LAB OFFICER'S REPORT

Roy Davis

General Leg Information

Expedition 339 scientific objectives focused on the broader significance of Mediterranean Outflow Water (MOW) on North Atlantic circulation and climate. The Expedition was 62 days in length and originated from Punta Delgada, Azores on November 17, 2011. It ended at Lisbon, Portugal on January 17, 2012.

Port Call Activities Overview

Pt. Delgada

Offloading of

• Ocean Freight
• Air Freight
• World Courier Frozen and Refrigerated

Delivery and loading of

• IODP Surface freights
• IODP Airfreights

Lisbon

Offloading of

• Ocean Freight
  • 3 ea refrigerated shipping containers of cores and residues for BCR
  • 1ea 40 ft container of return surface freight to CS
• IODP Airfreight
  • 4 boxes dry/blue ice sample world courier shipment
  • Return air freight to CS
  • Foreign air freight

• Trash
  • 3 ea. core liner boxes

Lab Activities

Core Lab

The core lab processed 5446 meters of sediment. Expanding cores were experienced. Multiple holes were drilled in the liners, and sections were cut short (140-145 cm) to allow for expansion. The liner patch "socks" were used to accommodate expansion.

Physical Properties

During Expedition 339 the Physical properties group used the Whole Round Multi-Sensor Logger (WRMSL), Natural Gamma Radiation (NGR) Logger, Special Tasks Multi-Sensor Logger (STMSL), ThermCon, Pycnometer, Gantry, Section Half Multi-Sensor Logger (SHMSL) and Section Half Imaging Logger (SHIL) instruments for initial characterization of upcoming core flow.

Paleomagnetics Lab

The SRM was filled with liquid Helium in Ponta Delgada, Azores by Dave Shuler, 2G. Training on refills was also conducted at this time.
This expedition was a high recovery sediment expedition and the SRM was the only instrument used. No samples were analyzed or measured in any of the other instruments. Bartington 36 mm MS2C loop was delivered to the P-Mag lab for measuring magnetic susceptibility of discrete samples during thermal demag sequences.

Core Description

Expedition 339 is the first high recovery sediment expedition that documents cores with the improved DESClogik version after the project deadline. As such, we had successfully completed a pre-cruise meeting with the senior sedimentologists (Larry Krissek, Roger Flood, Francisco Hernández-Molina) and received feedback from the paleontologists to set up templates before port call on the JR (Azores, 2011, Nov.18^th to 22^nd). The scientists checked the provided templates on board and added some more entries for sedimentology; the templates for the paleontologists were the subject of major changes on board. All templates were fully prepared before the first core was on deck.
A total number of nine sedimentologists and nine paleontologists worked with DESClogik during Exp 339. The templates were used for the following scientific disciplines: sedimentology, benthic foraminifers, planktic foraminifers, nannofossils, palynomorphs, ostracods.

Curation

A total of 13,396 samples were taken for Expedition 339. 10,946 shipboard samples, and 2,450 personal samples were taken. 7,012 shipboard sample residues were assigned to Sample Request Numbers. Personal samples were limited to: Microbiology (Jennifer Biddle, 1183IODP), Geochemistry (Dave Hodell, 1221IODP and Madeline Miller, 1241IODP), Palynology (Maria Sanchez Goni, 1231IODP), and an Alkenone pilot study (Alexandrina Tzanova, 1244IODP). In the last week of the cruise Roger Flood (1392IODP) was approved for a pilot CT scan study of 7 small U-channels (~5-7 cm). All other personal sampling will occur at a sample party held at the Bremen Core Repository (BCR) in June, 2012. I am including an excel spreadsheet with the sample information in the email that includes this report.

Imaging Lab

The Close up workstation was moved and rebuilt. The entire workstation, lighting included, can be moved by removing four bolts.

Microscopes

One of the new Zeiss Discovery V8 scopes has bad internal optics so the main body of the scope is being returned to the vendor for repair.

X-Ray Lab

Expedition 339 was a sedimentary expedition with high recovery. The XRD lab ran bulk samples on every core from the 'sampled cores' and clay separations (with glycolation and some heating to 550° C) on every forth core.

Paleontology Prep Lab

A total number of nine paleontologists worked in the Paleontology Lab during Exp 339. The expertise was nannofossils (using the UV light, smear slide preparation and vacuum pump system etc.), foraminifera (using sieves, filtration, needles, valves etc.) and palynology (HF preparation, smear slides, centrifuge etc.).

Thin Section Lab

There were a total of 25 thin section requests that included grain mounts, mudstone and sandstone clasts as well as unconsolidated sediment.

Electronic Technicians Report

See Report.

Publications Specialist

Overall, Expedition 339 seemed to be a steady, high recovery and productive expedition. There were changes and challenges to work through, and I think we, as a team, did a good job of communicating and trying to work through them as early as possible (updates to data entry in DESClogik and output through LIMS2Excel).

System Manager's Report

During Expedition 339 the IT infrastructure performed as intended with minimal impact to operations.

Developers Report

As often happens, the early part of the expedition was fraught with major problems, but these were slowly worked out as the expedition progressed. One of the more important items on this expedition was a more formalized format for Change Management.

Chemistry Lab

See report

Underway Geophysics Lab/Fantail

Navigation and Bathymetry data were collected during the 1,112 nm of transits. Magnetometer data was not collected in part due to winch and leveler concerns and the higher priority of preparing the laboratories for shallow water APC/XCB coring operations.
VSP operations were conducted at 3 site locations in accordance with marine mammal protection protocols. VSP operations at the last sites were discontinued due to sea chest metal wastage concerns.

ASSISTANT LAB OFFICERS Report

Steve Prinz, Chieh Peng

Summary

We recovered 5,446 meters of sediment. We experienced core expansion, multiple holes were drilled in the liners, sections were cut short (140-145 cm) to allow for expansion. The liner patches "socks" were used to accommodate expansion.
Two temporary technicians, Melissa Rotella and Hilary Hall, worked in the core lab. Both were quick learners and they both did an excellent job.

AMS/Inventory

• Similar issues observed in complete shipment reports, regarding missing location as describe below:

1. All SC0001 items show BLO as ship location
2. All DC0001 items show no location with "shore department" as owner.
3. All other and non-inventory items show no location with no owner.

This turned out to be an AMS reporting problems. All information has been filled out by users on shore. Emails were sent to shore, awaiting results.

• New items were added in inventory (please see attached spreadsheet).

Special projects

• All combo locks have been changed to 0933
• Tile saw shielding received and stored in UTSHOP
• ALO computer kept crashing. The hard drive has been re-imaged. A folder was created in JR1/ALO folder/ALO/HD339 to temporarily store all files/folder from old HD. If you see the blue screen of Windows crash, the MCS's best advice is to re-boot. During the re-boot process don't touch the mouse or keyboard for at least 5 minutes-even after it looks complete.
• D-Tube rack and close up photo table were re-arranged so that we can accommodate a second D-tube rack in the aft corner of the microscope lab. This arrangement has gone through the Curation lab-working group, and the technical staff on this crew prefers it. With the new sailing schedule for the rest of this year, we wish to keep this arrangement for all the upcoming expeditions, especially the high recovery cruises.
• The angle aluminum clamp down for the super saw was warped and was replaced.
• We had 328 D-tube boxes in the beginning of the expedition. All were stored in the HRS; we believe we can store another 100 boxes in the HRS.
• We can store up to 800 waxed core boxes in the storage bin in TBULK.

Challenges encountered

• We are able to store most if not all core boxes in the reefer. That's about 800 full boxes
• The following 'new' items were added to AMS Item Master:

PHYSICAL PROPERTIES

Y. Vasilyeva

Summary

During expedition 339 the Physical Properties group had been using the Whole-Round Multi-Sensor Logger (WRMSL), Natural Gamma Radiation Logger (NGR), Special Tasks Multi-Sensor Logger (STMSL), ThermCon, Pycnometer, Gantry, Section Half Multi-Sensor Logger (SHMSL) and Section Half Imaging Logger (SHIL) instruments for initial characterization of upcoming core flow. The total number of cores from 7 sites by Jan 12th of 2012 has reached 652 (~690 expected by end of Exp 339) in total. See detailed report in Appendix 1.

Instruments

All instruments performed satisfactorily and exhibited only minor problems, which were promptly resolved by the Developer/IT/ET groups – special thanks to T.Cobine, T. Blaisell and D. Hornbacher for their dedicated work. Some instruments – WRMSL, STMSL, Gantry - had been upgraded with an improved software interface and successfully used during Exp 339. The MadMax interface (installed during Exp 336) was further improved during Exp 339 and alongside continuously ongoing measurements (See: Tech Report by Tim Blaisdell for further details). Due to electrical noise/temperature instability problems, the location of the ThermCon measurement system was moved from the core lab entry to the Bio-Lab. Results were satisfactory and according to expectations, i.e., in terms of how fast data were collected with the full-space needle probe and also data quality (values were in the range of previous measurements in similar sediments, e.g., Exp 327 data).

Individual Measurement Systems

STMSL

STMSL had been operated with a new software interface. The operation went smoothly, without any major problems. However, sometimes core-sections with a disturbed end-cap (due to core expansion, etc.) had a tendency to get stuck in the plastic MS loop. Therefore, MS detector loops with a slightly larger diameter are expected to replace the old ones during Exp 340T.

WRMSL

WRMSL exhibited mostly no problems. However a couple issues need to be improved on that system:

• Similar issue with MS detector size loop as for STSML
• Minor software failure: Galil motor system sometime got "confused" about proper upcoming core section position on the track. In that case the "pusher" starts its movement from home position as in the middle of measurement: 2.5 cm step movement with the following measurement, without bringing a core-section under laser. As result, the data profile collects a few fake readings. Such failure was observed both with and without error message. By the end of expedition that problem seems to be solved by persistent work of developers T. Cobine and D. Hornbacher.

So far, it should be noted that the new interface for both MST tracks was brought to almost perfect level in terms of efficient handling of core scanning workflow. Upgraded UG for the new software interface (written by T. Cobine).

NGR

NGR performance was satisfactory. However, two times during the first weeks of the expedition, the NGR software failed in the middle of analysis. Restarting the software failed, exposing error message about server communication problem. This problem was fixed by united effort of developer/IT groups (see more details in Appendix 2-1) and for the rest of the expedition the NGR operation went smoothly, except for few minor problems with Galil motor system, which sometimes failed to deliver the boat to the chamber, showing the following error message:

When the user clicked Restart the machine continued to work, but it could be awhile before the operator saw the message. Adding sound to the error message to alert the user would be helpful.
Thomas Gorgas twice reported that the Galil-motor-pusher went out of moving range, causing vigorous stress to the motor and the emergency button was applied to disconnect the motor from the main power. However, the Stop button apparently doesn't disconnect the Galil motor from the power. Thus, as an additional adjustment/improvement of the NGR system, it is suggested to modify the Emergency Power Shut Down button of the Galil Motor so that it not only stops the track movement, but also the motor itself (see: Tech Report by Y. Kotze and T. Gorgas in Appendix 2-2 for further details).
During troubleshooting it was noticed that some parts (shutdown/startup procedure; apparatus/reagent/materials; software interface) of the NGR User Guide had become obsolete and needed correction.
Some suggestions for further NGR software/hardware improvements were submitted by the NGR operators after continuous operation. The full list of them is presented in Appendix 2-3. Additional core-section shelves were built under the delivery track by E. Claasen.

ThermCon

Thermal Conductivity was measured once in the middle of each whole round core-section for most sites within APC drilling depth as far as reading was staying in expected range. Measurements were stopped as soon as a cracked texture of the inner sediment started having a noticeable impact on the ThermCon reading.
Initially at its original location (close to the core lab/cat walk entry) the TeKa system was failing to show a satisfactory performance, primarily during the day hours; perhaps this was due to a higher level of electrical noise and/or temperature instability in this area. Thus, the ThermCon station was moved from its original location to the Bio Lab, where good results were obtained. At all locations the core section was covered with the black foam to reduce & minimize the effect of thermal instability in the measurement area. Remarkably, the system was working there OK without a UPS unit. Perhaps in the future, the location of the ThermCon system needs to be changed to a place relatively remote from traffic and electronic noise.
In general, we were obtaining acceptable results for QC measurements throughout the expedition, and TeKa operations went smoothly. The measurement setting parameters were as following: probe # 10702; heating power 1.8; serial (replicas) # - 3; no delay/pause time. However, a few minor problems with downloading software were reported to developer T. Blaisdell.

Pycnometer System

During this expedition the upgraded system continuously went through long-term testing of the new electronic and software Mad Max interfaces. In general, all system provided adequate operation to satisfy all research targets. However some minor users' frustration came from occasional failures either from hardware or possibly software. Despite a number of problems that emerged during this test, most of them were fixed by developer/IT/ET team in a reasonably short time.

List of the problems

• Cell 5 malfunction, occasionally cells 1 and 3 malfunctioned as well. The problem was investigated by D. Hornbacher and E. Claassen, who found that the ventilation valve had shown a systematic failure. ETs E. Claassen and J. Kotze had been doing careful investigation and rooted down the problem to weariness of rubber seals and o-rings inside the solenoid valves. More details are described by T. Gorgas in Appendix 3. Subsequently, the ETs suggested a major maintenance of each pycnometer cell, which would include replacing most of the rubber seals. Further investigation and observation of these cell operations are necessary to be confident in their correct performance. Perhaps a major cable connection needs to be replaced, since all cells 1, 3 and 5 belong to one side of the electronic board.
• Computer was getting "frozen", exposing a blue screen. Problem was fixed by ITs by swapping the hard drive and reinstalling all programs.
• Occasional Mad Max bugs/further optimization development was conducted by developer T. Blaisdell. However users are still facing issue of software getting frozen during "Accept result" procedure, when it happens too fast. Until this problem is solved, it would be recommended to do one "Accept result" operation per time: click "Accept" button and wait until result will appear in the main table, then proceed with other cell, and so on.
• The water bath for the pycnometer was found one day (Dec 15th) working with very loud noise. The ET-on-duty, E. Claassen, had lubricated the shaft of the motor, and the noise stopped. Conclusion: regular maintenance list for the Phys Prop instruments needs to be created, so things like proper lubrication of various parts can be performed in the beginning of expedition. This list should include lubrication of SHIL axes, Gantry P-Wave velocity axes, water bath motor shaft (occasionally) – see Appendix 5.
• SHMSL: The sedimentology group measured Discrete MS Point & light reflectivity data; no major issues were reported.
• Once (Dec 9th) after a 1-day break in the workflow, the instrument software was performed in the mode, when it didn't see VIS4000 (spectrophotometer) unit, sending message for choosing a USB port for VIS4000 unit. Reconnection of cables and system rebooting action seemed to resolve the problem.

Such failure tends to be happening after SHMSL has been in use for a few days. The major problem though appears to be that most of the time there is no error message, and scientist may not notice on time that VIS4000 instrument screen is missing, and waste their time on scanning of few core-sections before this problem is noticed. It would be very helpful, if software would send a warning every time one of the instrument connections is missing. This and other concern about further SHMSL software interface improvements can be seen in Appendix 4.

• SHIL: The sedimentology group obtained digital images at a high-resolution, and subsequently printed out an 11 x 17-sized hard copy of each image as a first step to perform a detailed core description on paper (all hard copies were collected in a number of 2-inch thick binders). For Exp 339 the printout format was modified such that now some basic columns are also included in the print-out (adjacent to the actual core image). From this paper record, data entries were performed into DESClogik.
• A previous problem (see reports from earlier expeditions) with dropped lines happened again after 1 week of instrument intensive operation. As in Expedition 336 it was caused by loosened cable (linear encoder head) connection behind the scanning track. T. Cobine has replaced mounted screw with a longer one, which is supposed to provide a more reliable connection. Also it seems, that systematic lubrication/cleaning of the shaft (seen on picture below) with the silica grease (WD-40 is not recommended by T. Cobine) may help to avoid problems with dropped lines.

(see details in Tech Report by the Imaging Specialist and Developer/Trevor Cobine).

• Once, on Jan. 8, 2012, the SHIL software stopped working – dialog window got frozen in "completing tasks waiting" status permanently. T. Cobine and D. Hornbacher traced this problem down to a malfunction of the scanner software. Due to the urgency of fixing the system ASAP, it was decided to replace the initial scanner with a regular type of scanner (Symbol Tech Inc., NY) installed on all other systems on the ship. T. Cobine provided a summary of the changes that were made:

1. Replaced Microscan MS-4 label reader with Motorola Symbol label reader.
2. Modified code to work with Symbol label scanner
3. Sample Entry Dialog box still has same look & feel as before.
4. Done by Dwight, Tim & Trevor

• Gantry operation was in the satisfactorily range. P-Wave velocity unit was used only for X-axis measurement. The upgraded interface had been working affirmatively, however a few suggestions of further operation optimization have been proposed by users:
• The resolution of transducer moving speed needs to be brought to higher level on purpose to provide more fine control of X-axes transducer movement (may be done already?).
• The software needs continuous testing to investigate a few accidents, when a part of the core-section was smashed as a result of uncontrolled transducer movement (TG comment: the user just needs to be educated on the fact that upon starting the software, the transducers always find their "way home" and thus close and open again to ready themselves for a measurement).

Other issues

Obsolete and broken parts were sent back to shore. As it was suggested by T. Cobine, an additional list of spare parts is being created.

Appendix 1 –Exp 339 Phys Prop summary on analysis

Before splitting all cores were scanned on WRMSL with a delay of 3 hours from their delivery time with step 2,5 cm for GRA density, Magnetic susceptibility (MS) and P-Wave Velocity (PWV). Alternative scanning on fast track (STMSL) was done only for some cores from Holes B-C without waiting time for the temperature calibration after core was received on the cat walk with step of 2,5 m for GRA density and MS. Following WRMSL track all cores were scanned also on NGR with scanning time 7 min in position II. During available extra time due to slow workflow, the scanning resolution for some cores was increased with step 1 cm for WRMSL and with 7 min of scanning time in both positions for NGR, ending with 14 min of total scan for the NGR. Total 118 whole-round core-sections were analyzed for the thermal conductivity using TeKa instrument. MST-PWV and thermo-conductivity data were taken only for the Hole A cores at each site within APC drilling depth before disturbance of the core started affecting results.
After core splitting, some additional PWL data was obtained from working section-halves mainly for Hole A cores within APC drilling range - total results by Jan 12, 2012 had reached 321. PWV measurements were taken in the middle of each section-half as far as signal was coming out properly. Also from each odd number of working halves MAD samples were taken and analyzed using the METTLER Balance and Pycnometer for the bulk density, moisture and porosity data (total samples by Jan 12, 2012 had reached 1121.
All archive section-halves were scanned on the SHMSL for discrete MS and color reflectance spectra at a 5 cm resolution, and also on the SHIL, obtaining high-resolution digital images.

Appendix 2 - NGR

2-1 NGR - "communication" failure. As it was found by developers T. Blaisdell and D. Fackler (on phone) in the following troubleshooting analysis, the signal from one of the Ortec NaI controllers was lost: in the MCB configuration window only the 6 NaI detector had been seen. Both times total system "shut down/ restart" procedure helped to restore the NGR adequate operation. Before all system was restarted, the core was manually removed from the chamber. For the following troubleshooting both developer and MCS group were called to investigate and find a reason for the sudden communication error, which had disturbed dramatically the workflow on the ship. MCS group replaced the computer with a newer unit to ensure a prompt software operation to exclude a possibility of communication error due to slow response from unit. Also all USB cables between Ortec NaI units and PC were replaced and rerouted to exclude a possibility of any type of hardware causing the communication failure. Detailed description should be provided by developers and MCS in their technical report for Exp 339.
2-2 NGR - Occasional failure (2 times) of Galil motor track delivery system was observed by T. Gorgas and worded out by out by ET-on-duty J. Kotze. The NGR developed some problems during the expedition, where ETs were not directly involved and could not find any technical faults for the problem with the Galil controller or stepper motor. The only indication would be an error instruction on the Galil controller, and the problem would clear itself after a program reboot or a complete PC reboot.
The symptoms are: for unknown reason the core boat is pulled back past the end stops and limits and keeps driving the stepper motor at the end stop of the track and continues to push further. After a couple of minutes the stepper motor would get very hot to the extent that it would burn out if not physically disconnected (what ET J. Kotze did in each case). The emergency button did not help either if it was pushed, which is an indication that the program is not running anymore and does no further extends executions entered from the keyboard or external peripherals. At the moment it is a soft driven emergency stop executed via the PC. The signal from the E/button just gives the PC the instruction to stop.
ET (J. Kotze) suggests the emergency button should be wired in line with the Galil motor supply, so as to cut off any further motion of the motor if pushed, as had been done in the past on the P-mag after similar problems, which solved that problem. The emergency stop is of limited use if it is software-driven, as the PC might still be busy with something else to be quick enough or, as it seems to be in this case, to be stuck in a "hang-up"-type of situation. That happened in most cases when the PC failed. In such a case the user needs the PC software to stop the track, which is not available.
ETs do not know the reason for the NGR PC failures, but it might be related to some data-cluttering as the PC takes a very long time to pick up the necessary registry files to boot and is slow to start up. This remains only speculative at the moment though. No ET-related NGR components were replaced throughout the expedition.
2-3 NGR wish list:
Software:

• Galil motor error messages should have a sound warning (perhaps continuous), so when the Galil motor fails to deliver a core-section inside the chamber, the operator will be aware (very often the operator is doing multi-tasks, so s/he can miss it for a moment when it happens, which causes a significant time-delay sometimes, and is not desirable before core-splitting operation, when many people (sedimentologists) may wait for NGR analysis to be finished). Issues with Galil motor failures need to be resolved (Galil motor sometimes fails to deliver the core-section to the chamber), so amount of errors will decrease to 0.
• Request count time in sec – then elapsed time needs to be in sec – not in min and hours. Also we need a live time line. Best of all: all three live, req. and elapsed time should have a choice of either sec, hour, and min count.
• Configuration tab with files and config data need to be protected with a password.
• Length line name needs to have a unit – cm
• Ngr.xls results file table needs to make a readable appearance for column heads
• Can we overlap result spectra?
• Can we add any type of warning for the plastic detectors indicating whether they are working or not?
• The depth scale on LIMSPeak data report needs to be corrected.
• Ideally it would be very helpful to have an option in "Scan Sample" main dialog window: "Add sample" in case, if operator needs to run two short core-sections, therefore it will reduce core-flow time for high recovery legs. In that case software needs to "see" beginning and end for each section.
• Grind down the top of calibration standard holding cup, so alignment procedure can be avoided, which will simplify the procedure slightly.

Hardware:

• Stop button needs to be arranged so it would stop the Galil motor immediately.
• Additional core holding racks possibly may be mounted below the Galil motor track area.
• For cases when the power goes down and a core-section is inside, we need to use some capability of Galilo control to be able smoothly remove the delivery track back to home position.

Appendix 3 -Pycnometer

Throughout the MADMAX experiments, and reoccurring problems with the cell performance, the ETs discovered that pycnometer Cell 5 developed a leak after numerous runs (one or two other cells sporadically did the same to a lesser extent). Upon detection of this problem, the cell was removed from the pycnometer battery and the expansion and vent valve were replaced. The cell was re-tested and then found to be working well. ETs (Claassen & Kotze) checked a number of removed seals on the valve "plungers" (a little rubber stomp, which seals the expansion chamber off) and found a common problem on all of them: the rubber seal on the plunger tip has a permanent indent/footprint on it, which causes leakage intermittently. After consulting and sending images to Graham Killip at "Micrometrics", he confirmed that the wear on the rubber seals are on the edge of their usable life once it reaches that level of imprinting. ETs ordered 25 plungers and will replace them all once a year for a first trial to determine a routine replacement interval. The plunger and seal unit only cost $10 each, which is a very justifiable cost. 18 plungers are needed for the first complete service overhaul and keeping 7 as spare parts. As it is not necessary to replace the valve but only the seal, it should be possible to maintain it at a reasonable price. ETs also ordered 30 O-rings for the cap lids; they are only $1 each, and need to be replaced from time to time.
The Pycnometer Test Box & breakout cable system were created by ETs J. Kotze and E. Claasen. The manual is added to Pycnometer manuals draw.

Appendix 4 – SHMSL user interface wish list

This failure of software described below needs to be brought to the attention of the operator with some type of error message: Software fails to open the VIS4000 dialog window (it happens sometimes after a computer is restarted). Apparently it fails to communicate (or activate) with the spectrophotometer. It was found that a total reboot of the system (sometimes it may require cables to be reputed) would fix the problem.
However some user may miss this failure (since other three dialog windows are open, including main scanning window) and run a few core-sections before they realized they are not getting color-reflectance data. To avoid such waste of working time, it would be very useful, to provide a warning message like: "The communication with spectrophotometer VIS4000 has failed. Do you want to continue the analysis anyway?" In addition, it would be desirable to investigate, how to prevent such failure.
During Expedition 339, a sedimentologist needed to run some hard rock sections. The section half surface in that case usually is represented by a chain of discrete rock pieces of irregular size and within random distance from each other. Therefore scanning steps provided the SHMSL software can cover only few spots with good contact between the detector head and rock pieces. Most of the other spots need to be excluded due to bad quality of the landing contact on the edge or cracks between the rock samples.
A possible solution using the current design of software would be to increase the scanning resolution to very small steps like 1 or 0.5 cm, so the amount of "good contact" will increase, and then delete all "bad contact" spots. However in that case the operator needs to use many "skip area" slots, which would usually require much more than seven slots as it's given in the SHMSL acquisition window. Therefore in the acquisition window of SHMSL software more slots (perhaps ~20) for skipping area need to be added for the hard rock samples operation. An alternative solution, which probably would be easier for the operator, can be done as an additional window, where the operator may "order" all desirable location – like 2.5 cm;  4 cm; 5.2 cm; 8.3 cm – whatever will provide the best contact between the detector head and core section half (something similar is used in the interface for the Avaatech XRF scanner in the shore lab).

Appendix 5 - Physical Properties "to-do" suggested list:

• Daily: check NGR "all plastic counts" numbers.
• Weekly: lubricate SHIL shaft/ Gantry shafts with silica grease (no WD-40) during high core-sampling activities on board;
• Monthly: clean, lubricate and replace (if necessary) Pycnometer O-rings; calibrate WRMTL, STMTL and NGR, if they are in operation;
• Before each expedition: calibrate all instruments, if they are planned to be used; go through daily, weekly, monthly list of tasks; lubricate the shaft of water bath motor (WD-40 can be used) –ask ETs for assistance.

PALEOMAGNETICS LAB

Trevor Cobine
Scientists: Carl Richter & Chuang Xuan

Summary

• The SRM was filled with liquid Helium in Ponta Delgada, Azores by Dave Shuler, 2G. Training on refills was also conducted at this time.
• This expedition was a high recovery sediment expedition and the SRM was the only instrument used. No samples were analyzed or measured in any of the other instruments.
• Bartington 36 mm MS2C loop was delivered to the P-Mag lab for measuring magnetic susceptibility of discrete samples during thermal demag sequences.

Issues

• Section sample boats lost pins. We have 1 working and 1 spare sample boat, with 3 others missing 2.5-3.0 mm aluminum pins. Spare pins may be coming.
• Twisted sample boat was straightened by lashing it to a piece of split liner and carefully heating with a heat gun, then letting it set for about 3 weeks before use.
• Motorola Symbol label scanner for the Agico KLY4s & JR6a was repurposed to fix the scanner problems on the SHIL. 2 replacements have been ordered.
• On order are 25 anti-vibration rubbers for FlexIT pressure barrel mounts. These should be here for next expedition.

Recommendations

• Replace the IODP plastic P-Mag Cubes with the Japanese plastic P-Mag cubes. These cubes fit the JR6a's automatic sample holder and would make the JR6a more useful on sediment expeditions.
• For core orientation, recording and displaying, "Time of Shot" for APC core would be very beneficial to the data analysis process.

CORE DESCRIPTION

Sandra Herrmann and Thomas Gorgas

Summary

Expedition 339 is the first high recovery sediment expedition that documents cores with the improved DESClogik version after the project deadline. As such, we had successfully completed a pre-cruise meeting with the senior sedimentologists (Larry Krissek, Roger Flood, Francisco Hernández-Molina) and received feedback from the paleontologists to set up templates before port call on the JR (Azores, 2011, Nov.18^th to 22^nd). The scientists checked the provided templates on board and added some more entries for sedimentology; the templates for the paleontologists were the subject of major changes on board. All templates were fully prepared before the first core was on deck.
A total number of nine sedimentologists and nine paleontologists worked with DESClogik during Exp 339. The templates were used for the following scientific disciplines: sedimentology, benthic foraminifers, planktic foraminifers, nannofossils, palynomorphs, and ostracods.
A brief, informal mid-expedition survey was conducted to allow scientists to provide feedback on the use of DESClogik, its functionalities, user comfort etc. (see: attached SURVEY.doc). The main recommendation was a well-developed graphical interface that was badly missed (as has been expressed ever since by various scientists over the years).
"Core description is heavily based on a graphical processing of information to approach a final interpretation, whereas a tabular approach for this entire process does not suit the nature of this complex task very well."

Issues

1. Generic Dynamic Columns (GDC):

The GDCs established after the precruise workshop on request of the lead sedimentologists caused trouble: a) download of data that should be auto-populated in these corresponding columns slowed down the entire system (cell by cell request needs to be changed to minimize the memory issues), b) the cells were not properly populated (more than 1 or 2 entries were pulled out). On Nov. 29, 2011 the decision was made to delete these columns again to avoid further problems. Some other fixes, e.g. auto-linked value lists, were solved pretty quickly. The sediment template usage works according to the expectations on Nov. 30, 2011.

1. Check overlap:

The check overlap function was activated on Dec. 1, 2011, for the sediment template (TAB GENERAL and CORE SUMMARY). The function caused a Launcher error and a major crash of DESClogik (reproducible). Tim Blaisdell worked on the issue right away – for details see his report.

1. Auto-linked columns in DESCINFO sites:

Some corrections of entries in the GENERAL tab of the sediment template caused changes in other (non-linked by template definition) columns. The issue was found to be a column definition in the DESCINFO sites. The issue was solved right away.

1. DESClogik and LIMS2EXCEL interaction:

The prefix classification showed up in the concatenation of Lithology A+B for core U1385B-10H, not for all the others.

1. DESClogik red X:

December, 14^th, 2011: Larry Krissek (lead sedimentologist 12 midnight-12 noon) produced a major crash of DESClogik by: downloading hole data for all tabs, changing entries in 2 tabs for several samples, thereby jumping around between tabs and finally hitting upload ¿ red X. Developers assume that there is a certain connection that is lost in translation between the server and program talking to each other.

1. Samples only show up after recalculate depth (Sample Master):

December 14^th, 2011: After having a wash core logged as ~ 4 m and not 290 m, the depths needed to be recalculated after every core on deck (section entries) to be able to see the sections/core in DESClogik. Software fix in SampleMaster needed.

1. Names of templates:

Import of template with a name of an existing template does not overwrite the existing template. The new one needs to be imported under a different name, the old one deleted and the new one renamed. Annoying, but doable.

1. Classification of value list entries:

December 21^st, 2011: Classification (in []) shows up while populating cells in some cases. It disappears for the entire column if one clicks in one of these cells. Fixed.

Change requests for DESClogik

1. Autosave per template is needed (accomplished during cruise).
2. Retention Schedule in the recovery settings needs an option between 5 and 100 autosaves and was requested (accomplished during cruise).
3. Integrate a sample query for data only entered by hole (without showing all the cores too after download).
4. Automatic switch in sample finder to the section that an entry from a section is extended to (request 2: also jump to the depth entry that was selected the last time (entry: section 1H-1A, 50-55 cm; should auto-jump to 1H-1A, 55 to...)).
5. Allow an "Insert" of a row where needed (instead of adding a new entry at the bottom of the tabular entry sheet, which subsequently is re-arranged into its corresponding depth interval. Accomplished as per 20111223 (DESC Version. 4.67).

Other information

Updates for the paleontological templates were performed regularly (1-2 days basis). Sediment template changes (adjustments for 80% of the value lists in the first week, small changes after this [weekly on average]) were implemented within several hours. Major changes on the STRATIGRAPHIC UNIT column were implemented on November 25^th, 2011 (additional 15 columns).

Changes to DESCINFO

DESCINFO2 within Google sites and the online DESClogik manager works fine on board. Fast changes are always possible and implemented in no time. No additional components are required, only completing and adding data.

Equations for calculating major lithology and prefix plotting space

In order to get the lithology plotted the way the sedimentologists on board want to see the plot, a formula in excel was created and implemented for the columns that need to be filled.
Once the publication specialist exports the tables through LIMS2EXCEL the formula just needs to be copied in to the equivalent columns. Two days later the scientists decided to use the usual A+B concatenation for lithology.

CURATION

Chad Broyles

Summary

Samples

A total of 13,396 samples were taken for Expedition 339. 10,946 shipboard samples, and 2,450 personal samples were taken. 7,012 shipboard sample residues were assigned to Sample Request Numbers. Personal samples were limited to: Microbiology (Jennifer Biddle, 1183IODP), Geochemistry (Dave Hodell, 1221IODP and Madeline Miller, 1241IODP), Palynology (Maria Sanchez Goni, 1231IODP), and an Alkenone pilot study (Alexandrina Tzanova, 1244IODP). In the last week of the cruise Roger Flood (1392IODP) was approved for a pilot CT scan study of 7 small U-channels (~5-7 cm). All other personal sampling will occur at a sample party held at the Bremen Core Repository (BCR) in June 2012. I am including an excel spreadsheet with the sample information in the email that includes this report.

Shipments

Core-There were 688 cores recovered on Expedition 339. 5,458 meters were recovered. There are a total of 814 boxes (Working and Archive). 814 are being sent to the BCR.
Frozen and Refrigerated Samples-All frozen and refrigerated shipments are being sent to:
Dr. Jennifer Biddle University of Delaware125 Cannon Laboratory700 Pilottown RoadLewes, DE 19958
USA telephone: 814-360-4899 backup phone: 603-770-8731email: jfbiddle@udel.edu
This shipment is being sent from the JOIDES Resolution in Lisbon, Portugal to Dr. Biddle via World Courier. The shipment contains 3 frozen boxes of microbiology whole rounds, and 1 refrigerated box of microbiology syringe samples.

Residues

The residue distribution is as follows:
Residue Destination

Sample request numbers and codes were assigned to requested residues in the database.

All requested residues were sent from the ship to the recipient or hand carried.

Thin Sections

A total of 25 thin sections were prepared by Gus on Expedition 339. The following table is a complete list of all thin sections produced:

One thing to note is TS_21 was broken by the scientists on board the ship.

Smear Slides

Sedimentologists prepared and described 1,175 smear slides. A complete list of smear slides is being emailed to the BCR.

Action Items

Borrowing Thin Sections:

Roger Flood (1392IODP) has requested to borrow all thin sections from the BCR made on Expedition 339. This has been approved by the shipboard Sampling Allocation Committee (SAC). His shipping address is as follows:
Roger Flood
Stony Brook University
School of Marine and Atmospheric Sciences, Rm. Endeavour 145
Stony Brook, NY
11795-5000
USA
Telephone: 631-632-6971
email: roger.flood@sunysb.edu
No other shipboard scientist has requested thin sections, so he is allowed to borrow them for one year.

Expedition 339 Curation & Sampling

Pre-site to Site Conversion

Site U1385 (APL "Shackleton" Site)

The Shackleton site was proposed by Dr. David Hodell, Cambridge University, UK. As the PI for this site Dr. Hodell served as part of the Sampling Allocation Committee for these cores. We experienced gas and core expansion beginning at Core 10H. Gas expansion occurred at similar depths for all remaining sites. As the cores equilibrated to room temperature for whole round measurements they continued to expand. Once the cores were split, we re-measured the section lengths, and updated the curated length in the database. Subsequently CSF-A depths were recalculated.

Hole U1385A Catwalk Sampling

Geochemistry: Low-resolution geochemistry samples for David Hodell (1221IODP) and Madeline Miller (1241IODP) were taken from the next to last section of odd numbered cores (Figure 1). This consisted of a 50 cc syringe (IWSy) being inserted into the bottom of the section. This sample was squeezed for pore waters. We attempted to take samples slightly off center towards the working half. This did not always work properly due to different consistencies in core material. Rhizome samples were also taken from this section.
Microbiology: Microbiology samples were taken for Jennifer Biddle (1183IODP) from the next to last section of even numbered cores (Figure 1). These consisted of 5 cm whole rounds from the bottom of the section. After this sample was removed, a 10 cc syringe was inserted into the bottom of the same section for cell counting. An additional 5 cm whole round and 10 cc syringe were taken from one Core Catcher for contamination testing.
Headspace gas (HS): Standard shipboard HS samples were taken from the last section of every core unless the chemist chose otherwise (Figure 1).
Paleontology (PAL): Standard shipboard paleontology (PAL) samples were taken from the Core Catcher in every core. This consisted of 5 centimeter whole round at the bottom to the Core Catcher. This was then subdivided by the paleontologists for Foraminifera, Palynology, and Nannofossils (Figure 1).

Hole U1385B Catwalk Sampling

Geochemistry: High-resolution geochemistry samples for David Hodell (1221IODP) and Madeline Miller (1241IODP) were taken from sections 1-5, for a seven-section core (Figure 2). This consisted of a 50 cc syringe (IWSy) being inserted into the bottom of each section. This sample was squeezed for pore waters. We attempted to take samples slightly off center towards the working half. This did not always work properly due to different consistencies in core material. 5 cm whole round Interstitial Water (IW) samples were taken from the next to last section of each core. Rhizon samples were taken for all sections besides the Core Catcher.
Paleontology (PAL): Standard shipboard paleontology (PAL) samples were taken from the Core Catcher in every core. This consisted of 5 centimeter whole round at the bottom to the Core Catcher. This was then subdivided by the paleontologists for Foraminifera, Palynology, and Nannofossils (Figure 2). PAL samples were taken in both hole A and B to confine the age date range, as the two holes were offset slightly.

Site U1386 Catwalk Sampling

Geochemistry (U1386A): High-resolution geochemistry samples for David Hodell (1221IODP) and Madeline Miller (1241IODP) were taken from Sections 1-5, for a seven section core (Figure 3). This consisted of a 50 cc syringe (IWSy) being inserted into the bottom of each section. This sample was squeezed for pore waters. We attempted to take these samples slightly off center towards the working half. This did not always work properly due to different consistencies in core material. For the upper 50 m only half the syringe was taken. From 50 to 150 m the entire syringe was taken. 5 cm whole round Interstitial Water (IW) samples were taken from the next to last section of each core down to 200 m. Below 200 m the IW sample increased to 10-15 cm with a resolution of every third core. Rhizon samples were taken for all sections besides the Core Catcher.
Paleontology (U1386A, B, & C): These samples were taken for the all holes in the same manner described for U1385A&B.
Head Space Gas (U1386A & C): These samples were taken for the all holes in the same manner described for U1385A & B.

Site U1387 Catwalk Sampling

Microbiology (U1387A): Microbiology samples were taken for Jennifer Biddle (1183IODP) from the next to last section of even numbered cores (Figure 4). These consisted of 5 cm whole rounds from the bottom of the section. After this sample was removed, a 10 cc syringe was inserted into the bottom of the same section for Biddle's MBIO cell counts. An additional 5 cm whole round, and 10 cc syringe were taken from one Core Catcher for contamination testing.
Geochemistry (U1387A): 5 cm whole round Interstitial Water (IW) samples were taken from the next to last section of each core down to 200 m. Below 200 m the IW sample increased to 10-15 cm with a resolution of every third core (Figure 4).
Paleontology (U1387A, B, & C) and Head Space Gas (U1387A & C): Samples were taken in the same manner mentioned before.

Site U1388 Catwalk Sampling

Geochemistry: Standard IW samples were taken in the same manner as U1387A. Standard Paleontology, and Head Space Gas sample were taken as before.
However, Site U1388 presented a series of challenges. The first APC core recovered was all sand. All holes on this site were alternating sand and mud layers. Recovery was low. The site was abandoned after the RCB bit became stuck in the hole. Eventually, the drillers were able to pull up the drill string without severing the pipe.

Site U1389 Catwalk Sampling

Five holes were drilled on Site U1389. Hole A penetrated to a depth of 350 mbsf using APC and XCB coring methods. Hole B was abandoned due to a missed mudline. Hole C achieved the same goal as Hole A, but was slightly offset for stratigraphic correlation. Hole D only used the APC method, and reached a depth of 94.52 mbsf. Hole E was washed down to a depth of 355m. The RCB coring method was used to achieve a target depth of 990m. Sampling for U1389 was the same as described for U1386.

Site U1390 Catwalk Sampling

U1390A followed the same sampling scheme as U1387A, except IW samples were taken for the entire core. U1390B was offset from U1390A, so shipboard PAL samples were taken for this hole as well.

Site U1391 Catwalk Sampling

Geochemistry (U1391A): High-resolution geochemistry samples for David Hodell (1221IODP) and Madeline Miller (1241IODP) were taken from sections 1, 3, and 5 for a seven section core (Figure 5). This consisted of a 50 cc syringe (IWSy) being inserted into the bottom of each section. This sample was squeezed for pore waters. We attempted to take samples slightly off center towards the working half. This did not always work properly due to different consistencies in core material. One IW whole round was taken for every core (Figure 5). This consisted of a 5, 10, or 15 cm (depending on depth) whole round taken from the next to last section in every core.
PAL and HS samples were also taken as described in previous sites.
For U1391C standard IW (Whole round 10-15cm), HS, and PAL samples were taken.

Exp 339 Section Half Sampling

Standard shipboard samples (All sites): These samples were taken from working half sections. This included Moisture and Density (MADC) samples (10 cc syringes, 3 per core), Paleomagnetism (8 cc cubes, 1 per section), CARB_XRD (5 cc tubes, 1 per core, shared for both analyses), and Nannofossils (toothpick samples, 1 per section). Thin Section Billets were taken as needed for sedimentology. Toothpick samples were taken from archive halves for sedimentology smear slides. Additional paleontology samples were taken when scientists needed to confine age dates between core catcher samples.
Tzanova (1244IODP) Alkenone Pilot Study: 18 (5 cc) samples were taken for Alexandria Tzanova's pilot study (U1389A & E). These were stored in the -86°C freezer to preserve the alkenones. Tzanova also took pieces of the IW and IWSy squeeze cakes for her study from U1385A & B, U1386A, and U1389A & E.
Flood (1392IODP) CT scan Pilot Study: In the last week of the cruise, Roger Flood was approved for a 5 cm U-channel CT scan pilot study from U1391B by the staff scientist and co-chiefs. 7 samples were taken from core catchers for this purpose.
Sanchez-Goni(1231IODP) Palynology Study: Maria Sanchez Goni took 5 cc plugs from all PAL core catcher samples for her palynology study.

Core Wrapping

Archive and working halves were wrapped in Glad Wrap until they can be shrink wrapped in the BCR. Several archive halves from U1386A may have been missed as scientists were adjusting to this procedure in core flow.

Preserved Macrofossils

From all sites, macrofossils were removed from section halves for close up images. I cataloged these samples, entered them into the database, and preserved them from future studies. I also kept a Macrofossil inventory in an excel spreadsheet. This is being sent, along with this report, electronically to the BCR. A box containing these specimens is being sent to the BCR with the core and sample shipment.

Problems Encountered

Core Expansion (All Sites)

We experienced a great amount of core expansion due to gas pressure for APC cores. In some cases the cores would expand >15 cm out of the liner once the section was cut on the catwalk. To deal with this problem, we cut sections at 140-145 cm to allow for the expansion. This was to ensure that the sections would fit inside the d-tubes, once split. We also had to devise extended endcaps that would fit over the expanded mud that had extruded from the liner. This consisted of cutting liner patch into 5-15 cm pieces, cutting it in half, and acetoning an endcap inside of the liner patch. The acetone did not always hold the extended endcaps onto the sections. These had to be attached to the core liner using the sonic welder.

Ejected core material from core barrel (All sites)

We also experienced a great amount of core expansion due to gas pressure for XCB cores. In many cases, XCB core material extruded from the plastic liner into the core barrel. This material had to be removed from the core barrel with water pressure. In many cases the tool pusher's crew had little control over this process. Several times, the core material ejected from the core barrel onto the rig floor. In other cases, the gas pressure itself caused material to be ejected from the bottom of the core barrel. We preserved this material in split liners. In many cases the core material was preserved but the orientation and sequence of this material was completely lost. This often caused Section 1 to have a shorter length. Core disturbance such as this was noted in the database. Also, yellow Caution stickers were placed on the section end caps, and d-tube end caps.

Exploding core

Core 339-U1387C-57R had a crumpled core liner. The core exploded out of the core barrel onto the rig floor and the catwalk up to the core catcher bench as a result of gas pressure. Whole round pieces of mud were collected and put into new core liners. As a result this core is extremely disturbed, and out of sequence.

Catwalk core cutters

A few of the catwalk core section cutters were cutting in a spiral. We believe this was caused by the blade cutting too deeply into the core. We adjusted the blades. This helped in most cases. However there were two core section cutters that we could not fix.

Computer Software And Database

LIMS database

In the second week of the cruise the database was at 99 percent capacity. This was solved by removing Expedition 320 data, adding more memory, and allocating a new system file. Sample Master slowed down when the database was almost full. This improved by the aforementioned database changes.

SampleMaster

The IODP-USIO sampling program, SampleMaster continues to have many issues. Each time I return to the JOIDES, new and surprising issues with the program arise. The latest version of SampleMaster on the ship is 2.2.3.3.

Dealing with core expansion in SampleMaster

Core sections continued to expand once brought inside the lab. This was due to the remaining gas in the cores and thermal expansion. This caused endcaps to break off the ends of sections. In many cases we had to add extended endcaps to sections. This caused the Curated Lengths of sections to increase by up to 6 cm. We treated this problem similar to hard rock curation, where the length measured on the Catwalk changes drastically from the final curated length. Once the cores were split, I remeasured the Curated Lengths for all APC core sections. I then edited this information in SampleMaster, recalculated offsets, and recalculated depths for the entire hole. It is important to note that this process must be done before the sedimentologists describe the core! Otherwise the section length and description information in DESClogik will be offset by the change in curated length.

Editing offsets (cm) on section halves (SampleMaster)

The program would not accept changes to offsets/intervals (cm) on section half samples. It is very common mistake for a user to enter the incorrect value for sample offsets/intervals on section halves. It is therefore very important for us to be able to correct these errors. For some reason Sample Master converts these edits from centimeters to meters, rounds to the nearest whole number integer, adds the length of the sample in meters, converts the number back to centimeters, and returns the wrong number on the sample label. For example, a sample was entered as 339-U1387C-48R-3-W 70/70 cm. I then 'edited' the sample to 339-U1387C-48R-3-W 71/71 cm. The current length is 0 cm in this case. The program converts 71 centimeters to 0.71 meters, and rounds it to the whole integer, 1. It then adds the current length (0 cm) to 1, resulting in an interval on section half of 1/1 cm when it should be 71/71 cm. This was found to be a problem in the web service (resteasy) that prints the labels rather than Sample Master itself. Tim Blaisdell fixed this problem. The latest version of resteasy-lims-webservices is 4.4.6.1.

Error printing section half labels on upload (SampleMaster)

When entering sections on a core, Sample Master prints 3 labels of both the Working (W) and Archive (A) halves for the core liner, d-tube, and d-tube end cap. The user can also select the box, "Print Labels on Upload." In many cases the program skipped the first section for W and A labels, and did not print them at all. The value was uploaded to the database, but the label did not print. This seems to be a problem with the print service that SampleMaster uses, and not the program itself. This issue was reported, and not resolved on Exp. 339.

Error printing the correct parentage information on sample labels (SampleMaster)

In some cases where a sub-sample is taken from a section sample the label prints the wrong information. For example a whole round PAL sample was taken on 339-U1387C-53R-6 from 65-70 cm. A gastropod was found in this sample and recorded in the database as 339-U1387C-53R-6-PAL-Gastropod 65-70 cm. The label printed the incorrect parent information as: 339-U1387C-53R-6-Gastropod. When looking at the label it gives one the impression that the Gastropod sample was taken directly off of the whole round section, when in reality it was a sub sample of the Whole Round PAL sample. This problem was reported, and not fixed on Exp. 339.

Web Tabular Report (WTR)-Section Summary

The section summary in WTR was displaying some sections out of numerical order. Tim Blaisdell corrected the problem in this report.

Special Projects

Thin Section Billet plastic templates: Etienne Claassen made several new templates (large and small format) for cutting Thin Section Billets on the ship. Several will remain on the ship, and several will be sent to the Gulf Coast Repository (GCR).




Figure 1: This is a visual representation of samples taken for U1389A. For odd numbered cores, 50 cc syringe samples were taken for geochemistry, from the next to last section in the core. Fore even numbered cores, 5 cm whole round microbiology samples were removed from the bottom of the next to last section. After this sample was removed a 10 cc syringe sample was taken from the bottom of the same section. For all cores one 5 cc syringe, for Head Space gas (HS) was taken from the top of the last section (Sec. 7 for a full core). 5 cm Paleontology (PAL) samples were removed from the bottom of the Core Catcher (CC).

Figure 2: High-resolution geochemistry samples were taken from sections 1-5 for a seven section core. This consisted of a 50 cc syringe being inserted into the bottom of each section. 5 cm whole round Interstitial Water (IW) samples were taken from the next to last section of each core. 5 cm Paleontology (PAL) samples were removed from the bottom of the Core Catcher (CC).

Figure 3: High-resolution geochemistry samples were taken from sections 1-5, for a seven section core. This consisted of a 50 cc syringe being inserted into the bottom of each section. For the upper 50m only half the syringe was taken. From 50 to 150m the entire syringe was taken. 5 cm whole round Interstitial Water (IW) samples were taken from the next to last section of each core down to 200 m. Below 200 m the IW sample increased to 10-15 cm with a resolution of every third core.

Figure 4: A 5 cm whole round, and a 10 cc syringe microbiology sample was taken from the next to last section for even numbered cores (0 to 150 m). From 150 to 300 m the resolution was decreased to one every fourth core. 5 cm IW samples were taken from 0-200 m. The sample size increased to 10-15 cm and the resolution decrease to one every third core below 200 m.

Figure 5: High-resolution geochemistry samples for David Hodell (1221IODP) and Madeline Miller (1241IODP) were taken every other section, e. g. sections 1, 3, and 5 for a seven section core (Figure 3). This consisted of a 50 cc syringe being inserted into the bottom of each section. One IW (5, 10, 15 cm depending on depth) sample was taken from the next to last section of the core. PAL and HS samples were taken as described in previous sites.

IMAGING LAB

John Beck
Expedition started by moving and rebuilding the close up workstation. The entire workstation, lighting included, can be moved by removing four bolts.
The image scanner started dropping lines and it was the same problem that Bill Crawford had mentioned in his Exp 336 Lab Report. Trevor secured the sensor and it corrected the problem. Two barcode sensors have failed and a hand held sensor was installed. The scanner started adding images above the standards block. I found a broken off home sensor switch. It was replaced and the problem corrected. The scanner more often than not is adding a blank white area at the bottom of each scan. This does not interfere with the image but does increase file size. Trevor is looking into the cause of this.
LIMS-to-Excel was modified by Dwight to allow download of images by selection of individual core or group of core rather than by entire hole or date.
The Audio-Technica ATW-R1820 wireless microphone receiver did not work. I had Jurie look at it and he recommended that it be returned for repair. It is in the shipment back.
The Metz strobe batteries would not maintain a charge. Jurie took both battery packs apart and made one that works. Rather than replace the packs at $170 each we have ordered batteries and Jurie will rebuild the packs at a fraction of the cost.
One of the computers in the imaging office would not boot. Grant Banta pulled the drives and placed them in another box for me. He determined that it was a bad video card and replaced it, reinstalled the drives and all is well.
At this point 4366 core section scans have been checked. All section scans have been downloaded to the imaging office, corrected to give a more accurate visual representation of the core and written to a drive for return to the beach.
Currently 167 close ups have been shot or produced from scanned section images.
Approximately 21Gb of PR images have been shot so far.

MICROSCOPES

John Beck, Sandra Herrmann
On arrival to the ship and preparing scopes, I discovered that the Spot camera on the scope in the bio lab had been left on and covered. Needless to say it was quite hot.
One of the new Zeiss Discovery V8 scopes has bad internal optics so the main body of the scope is being returned to the vendor for repair.
An Axioskope objective epiplan neofleur 50x pol inventory #115 was found with a loose lower element. It is being returned for repair or replacement.
The condenser pol filter on the thin section scope was not aligned properly as well as the handle for rotation being badly bent. To make a long story short the handle eventually broke off. I removed a filter and it's housing from another scope that was not being used and replaced the broken one. The broken one was realigned so cross poles worked properly and a new handle fabricated. This repaired housing and filter were then reinstalled on the scope not being used. The slider on this scope also became problematic. The slider would drag at a certain point in its travel. I removed the slider from the scope and found that one of the filters mounted in the slider had started to unscrew from the housing. This was corrected and reinstalled.
One of the Spot "IDEA" cameras stopped functioning. I removed it and gave it to Jurie who found a broken internal solder joint. This was repaired and the camera put back in service.

Configuration:

The microscopes were configured as per the request of the users. The microscope usage was light with a setup for microfossils (Axioskope, Objectives: 20x, 40x, 63x and 100x oil; Axiophot, Objectives: 5x, 10x, 50x, 63x and 100x oil; Axioplan, Objectives: 10x, 20x, 63x and 100x oil), three binocular for foraminifera analyses (benthic and planktic), and two microscopes for sedimentological investigations (Axioskop, Objectives: 10x, 20x, 50x, 100x; Axioskop, Objectives: 2.5x, 5x, 10x, 20x).

Instruments

Received and added the following microscope replacement and supplemental parts into the inventory (Microscope_inventory_20111128.xls):

Parts shipped out to CS after Exp 339:

XRD LAB

Heather Barnes

Summary

Expedition 339 was a sedimentary expedition with high recovery. The XRD lab ran bulk samples on every core from the 'sampled cores' and clay separations (with glycolation and some heating to 550°C) on every forth core.
Total XRD samples: 435

Equipment and Software

The Bruker Diffractometer ran without any problems. The parameters for the scans were:
35 kV, 40 mA
Scan angles: 4 – 70° 2 ¿
Step Size: 0.0174
Scan Speed: 1 s/step
Div. Slit: 0.3° = 0.6 mm
The sonic dismembrator was set up in the ICP prep. lab for dispersing the clays. The dismembrator is programed to run for 1 minute in pulses (hit the start button to run). Pulse, instead of continuous sonification prevents the sample heating up.
Freeze Dryer vacuum pump oil was changed. Keep eye on color of oil in vacuum pump, when it starts to darken it is time to change.
Five new XRD software licenses are onboard with the IT department. The new software user interface is different than the current program we use for evaluating the scans. Expedition 339 did not allow time to set up and test the new software. Curacao tie up/dry dock may be a good time to install and test the new software. In addition, a new quick user guide needs to be written.

Fisher Scientific muffler Furnace (taken from ET Report)

The furnace is in good condition although the element will need replacement for the Lesser Antilles expedition (temperature is reaching just above 1000°C). The oven LED displays the temperature a bit lower than the actual temperature - at a max indication of 985°C it actually is at 1005°C measured with an electronic probe. We decided to stretch the element's use till we really need the higher temperatures above 1100°C.
We will consult with the upcoming ETs to find out if they know if we have a spare heater. We cannot locate a spare element for the furnace. I'm sure we will be able to get one from Fisher Scientific as they still do supply spares for our furnace, seeing that Garrick got a spare fan earlier. We will confirm with them in case they know if we have a spare element stashed somewhere.
It is a Fisher Scientific muffler oven Model 750-58/240V/12.5A. The catalog that the oven label refers to does not exist anymore. I guess we will have to get in contact with the vendor by telephone for P/N details.

Methods

Clay separation was used during Expedition 339. Method used is listed below, as described in the X-Ray Diffractometer User Guide onboard:

1. In 50 ml centrifuge tube mix ~1 cc of bulk sample (fresh, not freeze dried) with ~1% Borax Solution (total of 30 ml of solution). To mix thoroughly, sample and borax solution was placed in sonic dismembrator for 2 minutes.
2. Sample/borax solution centrifuged at 1500 rpm for 5 minutes. (Removes the > 2 µm particle size fraction).
3. Decanted the borax solution (containing the suspended clays) into new centrifuge tube and spun at 1500 rpm for 15 minutes to remove the remaining ~ 2 µm particle size fraction.
4. Decanted the borax solution (discarded into sink) and washed remaining clay residue with distilled water (added DI water, ~15 ml, to remaining clay/sample in bottom of centrifuge tube and shaken by hand to mix).
5. Centrifuged distilled water and clay residue at 1500 rpm for 15 minutes (to help remove any borax from clay residue.)
6. Repeated Step 4.
7. Made an oriented clay mount on zero background single crystal quartz discs by placing several drops of solution onto the quartz discs and letting dry in desiccator or oven at low temperature (40°C).

Scan parameters for Clays:
Clay mounts were scanned with the following parameters:

• 35 kV, 40 mA
• Scan angles: 4 – 35° 2 ¿
• Step Size: 0.0174°
• Scan Speed: 1 s/step
• Div. Slit: 0.3° = 0.6 mm

XRD Lab Projects for Tie-up

• New XRD Software: Five new dongles/licenses for the evaluation software plus operations software (came with the licenses) are onboard and need to be installed and tested. Install on 5 designated computers (all in Core lab and if possible save one dongle for a scientist's laptop if required). If any problems, contact Bruker. Write new Quick User Guide for scientists. What about the updated Operations software – if we can use it we should update the Operation software as well. If the updated software is drastically different than current software please test thoroughly before Lesser Antilles expedition – with only a one day transit to the first site we do not have time to test thoroughly.

• The wooden shelves in the XRD/ICP lab are poorly mounted. If time and resources are available please improve the shelves in the XRD and ICP prep lab. Extend the XRD shelf under the oven.

• The Shatterbox is poorly emplaced. Improve the padding. Is there a better way to set up that area?

• Door of oven in XRD lab is broken – it will not shut. See about repairing or switching the oven with another oven onboard. Chieh said we could change with the oven in the movie room.

PALEONTOLOGY PREP LAB

Sandra Herrmann

Summary

A total number of nine paleontologists worked in the Paleontology Lab during Exp 339. The expertise was nannofossils (using the UV light, smear slide preparation and vacuum pump system etc.), foraminifera (using sieves, filtration, needles, valves etc.) and palynology (HF preparation, smear slides, centrifuge etc.).

Issues

After connecting the filtration system to a vacuum pump that runs with oil, it was decided to switch to another pump (reason: space issues and the oil vapor.

THIN SECTION LAB

Gus

Summary

There were a total of 25 thin section requests, which included grain mounts, mudstone and sandstone clasts as well as unconsolidated sediment.

Special projects

A section of vertical unistrut was added to the forward bulkhead. The concave LP-50 lap wheel has been returned for flattening.

Problems encountered

• Replaced seized LP-50 roller arm bearing.
• Repaired leaking LP-50 vacuum pump fitting.
• Replaced Petrothin digital micrometer battery.
• Reconfigured Petrothin LED strip lights to operate from one power supply.
• Adjusted several PM-5 weight holders and stops.
• Tightened PM-5 slurry scrapper post.

Miscellaneous

Performed:

• Routine equipment maintenance as necessary.
• End of cruise cleanup as required.
• Removed oven and returned to chemistry lab.

ELECTRONIC TECHNICIANS REPORT

Etienne Claassen, Jurie Kotze

Core lab

Pycnometer cell five developed a leak after numerous runs, (one or two other cells sporadically did the same to a lesser extent), we removed the cell and replaced the expansion and vent valve, the cell was tested and was found to be working well. We checked a number of removed seals on the valve plungers and found a common problem on all of them, the rubber seal on the plunger tip has a permanent indent/footprint on it, which causes leakage intermittently. After consulting and sending images to Graham Killip at " Micromeritics" he confirmed that the wear on the rubber seals are on the edge of their usable life once it reaches that level of imprinting. We ordered 25 plungers and will replace them all once a year for a first trial to determine a routine replacement interval. The plunger and seal unit only cost $10 each and that is not much for a yearly service. We will need 18 for the first complete service overhaul and we will keep 7 as spares. As it is not necessary to replace the valve but only the seal, we should be able to maintain it at a reasonable price. We also ordered 30 O-rings for the cap lids; they are only $1 each and only need replacement from time to time.
A test circuit was built and fitted in a box to enable the Tech or ET to quickly check any suspect cell still in place with no interruption to operation of the instrument and to check the cells while in use or otherwise, this way repairs can be done without interfering with the science time. A interface breakout cable was made up as well that plugs in line with the cell and electronics and can be logged with an analyzer or just a multimeter to keep an eye on it while it's working. It measures the output of the transducer that can be measured and logged, and compared to the calculated PC display. It has no effect on any other part of the normal operation of either the cell or instrument while working. This way it is easy to determine where the problem lies, either on the software/electronics or the cell hardware.
A Text box user manual was compiled and distributed and will be saved in ET's archive, a copy was printed and put in the pycnometer spares drawer.

Cellophane Bag Sealer

Cellophane Bag Sealer was repaired for the sample table; the hot wire broke, removed and repaired.

Super Saw

Super saw lapidary blade replaced after the one in use was worn out to the end of the cutting edge.

NGR

The NGR developed some problems during the expedition, we as ETs were not directly involved as we could not find any technical faults for the problem with the Galil controller or stepper motor. The only indication would be an error instruction on the Galil controller, the problem would clear itself after a program reboot or a complete PC reboot.
The symptoms are: for no known reason the core boat would be pulled back past the end stops and limits and continue driving the stepper motor at the end stop of the track, pushing to go further. After a couple of minutes the stepper motor would get very hot to the extent that it would burn out if not disconnected (which we did in each case). The emergency button does not help either if it is pushed, which is an indication that the program was not running any more and does no further executions entered from keyboard or external peripherals. At the moment it is a soft driven emergency stop executed via the PC. The signal from the E/button just gives the PC the instruction to stop.
I suggested that the emergency should be wired in line with the stepper motor supply, so as to cut off any further motion of the motor if pushed, I did that on the P-mag after similar problems in the past, which ended that problem. The emergency stop is of limited use if it is software driven; the PC might still be busy with something else to be quick enough or as in this case seemed to be in a "hung" situation. That happened in most cases when the PC failed. In such a case you need the PC to stop the track, which is not available any more in this case.
We (ETs) do not know the reason for the NGR PC failures but by the looks of it there might be some data cluttering as the PC takes a very long time to pick up the necessary registry files to boot and slow to start up. By giving the PC hard drive a good maintenance defragmentation and registry scan might help if there is sufficient space available on the hard drive to do that, the drive needs about 10% free space to have available as "scratch pad" to be able to do a proper maintenance exercise and it will take most probably most of a day to complete. Maybe a good idea to do it while the ship is in upcoming port call.
We did not replace any ET related components throughout the expedition on the NGR.

Paleo Lab

Welch vacuum pump for the paleo lab was replaced with a spare and it was sent in for a factory rework. The tolerances on the pump and motor bushes became worn out of limits causing the pump to bind after running for about an hour; it will need to be replaced/machined with bushing inserts. A second pump was booked for a service as well.

Chem lab

Ampulator

Assisted the Chem-tech in adjusting the ampule sealer to get the gas flame to the right intensity to seal off ampules, it was a bit cold and did not seal properly. Working well again.

Water isotope analyzer

Assisted Dave Hodell with third party instrumentation (water isotope analyzer) that had instabilities after being put into operation. We worked in accordance with his Universities' instructions to clear the problem. At first we suspected possible mains interference but after measuring and logging the mains it was ruled out. Further assistance was given to hardwire its gas flow valves in its open condition in the attempt to dry the measuring cell with Nitrogen gas flow through it as moisture was detected inside of the instrument housing. After 24 hrs of Nitrogen flow through the measuring cell the readings were normal.
Manufactured a drilling template/jig to drill holes at 3 cm intervals in the core liner and insert sucking syringes to extract pore fluids at 45° angles.

Fisher Scientific Ashing Furnace

The furnace is in good condition although the element will need replacement once we need to get higher than a 1000°C, we can replace it once we start the Lesser Antilles expedition. The oven controller displays the temperature a bit lower than the actual temperature; at a max reading of 985°, it is actually at 1005° as measured with an electronic probe. We decided to stretch the element use a while till we really need the higher temperatures above 1100° C.
We will consult with the upcoming ETs to find out if they know if we have a spare heater element. I cannot locate a spare element for the furnace, I'm sure we will be able to get one from Fisher Scientific as they still do supply spares for our furnace, seeing that Garrick got a spare fan earlier. We will confirm with them in case they know if we have a spare element stashed somewhere. It is a Fisher Scientific muffler oven Model 750-58/240V/12.5A. The catalog the oven label referred to does not exist anymore. I guess we will have to get in contact with the vendor by telephone for P/N details.

Downhole lab

APCT-3: Temperature tool runs were deployed on all the sites and loaded onto the network. One set of fresh batteries was replaced on the running APCT-3 tool.
SET Tool: A set of fresh batteries was installed on the SET tool on board per Mike M's request.
All the tools ran perfectly without any problems.

Underway

VSP Guns were deployed on the first four sites before we stopped because of the sea-chest issue.

Gym

Cybex 750T treadmill: A 3 kvA UPS was installed on the new Cybex treadmill as a test following previous power problems on the older treadmill during the previous expedition. Supply problems were ruled out, as power from 3 different sources did not make any difference in the problem occurrence (ship supplies, regulated supply and direct UPS supply were tried) and no difference was made. We made a range of diagnostic recordings on the circuit boards driving the 3 phase speed controlled motor and found that the motor controller would go into some erratic behavior at no specific intervals, the recordings were sent to Cybex for analysis and they offered to do a free exchange for the 115V controller and incline motor for a 220V system. We will do the interchange after the arrival of the new components and ship the present 115V system back to them. Cybex has some queries about the 115V controller that still has some unresolved issues. We will install a 5kvA 115v/220v transformer that we have spared to step up the supply to 220V.
We will walk this through with the upcoming ET' to make sure it will be exchanged/modified correctly. They should work with Siem Electricians to make sure about the switchover to a 220V system and still comply with Siem regulations.

Movie room

Optima projector globe went open circuit and was replaced with new one. It's back working again. The Audio Power amp runs too hot and extractor fans were ordered for installation on top of the amp to help with the airflow. A UPS was installed on the power line to protect the equipment and mostly the optima projector, as it is prone to have problems with the power on the ship.

Rigwatch

Rigwatch ran smoothly with no problems.

General

Numerous smaller odd jobs were done as we went through the expedition and Etienne helped with the close-up digital imaging table repositioning to the new spot.
We did constant lubrication and cleaning of battery operated drills used on the Catwalk to keep them from corroding, as it was a high core recovery expedition. We might have to purchase a bunch of extra 3 to 4 mm drill bits as we use them at a high rate while core liners are vented. Some get blunt from the abrasive mud or are broken.
Spares for specific equipment were ordered as well as general stock items that got low or were used up.

PUBLICATIONS SPECIALIST

Paul Pleasant

Summary

Overall, Expedition 339 seemed to be a steady, high recovery and productive expedition. There were changes and challenges to work through, and I think we, as a team, did a good job of communicating and trying to work through them as early as possible (updates to data entry in DESClogik and output through LIMS2Excel). As a first-time yeoperson and publication specialist, there was a learning curve to get up to speed. There were quite a few VCD template decisions that the co-chiefs and scientists needed to make within the first couple weeks so that I could map the data, create patterns and produce results. After some of those global decisions, bugs and templates were fine-tuned; the expedition became smoother and more production work to keep everything flowing through. There have been minor issues to try and solve, but the main goal (as I see it) – of collecting accurate data, producing Visual Core Descriptions and collecting all the reports and observations that the scientists made – has been successful and well organized. I think we have a great team of enthusiastic people invested in solving the challenges involved with collecting vast amounts of scientific data and observations from the core samples.

Equipment & Software Performance Summary

• The latest version of Strater was used on the Publication Office PC and ran smoothly.
• Adobe Illustrator, Photoshop, & Bridge ran fine. No issues to report.
• The Publications Office Mac and PC ran fine. No issues to report.
• Microsoft Excel & Word worked fine as well.
• GroupWise worked fine for emails.
• The copy machine printed out darker than expected, and the black toner faded to a lighter tone at the bottom. I ended up printing all the VCD prints out of the Core Lab printer, since it had more accurate colors, tones and consistency. The MCS staff tried to improve the quality of prints from the copy machine, but will probably need to get it serviced at the next Port call.

Database, entries, and data upload or download related

There were quite a few updates on this expedition, both with data-entry/valuelists in DESClogik and data output with LIMS2Excel. I think we had a good team and collaboration between developers, DESClogik support staff, scientists and myself. I think there was good communication between various parties and good effort in trying to resolve all issues.
A couple upgrades of DESClogik were released during the expedition, with a new Sediment template, value-lists and export options. The DESClogik support staff and developers worked well together to enhance, troubleshoot, and solve issues. After a few issues were worked out at the beginning (noted below), DESClogik seemed to run pretty smoothly, was stable and exported Excel spreadsheets that I was able to plot in Strater.

• The new DESC Sediment template included percent abundances of Major and Minor lithologies, which worked out okay. A request and attempt was made at the beginning to include a separate (fixed) percentage column for prefixes of Major lithologies, but this caused complications in DESClogik; so we decided that the Publications Specialist would create separate patterns for each combination of prefix+principal for MAJOR lithologies and plot only principal MINOR lithologies. There was the potential to create many, many combinations (if one creates a separate pattern for each and every possible prefix+principal lithology), but it ended up not being too bad. For this expedition, I used 23 principal lithology patterns (chosen from USGS patterns) and created 36 additional patterns, as combinations of prefix+principal. By creating separate patterns in Illustrator, it eliminated the complications in DESClogik and helped it run smoothly and stablely – which was helpful for everyone.
• The feature to export all tabs in DESClogik for an entire hole, with Expand sample column checked, has been very helpful and useful. After trying several times to troubleshoot with the developers why LIMS2Excel kept getting incorrect DESClogik data, I began to use the DESClogik export option instead and found it to be more reliable. It exported just what the scientists were seeing in DESClogik (with no incorrect, cancelled or old data), so I found this feature to be very helpful in streamlining my plotting process for VCDs. I would export all DESClogik data in a spreadsheet from DESClogik, and use LIMS2Excel to pull all of my track data, titles, samples and depth scales. The only DESClogik tab I would export through L2E was the Core Summary tab since L2E offers the ability to place carriage returns (a work-around for Strater since it currently does not offer word wrap for the Header pane; which was requested for future versions of Strater). This process of getting DESC data through DESC and track data through L2E worked out great, and required less corrections and trouble-shooting.

Several upgrades of LIMS2Excel were released on this expedition, and the developers were helpful in trying to see, understand and solve the issues that came up, which included:

• Incorrect/old/cancelled DESClogik data being exported (still an issue, but resolved for VCD-purposes, by exporting DESClogik data straight out of DESClogik, and other data through L2E);
• DESClogik tabs not mapping correctly or at all (due to XML differences and changes in the name formatting, resolved again by exporting DESC data straight out of DESClogik);
• Including an option to select only certain cores instead of the entire hole (which seemed helpful for the Imaging Specialist, but not as much for the Publication Specialist);
• The "From DESC Template" was updated and simplified – making it much more useful, but since L2E was still exporting incorrect data it was not as reliable as exporting DESC data directly from DESClogik.
• The option to Filter by Whole Round for Magnetic Susceptibility was updated and useful. The developers worked hard to try and resolve various issues encountered and improve database export tools.

As for plotting data on Visual Core Descriptions, I would provide draft VCDs each day to the scientists and co-chiefs, and marked corrections for the scientists (with DESClogik entry corrections), discuss with DESClogik support staff and/or the curator, or possibly ask a scientist which set of duplicate data the developer should remove. I tried to provide draft VCDs for feedback as soon as possible so that various parties could make adjustments to their process or data entry and resolve issues. I would also printout updated VCDs after corrections were made, images were lightened (with a Photoshop action, after an entire hole was imaged & downloaded), and after Ages and Lithologic Units were added at the end.

Volume Materials

Since this was a high-recovery expedition, there were quite a few documents and reports to keep track of. I found that good organization tools, communication and feedback were helpful in letting people know what we need for publications. The Staff Scientist also did a good job of communicating goals, expectations, scheduling at the beginning and feedback as the reports started to come through. There were clear deadlines; the co-chiefs and staff scientists would review the reports and send revision requests to the scientists; after revisions were made, the co-chiefs and staff scientist would approve it and then pass it to me. I would then check the files and prints to make sure we have everything needed for publications.

• I tried and successfully used Google Docs Spreadsheets for volume tracking, communication and progress reporting with both the Staff Scientist and staff on shore. So far, we have 47 [/88] Reports, 175 [/?] Figures & 89 [/?] Tables. I also used it for my own notes for Visual Core Descriptions (so far, printed 614 of ~700), plus 19 [/25] Hole Summary VCDs (which required a little more work). Google Docs seemed to be a good solution to help keep all the information up-to-date, organized and in one place. I also updated a chart outside the Publication Office for scientists to see the Volume tracking progress.

• I was able to initiate and help automate a process for digitizing the hand-drawn Visual Core Descriptions. Tim created a template in ImageMagic with the section line-scan image, section file name at the top and columns for hand-drawn sediment description. With the help of the Marine Computer Specialists, we were able to setup a feature on the Forecastle Deck Copy Machine, where a user could simply select a group of settings for VCD scanning and load their documents with notes into the feeder to digitize them. The copy machine would scan in the documents, create a multiple-page PDF (from the set of papers), and use Optical Character Recognition to see the text at the top of the page and try to name the PDF accordingly (which in our case was the image file name). The user could then go to the CanonCopier folder on the server, and find their PDF there. They might need to rename it, but it saved a bunch of time! With this automated process, one could scan in about 45 cores/hour (roughly 300 sections or pages/hour) – as compared to manually scanning in each page, compiling a multiple-page PDF and naming each file. This was a helpful feature and improvement, used by scientists and staff members to easily create PDFs of their documents.

General Duties Performed

• I worked with the scientists and staff scientist to work out and finalize a Visual Core Description template at the beginning of the expedition; continued to update the Methods figure and create new lithology patterns as they were found in the cores.
• Draft VCDs were plotted and printed out quickly to provide scientists with feedback on what data are in the database, and if data needs to be corrected. I would look over the VCDs and make notes where I saw gaps, overlaps, duplicate readings (zig-zag patterns), or possible issues that I could see on the VCDs.
• Provide VCD output and try to work with various people – scientists, developers, support staff – to try and troubleshoot where issues might be coming from (data entry, duplicate readings, software bugs or workflow issues.)
• After the scientists' site reports were reviewed by the co-chiefs and staff scientists, I would collect and track all the files. I would also make sure that we have everything we need from the scientists to format and publish their reports. I provided help with files, feedback on progress and how many reports are complete.
• General Yeoperson duties included Port Call activities – checking in staff and scientists; checking out off-going staff; keeping track of who stays on the ship when at port; coordinating with IODP Shore-based staff and keeping accurate & secure personnel records for the Siem Radio Operator, which will be passed to customs, immigration and port authorities.
• Distributed and completed necessary expedition paperwork, to include wireless device, communication policy, photo release, manuscript, and photo copyright forms.
• Assisted and coordinated social events, including: birthday cards and celebrations, holiday celebrations, and the expedition t-shirt design contest.
• Created artwork and designs for the Christmas menu, the New Year's menu and an Expedition 339 t-shirt design.
• Provided feedback and helped scientists create high-resolution graphics and vector files that will be useable for publications.
• Helped the Assistant Lab Officers with the store in providing IODP merchandise.
• Helped keep the DVD movie collection up-to-date and organized. Also communicated the movies available on the server in the Movie room.
• Ran the Virtual Photo Table Controller software to help create Core Composite photos for the database.
• Exported and collected Smear Slide data from DESClogik.

Additional duties

• Helped create Hole Summary VCDs and Site Summary plots for recovery and lithology to be used by the co-chiefs and scientists in reports.
• Provided feedback and tried to help the staff & developers troubleshoot issues in the database, with L2E or DESClogik.
• Restocked Publication supply cabinet as needed, and provided science party with supplies per request.

Suggestions

• If Visual Core Description template decisions cannot be made until the beginning of the expedition and the Publication Specialist gets swamped, it's helpful to know that shore-based staff can help also. I'm grateful for the help that staff on shore was able to provide in creating Strater schemes, making new Lith symbols, and mapping out the 114 valuelist-symbol combinations.
• I found the Google Doc Spreadsheets to be helpful in communicating progress, keeping notes, and keeping organized for the high volume of reports and VCDs. I think this would be helpful for future Publication Specialists. I also put stickers on a chart outside the office for scientists to see, and mark the finished folders with the color green on the server. I think these organizational tools are helpful.
• I think it would be helpful for management to look at how identity data, in general, is stored and handled – needed for travel, customs, tours and ports. The information flows between multiple offices, organizations, and people from different countries through emails and spreadsheets. I was a little concerned about the security of such information. I talked with the MCS and made sure that all of my files were always behind a secure password. I wouldn't want a virus or an unauthorized person, to be able to access this information, and have the personal data of everyone aboard compromised. I think, at the least, a protocol should be made for how Yeopersons should deal with this information, and who should have access to this. At best, I think it might be better to have this identity information only kept on a secure server and accessible only by those who need it. A central place would also allow for corrections to easily be made, and a copy of the information could be transferred to those who need it (with consent, knowing that they're responsible for the security of that data). I think this overall process could be looked at and improved.
• I also appreciated that my supervisor was able to travel to the ship to assist me at the beginning for Port Call. There is a big learning curve for a first-time Yeoperson/Publication Specialist, and it's helpful to be there a day before the scientists arrive – to get your bearings, to try and learn all the things you're supposed to help communicate and provide good customer service to our clients – the scientists.
• As a first-time Yeoperson, it's hard to anticipate what you might experience out here, but I think with the pre-cruise template workshop, and working as a team early, I was prepared.

SYSTEM MANAGERS' REPORT

Grant Banta and Mike Cannon were the Marine Computer Specialists for Expedition 339, Mediterranean Outflow.

Summary:

During Expedition 339 the IT infrastructure performed as intended with minimal impact to operations.

Servers

Microsoft:

The Microsoft servers performed well during this expedition with no issues to report.

Novell:

Web mail continues to fail occasionally requiring a restart of the service to restore functionality.

Solaris:

• We had an issue with the Oracle database that caused some problems early in the expedition. Some table spaces in the database had run out of space and required our DBA to expand the space available to these table spaces. Once completed, the database returned to normal operation.
• Cumulus continues to consume disk space in the logging directory requiring an occasional restart of the Cumulus service to free it up. This is an issue with Cumulus itself and should be fixed in the next update of the product.

EVA4000 Storage:

No problems were encountered with the EVA; it performed as expected.

Network:

The networking equipment performed as expected with no issues to report.

PC Workstations:

• A couple of systems became infected with a virus when users clicked on malicious links while using the Internet. This required a complete re-installation of the system to ensure the infected files had been eradicated. We were able to accomplish this with no loss of data.
• The NGR was having issues locking up so we elected to replace the PC and connect all USB connections directly to the system to remove the hardware from the equation.
• We have identified the cause of an issue with our XW4400 workstations. Occasionally during initial startup the system might crash and require a reboot. We have determined that this is caused by an incompatibility between the storage hardware's firmware and the operating system's driver software. The only way to correct this condition would be to upgrade the firmware to a more recent version. However due to this platform's age, this hardware is no longer supported by HP. Although it is not likely that they will release an updated firmware for this system, we are discussing the issue with them at this time. For now, once the system is completely started and is passed this initial startup phase it is reasonably stable and is still a workable platform.
• The Dtech system in the core lab developed an issue that caused it to blue screen and reboot constantly. It appears a portion of the operating system had become corrupt, preventing a clean boot up. We restored the system from backups and the system returned to normal operation.

Apple Workstations:

A video card failed in one of the systems in the imaging office. We replaced it with a video card from our spares inventory and ordered a replacement card.

Printers:

• The copier developed an issue where color printing resulted in uneven coverage. We replaced the toner cartridge and drum kit following suggestions from our service manual. This did not correct the issue. After further review of the service manual we decided to have the copier serviced at the next port call by a Canon service tech.
• We added a function to the copier to allow users to scan documents directly to a shared location on VOL1 via Samba. This is a much more streamlined process over the previous method of sending scanned documents via email.
• The 42 in. plotter in the user room developed a problem with its carriage belt. The belt was disintegrating and separating from age and use. We replaced the belt from parts in our spares inventory and restored operation.

Satellite/Internet/Phones:

• We had some intermittent signal quality issues with the aft antenna. We conducted troubleshooting procedures with RigNet to determine the cause of the problems. During the course of troubleshooting the problem seemed to clear up on its own, hampering any further investigation of the cause of the issue. We are continuing to monitor the aft antenna for any signs of reoccurrence.
• We installed new software allowing remote monitoring of the antenna control units.

Other Equipment:

The tape library had a drive fail on Exp 336. We received the replacement drive and successfully installed it into the library. The library is fully functional again.

DEVELOPERS REPORT

Tim Blaisdell, Dwight Hornbacher

Summary

As often happens, the early part of the expedition was fraught with major problems, but these were slowly worked out as the expedition progressed. We have very few issues left with the majority remaining with SampleMaster. The biggest issues we encounter (with software) involved LIMS2Excel, SampleMaster, DESClogik, the Affine/Splice Uploader, and Resteasy-Lims-WebServices. The ReportOverview was deployed for the first time on ship, and appears to be working quite well; the population scheduled events also appear to be populating the x_overview table quite efficiently. A newer version of the ChangePassword application was also deployed for use on the ship. There were a few issues with the loggers, most of them being user errors, but there were also some hardware issues that cropped up. As of now, all appears to be ready for the next expedition.
One of the more important items on this expedition was a more formalized format for Change Management. After discussions with James Rosser, Paul Foster, Algie Morgan, James Zhao, Tim Blaisdell, and Dwight Hornbacher, it was decided to adhere as closely as possible to a more formal change management policy. We felt that this went very well, and was well received and clarified communications a lot. We created a new e-mail account, JR_Change_Mgmt which would alert the appropriate parties to a change and get permission from the LO and Staff Scientist before deployment. We used the following email template in these communications:
Subject:
Change Management Request: [application or hardware] [new version number]"
Body:
This email is to formally notify EPM and Lab Officer about software upgrades that are available and to request formal approval to proceed with deployment.
Software Update: [Application or hardware and new version number]
Description: [A non-technical description of the software or hardware change, the reason behind it, and what was done to resolve the issue]
Risk to Science/Ops Operation: [Risk level: Low, Medium, High, etc. Include an honest, straightforward assessment of any possible risks and impacts]
Rollback Plan: [An explanation of what will be done if this deployment creates more problems than it solves - essentially an estimate of the time required to restore back to the previous version]
Benefits of the Deployment: [How will this change increase the effectiveness of the operations?]
Scheduled deployment: [When you or others are expecting the change to be deployed]
Once deployment had been completed, an identical email would be sent to the same address list, with the subject changed to "Change Management Deployment." (I [Tim] would also remove the "Scheduled deployment" line, since the deployment had already been made.)

Loggers

The following is a brief overview of what was done with respect to specific loggers and applications. This is not in any specific order.

SRM

Major issues were user errors; mostly, loading data to wrong sections. We were not able to update the file name in Asman for these cases; this needs to be addressed since this will continue to be a major hurdle in metadata assignment. Also, we would like to suggest a cradle next to the logger channel that would hold the next section and also scan the label on the section while waiting.
There was also a database issue with one of the SRM constants regarding the orientation component. Originally, SRM had numeric values for double or single line orientations, but with discretes it became necessary to use strings to indicate orientation in reference to the arrow on the sample and its relationship to the opening of the SRM cavity. So the change was made in the LIMS constants to change the field to T instead of numeric to allow for the string functions to apply.
A major problem in location of sample in the SRM cavity appeared when the users did some point source testing. They added a point source to the tray then added a lead weight to keep the tray from rotating. The max intensity was four centimeters off of location. Trying a discrete tray with no weight gave maxes, which were right on target. Then using a section half with a point source impregnated into the sediment, also showed a four-centimeter offset of the max intensity. It appears that the slack in the line, which moves the tray, is affected by the weight of the tray causing a proportional change in the offset with increased weight obtaining some maximum at about four centimeters. We recommend a change in configuration for tray movement. Use two motors in a push-pull association so that the line is shorter and kept taut during measurement.

SHIL

Added a dropped line text box to the left of the resulting image display; the previous version only showed a pop-up box which went away when the user trimmed the image. This caused a loss of location information. We did see an increase in dropped lines and were able to find two causes for this problem:

• First, the encoder on the side, away from the user, became loose. Tightening the screws resolved this issue. These screws should be checked on a regular basis since it is obvious the tremor of the ship causes the screws to loosen with time.
• Second, we found that the metal rod on which the encoder rides gets grimy, causing dropped lines; it needs to be cleaned and a light oil applied sparingly to the rod regularly especially on high recovery expeditions.

The Microscan 4 label scanner failed repeatedly, and we were eventually forced to replace it with a hand laser reader. The user now reads the end caps with the gun and needs to be aware that the cap must be kept with the half-section or data will be set to the wrong metadata. As it stands now, the image portion of the display (where the camera image from the Microscan reader used to be shown) is no longer used for anything.

SHMSL

The SHMSL would sometimes lose its reflection panel. Check the utility that sets elements on or offline and make sure it is not set to offline. Also, if not offline, then the application will have to be re-started. As a last resort, restart the computer. Again, the end cap is used which means the user has the possibility of assigning the wrong metadata to the half-section.
I, Dwight, do not believe the reflectance is giving the right spectrum data. I tested the tiles using both the saran wrap and without. There was not much difference between the results, but, when comparing the results to the tile certified results, there appears to be a major difference. Houpt believes the white calibration lens needs to be cleaned, but I do not believe cleaning will improve the quality of the data.
A software defect that was frequently seen: Upon launching the SHMSL logger software (the LabVIEW program), it would sometimes come up without the reflectance portion – as if the device were not being detected. Restarting the computer and trying again would clear this up, but it's an annoyance.

NGR

Twice during the expedition, the NGR workstation lost communication with two of its 8 "detectors." On both occasions, this resulted in a major interruption of core flow through the lab. Although we are tentatively hopeful that the problem has been resolved (as I shall describe below), we cannot be sure that it won't happen again.
The detectors communicated with the computer via USB, and (at the time of the failures) through an external USB hub. Once the failure has occurred (the loss of the detectors), the only solution seems to be a complete shutdown and restart of the NGR hardware. However, we strongly suspect that either the external USB hub, or the internal USB hardware, is at fault. Once the failure has occurred, the NGR hardware is in an unknown state, and cannot be recovered except by doing a complete shutdown (a lengthy process). After the last failure, we replaced the workstation hardware (placing the existing hard drive into a different CPU) and rewired the USB connections so that none of the detector cables pass through the external USB hub. Since we did this, the problem has not recurred, but we can't be sure that we have resolved the problem. Dwight believes the internal USB hardware was at fault; it is my (Tim's) opinion that the external USB hub was the culprit. In any case, both have been replaced now.
There is also the physical problem of the inner rails being higher than the outer rails. Upon run-in of the section, a Galil error occurs because the pusher has to use more current to overcome the hump. In the case of the heavier cores, the current limit is exceeded, and an error is generated. A user just closes the error message and restarts the process.

Special Tasks

This logger worked well throughout the expedition.

WRMSL

We had a problem with the section not always stopping when the laser beam was broken. Trevor discovered the laser was returning corrupted values, which caused this problem. We resolved the issue by checking the output of the laser and ignoring those, which did not meet criteria. The logger works well now. We did have an issue with the switch at the end, which triggers when a core slides over it. That now works, but the users want to turn down the volume because they do not like the noise it makes. We do not want to change that because we need the users to be aware and react quickly in making sure the core does not drop on the floor. The PWL still has problems with voids in the spaces. The user no longer sees the chart of the velocity, and we do not plot these points on the view since they are plots of the velocity through the core liner.

Thermcon

Had the usual problem with users not assigning metadata correctly; need to emphasize to the techs the importance of training the user in properly defining the metadata. Moved Thermcon down to the back section of chemistry where they obtained better results.
It is my opinion (Tim speaking) that the ThermCon Uploader application needs a major overhaul. I feel strongly that we ought to move its functionality into MUT, and when we do, we ought to take care to make its interface more intuitive (this latter needs to be done whether we move it into MUT or not). Note that, relative to many of our other projects, the work required here is small.

Correlator

Worked well with all but the uploaders; only one set of data was adequately loaded to the database. There are issues, which still need to be addressed. Among these, the loader is not always loading the values into the x_sample_depth table. And some of the affine values are not being loaded. Need to check the xml parsing. Had a problem with the user name, Lorenz, in logging into the database. His name would work in all the programs where a login was required, but would not login at the correlator logins. I, Dwight, have not been able to resolve this issue. He used the Acton account for the correlator upload.

Gantry

Appears to work well, except the laser stopped ranging for a short time. Do not know why and haven't seen the problem since.

SampleMaster

There are still several problems with SampleMaster (unexplained crashing, unresponsiveness, etc.), and the general consensus among those who use it (Chad and others) seems to be that it is in need of a major overhaul, if not a rewrite.
In the course of this expedition, several problems were fixed related to SampleMaster, but all these were found in the webservices (resteasy-lims-webservices primarily), and no new version of the SampleMaster software itself was deployed. Most of the problems fixed had to do with code that updates the parent samples' depth or length information when edits occur after initial upload.
One issue that remains unresolved is that sometimes it will skip printing the first label in the series of labels printed upon upload of a set of core sections coming off the catwalk. It is my belief that this problem does not lie in the SampleMaster application, but in the resteasy-printer webservice. When this happens, the user can just re-print the label and it comes out fine. I have not discovered the source of this defect.

MADMax

Had issues with the solenoids on cell 5. The vent and the expansion solenoids were not opening. They were replaced, and the cell has been operating well. We took one of the solenoids apart and realized that the spring and the rubber plugs were the possible points of failure. We are planning a yearly maintenance program where we will replace the plugs, springs, and O-rings. I, Dwight, am working on a new test program so that the ETs can work with the cells without removing them from the box. They have also created a test set up where they can test the cells outside of the box.
(Tim speaking) MADMax performed very well throughout the expedition, I felt. However, the main issue that still eludes me is why it will lock up when multiple PYC windows are allowed to close at close to the same time. This problem has not been resolved, despite my efforts.
One major hiccup occurred when the MCS did some work on the MADMax workstation itself and rewired the balances differently than they had been wired (he wired them up correctly, it seems, but they must have been incorrectly wired before). The result was that the "Reference" balance became the "Unknown" balance, and vice versa. For an entire day, the technicians using MADMax didn't notice this change, and were putting the samples into the "Reference" balance and the standards into the "Unknown" balance. This caused a lot of rework. At present, the cables connecting the balances to the computer have been re-labeled on both ends, so hopefully this will not recur.


During the expedition I completed and deployed a new version of MADMax with the "send this result to…" and "swap this result with…" features enabled. This was done late in the expedition, and was probably not used a lot, so that's something to keep an eye on. I also implemented several minor changes related to user requests/wishes.

DESClogik

For the first few weeks of the expedition, DESClogik was a major source of frustration to those who used it – particularly Larry Krissek and Jun Kuroda (the heaviest users). The biggest issue turned out to be a change that had been made that (inadvertently) was causing large amounts of log data to be transmitted to a LIMS table intended to capture information about crashes and the like – instead, every trivial log entry was being sent over the network into LIMS. Once this was rectified, user satisfaction with DESClogik immediately went up several notches.
Several other changes were made as well. Larry and Jun (and others after Larry left), being almost constant users for much of the expedition, found quite a few problems. Most of these were fixed. However, the "check for overlaps" feature was disabled due to problems found with it. This needs to be addressed soon.

Virtual Photo Table (VPT)

A new version of this was deployed, which is significantly enhanced, mainly to be more interactive, and show more information on screen about what it's doing. This was done mainly because it looked like the decision was going to be made to put oversight of this application into the domain of the pubs specialist. The application now shows detailed information about its activity on-screen, and minimizes to the system tray to keep it out of the way of the pubs specialist's normal usage of his workstation.

Web Applications

Web Tabular

The lat-longs for the hole-summary report were not being downloaded to the file. The problem was found in the RESTEASY-LIMS-WEBSERVICES and corrected. Also discovered Column gaps in the SRM reports; two extra columns were inserted and all subsequent data was placed under the wrong columns. Again, this was a REST-LIMS-WEBSERVICES problem and was corrected.

Changepassword

The application was updated and mavenized. It was upgraded to work correctly; before, it did not always change the password in the database. It is now at version 4.0.

Report Overview

This was deployed for the first time on the ship. It appears to be working well and the scheduled events populate the x_overview table properly and the functions are working very well. There have been no known issues on the ship as of yet.

NAV Loade

The navloader no longer runs on Krakatoa; it is currently running on the build box in firedaemon. The application was upgraded to run OJDBC6 and to use the new format for connecting to the database. I, Dwight, have created a new navloader using a better scheduled timer which came out with Java 6; this upgraded version can be operated by the underway tech.

LIMS Database

Had a major space allocation problem with the LIMS Database; there were only 20 megabytes left in the tablespace. The onshore DBA increased the space for several of the tablespaces. However, at present the "LABWAREIDX" and "LABWARE" tablespaces in yellow and around 80% full.

LIMS2Excel

LIMS2Excel was upgraded from shore to include the new DESC format in its data gathering process. It required several major changes before it was able to adequately handle all of the needs of the pubs specialist. It was not handling canceled values correctly, which required a major review of all SQL queries. The queries were also tuned so performance increased markedly. Since both the Special Tasks and WRMSL loggers were both working, the application required a filter to select which values were desired from these two. It was also discovered that the offset column was not always returned as part of the SQL data query; it now checks the number of returned columns and adjusts the data gathering properly.
The saved templates for loading menus would not save properly for DESC constraints because of spaces in the settings name and colons in the identifier. The DESC tags now have two additional attributes, template and setting. Now the user can save and reload the constraint templates without problems.
There were also issues with spaces in the settings name in the data collecting process. The application was removing these from the name, but, when the application would try to match the values with those in the result table, they would not find a match, and data would not be returned. These filters were eliminated where appropriate. When classifications were part of the download, authors' names containing apostrophes or single quotes, such as D'uBigne, would not be properly returned. Now the application looks for these and assigns an escape character before them so the database does not consider these as end or begin quotes for a string.
The core list table was fixed so that the cores and core types are now in ascending order, not string order. At the same time, the list selection mode was changed in order to allow random selection of cores. This allowed the expedition photographer to download only those photos he wanted to check. Another major issue came with the user of the jxl jar files for excel file reading and writing. This jar has not been updated for the newer excel file format and had a limit for the number of rows that could be created. The newer jars from Apache, the poi jars, now replace the older jar, the row limit was removed. The update created an unforeseen problem; the core scaling was not done properly. Solved this problem in the sheet creation for the core scale, now all scales correctly.
The follow the splice part of the application has been worked through and has worked for one set of data, Site U1385. But there is no other correctly loaded set of splices so it cannot, at the present time, be shown that it works properly in following the splice for MCD depths for other sites.
There is one issue that has not been resolved. If a user describes a section at a longer scale, then does the same for intervals within this larger interval, there will be an apparent overlap of the data in the Lims2Excel DESC report. This will require further study since DESClogik handles description data differently than can Lims2Excel. Lims2Excel is a data gatherer and does not know how applications put together the data, so it is limited in how it reports the results of its collecting.
[Tim speaking] There are still unresolved problems with the way LIMS2Excel retrieves DESC data. Essentially, the problem is this: the exact contents of the DESC data retrieved by LIMS2Excel does not always match what DESClogik shows. In some cases, this may be because of post-processing DESClogik does before displaying the data, in other cases it may be that LIMS2Excel's SQL queries need to be tweaked to create a result that matches exactly what the user sees in DESClogik.
The upshot of all this is that Paul Pleasant was eventually forced to retrieve data for the VCDs directly through DESClogik, rather than using LIMS2Excel. As it turns out, however, this may end up being the best way to do it, since it may be impractical and redundant to exactly replicate all the behavior of DESClogik in LIMS2Excel. DESClogik was designed with Strater in mind anyway (it has specific export functions designed to produce output compatible with Strater), so in my [Tim's] opinion it would be a good idea to use it going forward as the preferred method of retrieving DESC data for the VCDs.

MICROBIOLOGY LAB

Not in use this Expedition

CHEMISTRY LAB

Chris Bennight & Erik Moortgat
(Jan 11, 2011: one more RCB hole to drill/sample)

Details to be provided in lab notebook (\\JR1\TAS\Lab Notebooks\Chemistry\Chem 339\Open Notebook.onetoc2)

Gas lines/manifold

No issues to report.
A restrictor was put in-line on the lab air supply at the squeezer drying line.

Ampulator

The ampulator was used to seal 5 mL, 10 mL, and 20 mL vials.

Vial seal integrity

If the flame is set too far from the top of the vial then there is a tendency for the glass to "break" off when any pressure is applied. This can be tested by pushing gently on the glass seal on top after the vial has cooled. A few vials exhibited this behavior (10 and 20 mL vials, but not the 5's) and had to be resealed. Ideally the flame should be 2-4 mm from the top of the vial and the issue will not occur.

Tray actuator arm

There is a tensioner, which keeps the arm that moves the vial tray from popping inside of the case. This broke during the leg and the top of the machine had to be removed so the arm could be re-located. It was re-assembled without this arm and appears to work properly – but if pushed the arm can pop inside the case again (and will need to be dissembled and pulled out).

Belt maintenance

It had been noted on previous expeditions that there was difficulty getting the vials to spin properly. Whenever this occurred a quick wipe down with isopropyl alcohol remedied the issue (place some IPA on a KimWipe and hold it against the belt with the belt power turned on). Eventually the belt will dry and crack and needs to be replaced – this should happen no more often than 2-3 times a year though (and the belt is an inventory item). The belt was changed out this leg.

Balances

No problems were encountered with either the Mettler balances.
The Cahn balance at one point had a corrupted configuration file and Dwight was required to come to the chemistry lab to fix it. Typically we keep a zipped up copy of valid configuration files, so when they become corrupted (it's normally something to do with tare values) the zipped copy can just be extracted over the valid copy. Note that this might require re-adding users.
A spare balance arrived in the shipment. Tag #RF52371. This balance had been placed on the shelf over the GCs and is a potential spare for the chemistry, XRD, or Phys Props systems.

Carver Presses

The leftmost Carver Press was leaking from an elbow to the pressure gauge (on the press portion). Roy Davis worked with this and managed to fix the issue. He also noted that the press pumps appeared to be low on hydraulic fluid. There is a fill plug in the back and with the pressure released (transmission in the leftmost position) the fluid should be ~1 inch from the first thread in the fill plug. All the presses were topped off.
There still appears to be a source of leakage in the middle pump unit, but we believe it to be from over-filling. The situation is being monitored.

Cary Spectrophotometer

A Cary 100 spectrophotometer was delivered and installed this Expedition – in the location where the DA was previously set up (the DA has been re-located but is still operational – see DA section). The software to run this has been installed and configured on the shared DA/IC computer, and spare parts have been located in drawer D-D4.
The spectrophotometer was used extensively for ammonium determination this Expedition, and offered excellent precision and accuracy. No other methods were run on it.
A manual has been created and submitted for review.
It should be noted that the Simple Reads software must be on and running on the computer for the Fill/Return button on the routine sample accessory to work.

Discrete Analyzer

The discrete analyzer was relocated to under the cabinet – as seen above – to make room for the spectrophotometer. This was done due to usage patterns of the machine – the technician must change each sample manually on the spectrophotometer, while the DA can be loaded once for the entire run. The DA is connected to power and to the same original computer and still works as expected. The frame can be opened far enough to get to all pieces inside the DA – but not far enough to lock in the second position – it must be held up either manually or with a bungee cord attached to the desk above. But there is sufficient room to work.
No samples were analyzed on the DA.

CHNS

The CHNS was used heavily this leg – primarily as a component of the organic C/N ratio.

Calibration standard

Early in the Expedition we had issues with impossible C/N ratios. The standards (sulfanilamide), check standards, etc. were all coming in reasonably well (<5%) and the chromatograms themselves looked reasonable – so nothing stood out as immediately erroneous.
After further investigation it was determined to be a calibration range issue – the total carbon delivered to the column for the samples was bracketed in the calibration range, but because of this the nitrogen values delivered by the samples were falling well short of the actual calibration range – because sulfanilamide has a significantly greater %N per mass than the sample do. Though separate calibration curves could have been constructed, it would have been difficult to weigh out sulfanilamide in small enough quantities to create a proper curve – so a new standard was selected. We had a Thermo CN standard which was ~ 0.2% nitrogen and 2.1% carbon – this provided to be a much closer matrix to our samples and so this was used instead. After this the C/N ratios were coming in correctly
This issue was submitted to the lab working group but we never heard anything back from them on the boat and were not able to obtain any sort of meeting minutes/notes/action items.
We should discontinue the use of sulfanilamide as a standard though and instead move to items which better match the C/N ratios of the samples we are measuring.

Issue with excessively high baselines

An issue had been reported by the previous Expedition of high/wandering baselines, an inability to stabilize to 1000uV, etc. When the instrument was first fired up this problem persisted and we were able to troubleshoot it. It was caused by damaged fittings to the perchlorate water trap – there are silicone O-rings and stainless fittings on the sides, and these (the stainless) fittings had significantly corroded – and one of the silicone O-rings was missing. After replacing these parts the baseline immediately stabilized to 1000uV (after adjustment) and did not exhibit any wandering.

Issue with missing sulfur peaks

It was also reported that sulfur was not showing up on the instrument. We also observed missing sulfur peaks – it was determined that this was due to a column retention time limit – the sulfur peaks would come off the column after the run was over/as it was ending. We adjusted the run time to 900 seconds (from 750) and were able to view sulfur peaks as expected: (No hydrogen peak as the perchlorate water trap was installed).

Coulometer

Instrument Connectivity

During one run the coulometer software seemed to lose connection with the instrument, but power cycling the instrument restored connectivity.

Premature Run Completion

In a few runs it was noted that the measurement would "complete" before the sample had been fully delivered to the solution –

This is typically caused by hitting the measure button to soon. Best practice is to slowly aliquot the acid in to the vial, and only then press the measure button in the software. It takes _{15-20 seconds for the CO}2~ created in the reaction to make it to solution and start effecting a change.

Flow meter

It was noted that there was no flow meter attached to the coulometer gas supply so one was added. This should allow for more consistent measurements (and is required to properly setup the system).

Silver nitrate frit cleaning

It had been noted previously that the frit in the silver nitrate trap would clog up and some preferred not to use them because of this. The frit can be cleaned very simply by allowing it to soak for a few hours in an ammonium hydroxide solution and then rinsing with copious amounts of DI water. Compressed air should first be used to blow out and loose silver chloride/sulfate.

Freeze-drier

No issues encountered with the freeze-drier. Most of the samples for CARB/CHNS analysis were dried in the XRD lab.

GC3/NGA

All headspace samples were analyzed on the GC3. No issues were observed with the instrument itself. A few times the MUT appeared to not be processing results, for no apparent reason we could determine, and had to be restarted. We are not sure if this was user error or not, but people should check for this in the future to see if it is a new issue.
The NGA was calibrated midway through the expedition when we started seeing a little propane, but only one sample was actually analyzed on it.
An attempt was made early in the Expedition to retrofit the FID from the NGA onto the GC-PFT instrument to allow for an alkenone analysis method, but it would have required to substantial of a change to the NGA to achieve this so the project was scrapped. The FID, detector board, electrometer, and EPC from the GC-MSD have been removed and are en-route to the ship and will be installed as a second detector in the GC-PFT device to allow for this capability in the future.

Hydrogen generators

No issues to report. The cartridge on the new generator was changed.

IC

This expedition was this crew's first exposure to the significantly updated Chromeleon 7.1 software package. There were also reports of "problems" with the sulfate data from the Chemistry LWG, but we were never able to get any further information or response from the group on what the problems were (reproducibility, accuracy, etc.).

Pump pressure issues

It was indicated that there had been issues with the pump pressure (high variability in pressure, saw tooth patterns, etc.). We found a loose screw on the primary pump head of the system 2 (cations) pump and that seemed to help with the cations pressure. We also sonicated the pistons in HPLC grade methanol then DI water per the manual, but that didn't have a noticeable impact. We attempted to change out the check valves but it turned out that the part number we had for the check valves was incorrect.

The valve on the left, are the spares we had, the valve on the right are what was in the machine. After dialog with Dionex it was determined that we need an updated part number – 045994 . This has been added to the checkout sheet. Because of this we were not able to see if changing out the check valves would help clean up the variability on the pumps, but when the new parts come in this should be evaluated.
Gradient mixers will effect pressure as delivered to the column – we were going to change them out as well be again we had the wrong parts – somehow we had 4mm gradient mixers instead of 2mm. The part number and description was updated on the checkout sheet.

Firmware

It was noticed that the firmware validation matrix which came with Chromeleon 7.1 noted that the supported firmware versions for the various IC parts were much greater than what we had. After discussion with Dionex, we obtained and updated the firmware for the IC (main module), and the autosampler. The eluent generator and DP pump system were already at the proper firmware.

Simultaneous run mode

The instrument configuration was re-created as two systems/timebases in order to allow the anions and cations to be run simultaneously; as it was currently configured, the two systems could not be run independently. Dilution methods were created for the anions run (as it is slightly shorter than the cations run). When starting, if you are having the autosampler do dilutions you need to ensure that you hold off on the cation run long enough so it doesn't "catch up" and try to run a solution which hasn't been created yet. Typically waiting till 1/3 to 1/2 of the way through the anions run is sufficient.

Cations method development

The cations have always performed reasonably, but potassium has always had poorer reproducibility than magnesium or calcium. This (and the poor reproducibility of sodium) is due to the fact that potassium is eluting as a rider essentially on the sodium peak. We were able to increase the separation of the sodium/potassium peak, but still keep a tight peak shape on the divalent cations by running a gradient elution. This is the method currently configured and works well. Typically reproducibility for replicate runs was < 2RSD%.

Reproducibility's for various captions over the expedition (average of 1:200 IAPSO check standards)

Anions method development

When we started the leg the anion retention time was down to 50% of what it should be (indicating a significant loss in theoretical plates). This is a situation we have seen before. After discussion with Dionex they indicated it is likely because we have the IC pumping DI water without the eluent generator or suppressors running. They stressed that we should generally always have the suppressor and EG turned on when running the system. We have followed that advice this leg and have not seen any significant shift in retention time.
With regards to "sulfate" issues though we couldn't get any guidance from the LWG on this we investigated. I am guessing that these issues are reproducibility and maybe detection limits. I suspect this is all attributable to high baseline noise – in comparison to the peak size. See below for three replicate measurements of a 10% IAPSO (1:2000) standard.

You can see we had 20% variability in area of measurements, out of the exact same vial. I'm not sure if there is actually an issue with our baseline noise, or it's a function of our configuration (running a bicarb eluent is going to be nosier than a hydroxide eluent).
Sulfate was typically analyzed by height as that produced better reproducibility and accuracy than the area method. A 10% RSD was typical for the height method.
Further follow-up with Dionex is needed to address this.

Misc software configuration

The report template was configured so that all the previous steps included in the manual for exporting data are now automatic (selecting a directory, channel, excel, excel options).
A new custom variable, "TextID" was added to the existing and default sequences – and incorporated into the report designer. This allows the operator to enter both the text ID and a typical sample name (330-U1390A 34R4, etc.) – which helps put the data in context when viewing it in the software.

ICP

The ICP was initially used for both majors and minors this expedition, but about halfway through the science party indicated they were satisfied with the IC cations data so the ICP was only used for minors after that.
At the start of the expedition the initial majors run was exhibiting extreme scattering of the replicates on some of the standards (the higher concentrations standards). We hit the typical reproducibility points (sample introduction, glassware, etc.) but still had the problem. Eventually it turned out we were outside the operational range of the detector (doesn't hurt anything, but reproducibility goes in the pits). We ended up adjusting the majors' method from a 20 second view to a 1 second view and the calibrations cleaned up greatly.

Calibration with 20 second axial view
















Calibration with 1 second axial view







Not sure why this issue hadn't cropped up more often before, but regardless it seems fine with the new method.
Otherwise there were not significant issues with the ICP this expedition.

Salinity

No problems encountered with the digital refractometer.

SRA

Installed new PCB main board (req # 1111029DH) to replace broken one. Broken one to be sent back to Weatherford Labs (via David Houpt).
Note about USB cables:

• When you change USB ports you have to find the COM port in Device Manager that corresponds to the correct USB port
  • in PORTS - USB SERIAL PORT
  • in SRA.INI, you have to make sure that this COM port (from above) is the same number as in the parameter USBISCOMMPORT

FID issues:

• The PCB main board exchange does appear to have remedied the lighting issues.
• Prepped standards to be run. FID stays at constant 2.5V during run. E-mail sent to Weatherford.
  • They say that 2.5V is the ceiling of the FID so a short must have occurred.
  • Jurie (ET) confirms an electrical short in the FID glow plug. It is replaced with one from the GCs.
• Prepped standards to be run. FID will not auto-light but will light when a flame (cigarette lighter or propane torch) is introduced at the FID outflow port when the pedestal is raised and the software indicated that the FID is being lit.
  • Time was very limited so we could only confirm that the instrument 'works'. Reproducibility of the standards was however, poor, but time was not available to manually light the FID whenever a new sample was to be measured. There was also no time available to troubleshoot the FID auto-light issue.

Titrators

Alkalinity

We had the standard 1-3 crashes this expedition – only one was the –INF pH error though – the rest were Labview runtime crashes.
Electrode cable needed to be replaced. Requisition made to order two new ones.

Chloride

A chloride auto-titrator was brought out for the first time this expedition and used very heavily. It was installed next to the alkalinity titrator and connected to the same computer. A PCI serial port card was added to the computer to allow for both computers to be connected. (A FTDI usb<-> serial converter was tried first but didn't work).
We were able to achieve < 1% RSD on replicate measurements of IAPSO (~5-10 minute run, 500ul of sample) – here's a typical set of data.

When viewing production measurements actual precision was <2% RSD – the increase is due primarily to pipetting errors.
The method we adopted was to measure each sample twice (1mL of total sample) – which was still faster than the alkalinity device. If the measurements differed by more than 2% we added in a third measurement. This worked very well and we only had to add in a third measurement on 3% of the runs.
Initially there were issues with reproducibility of the data, but this was finally narrowed down to pipetting issues - and after some practice everyone was on the same page and producing acceptable data. It should be stressed that pipetting is absolutely critical here and should be stressed when training new operators.
The software was also modified to allow a grid type view of the history (listing sample, chloride concentration, etc.). This view also allows the end user to cancel and re-upload measurements as desired.

DIC-DOC

A new proton gas generator installed and is fully functional.
The DIC-DOC instrument itself was in a strange state. During 329 it appears that the science party re-plumbed quite a few of the lines in a nonstandard manner. These were all documented in the lab notebook and set back to stock. After some cleanup runs a calibration was run on the DIC portion only and the instrument appears to be working properly (at least that system)

The wet and combustion based TOC modes were not evaluated due to lack of time. This instrument really needs to have some resources dedicated to it to create a manual and some SOP's. There are definite workflow issues to be addressed (standard sample entry, data export/upload, but also things such as sample volumes – the autosampler containers are generally too large (5-40mL of sample) to be used for routine sampling.

Water system

Completely ran out of Barnstead RO carbon cartridges ship wide. AMS stock level therefore increased. When the new cartridges come in the RO cartridge should be changed out ASAP.

Miscellaneous

Picarro

See report from Dave Hodell (inorganic geochemist) for more information.

Shipping equipment

: Hamilton Microlab diluter (tag #01650): hand pipettors (2) – to be cleaned/calibrated
: SRA main electronics board: titanium base plate - to be machined
: Titrino titrators: IC gradient mixers (3)
: TOC gas generator (tag #90713)
: Hazardous waste from Exp336 left on-board per Mitch Mitchell's request. Was to be sent to Lisbon anyway.

UNDERWAY GEOPHYSICS LAB

Roy Davis/Erik Moortgat

Summary

The magnetometer was deployed on the transit across the Pacific. Bathymetric data was collected on the transit from Auckland and L1T, L2T, L6T, and L7T of Exp 334. The sonar was not used when making return visits to the 334 sites, as an accurate PDR had already been obtained. Navigation data was collected throughout the entire transit and expedition. SHIP WAS NOT IN THE PACIFIC THIS EXP. **

Data Summary

Expedition 339 consisted of eight transits (1,112 nm) and seven sites.
TransitsPonta Delgada, Azores to U1385(L1T ≈ 738nm)
U1385 to U1386 (L2T ≈ 122nm)
U1386 to U1387 (L3T ≈ 2nm)
U1387 to U1388 (L2T ≈ 55nm)
U1388 to U1389 (L2T ≈ 25nm)
U1389 to U1390 (L2T ≈ 22nm)
U1390 to U1391 (L2T ≈ 103nm)
U1391 to Lisbon, Portugal (L2T ≈ 80nm)
Sites: U1385 A/B/C/D/E U1389 A/B/C/D/E
U1386 A/B/C U1390 A/B/C
U1387 A/B/C U1391
U1388 A/B/C
Site fixes were performed at each site/hole.
Event data points were gathered every sixty seconds when underway and every thirty seconds when on-site.

Equipment Performance Summary:

WinFrog

WinFrog2 was used entirely for primary navigation acquisition. There were no problems encountered. WinFrog1 was available as a backup.

Gyro

NMEA GYRO #3 from DP was the gyro used for the duration of the Expedition.

Trimble/Ashtech GPS

The aft/forward Trimble GPSs were the primary GPSs used for the duration of the Expedition. No problems were encountered. The Ashtech GPS unit was available as a backup.

WinFrog

WinFrog2 was used entirely for primary navigation acquisition. There were no problems encountered. WinFrog1 was available as a backup.

Bathy 2010

No problems were encountered during the Expedition.
It was, however, noticed that the water speed was incorrectly set in the software, sometime during the prior Expedition. This has a major influence on the PDR depth, as noticed in the following cartoon, before and after set to 1500 m/s.

SeaSpy/SeaLINK

Magnetics data was not collected during the transits.

EPC Recorders

The EPC Recorders were not utilized on this cruise.

VSP

VSPs were performed at sites U1386C, U1387C and U1389C. Marine mammal watches were conducted with no marine mammal sightings.

Items Ordered/Received

Trimble GPS receiver.

Data Backups

data files for the Expedition were copied to:
\\JR1\Vol1\data1\1.5 Ops Navigation
\\JR1\Vol1\data1\1.6 Ops Bathymetry - PDR pulse depth recorder

FANTAIL

Gus

Sum mary

Navigation and Bathymetry data were collected during all transits. Magnetometer data was not collected in part due to winch and leveler concerns and the higher priority of preparing the laboratories for shallow water APC/XCB coring operations.
VSP operations were conducted at 3 site locations in accordance with marine mammal protection protocols. VSP operations at the last sites were discontinued due to sea chest metal wastage concerns.

Special projects

• Fantail high-pressure air supply ball valves were replaced.
• G-gun cluster rigged for VSP use.
• Streamline and paint float hangers.
• Minimize play in seismic winch directional control valve lever rod.
• Replace broken tension spring on fleet angle sensor guide rods.

Problems encountered

The old gun float was retired and replaced with a new float.

Miscellaneous

• G-gun cluster is assembled for use and is covered and secured to the starboard railing by the gun line winch.
• The VSP gun line is stowed on the hooks under the helideck.

MARINE MAMMAL REPORT

Summary

During Expedition 339 at 3 sites vertical seismic profiling (VSP) logging runs were preformed at Holes U1386C, U1387C and U1389C. No protected species were spotted during the watch periods for the VSP runs.
A Pre-Seismic Operations Planning meeting was held prior to use of the air-gun source used for VSP. The following personnel attended:
Expedition Project Manager, Co-Chief Scientist, Captain, Offshore Installation Manager, Operations Superintendent, Logging Scientists, Logging Engineer, Laboratory Officer, Assistant Lab Officer and Underway Technician.
The following information was discussed:

• The Logging Scientists provided the type of source to be used and a copy of the shooting plan.
• The Co-Chief Scientists and the Captain discussed the potential for marine mammal encounters and the actions that will be taken if an encounter should occur.
• The Operations Superintendent and Expedition Project Manager reviewed the plan and ensured that it complies with the instructions given by the Manger of Science Services during pre-cruise planning.
• The Operations Superintendent provided an estimate for the dates and times logging operations were expected to happen.

VSP/Check Shot Operational Procedures for Expedition 339

WATCH IS FOR MARINE MAMMALS AND SEA TURTLES (Protected Species}
When conducting a seismic VSP/Check Shot operation, the following guidelines will be followed:

Daytime Startup

h7.Observation:
1-hour prior to the use of seismic sources, the Mate on Watch on the bridge and the Protected Species Observer on the aft end of the ship will begin observations for marine mammals. Observations will continue until the seismic operations are completed. If a marine mammal is sighted within the safety zone, (940/1850 meters) prior to the soft start, the soft start will be delayed until the protected species has left the safety zone.
Soft Start:
Beginning at a pressure of 500 psi, an individual gun will be fired at 30-sec intervals gradually increasing the pressure to the "operational" pressure, (2,000 psi) over a 30-minute period. On site, during a VSP experiment, if the source used is interrupted for 30-minutes or more the Soft Start procedure will be used, even if no protected species have been sighted.
Note
Seismic sources can only be operated during daylight hours. These sources can only be used after sunrise and should be shut down by sunset. This will allow the observers enough sunlight to adequately detect protected species.
Operational Pressure:
The operational pressure should be kept at the lowest practicable levels through out a survey. The maximum operational pressure available is 2000 psi.

Protected Species Encounter

The Safety Zone (Exclusion Zone Radius) used for Expedition 339
Water Depth

• Shallow- less than 1000 m is 1 nautical mile or 1850 meters
• Deep- more than 1000 m is 0.51 nautical mile or 940 meters

• If a protected species is detected within the safety zone by the forward or aft observer, the information will immediately be sent to the mate on watch on the bridge and the Technician on Watch running the VSP. The Technician on Watch will suspend operation of the guns by disabling the trigger leads and lowering pressure of guns to 500 psi.
• A soft start will be required once the protected species leaves the Safety Zone.

Integrated Ocean Drilling Program
Log of Seismic Source Use During a Seismic Survey
Used in Conjunction with the Marine Mammal Observation Form
R/V JOIDES Resolution
Record the use of seismic sources while surveying or performing a VSP.
Indicate start time, stop time and any changes. (Times are in GMT)
Expedition: 339 Observer: Forward Mate on Watch, Aft, Tech on Watch

339 VSP # 1 Site: U1386C

N 036 49.6773 W 007 45.3165
Water Depth 577 meters Exclusion Zone 1850 meters

Integrated Ocean Drilling Program

Log of Seismic Source Use During a Seismic Survey
Used in Conjunction with the Marine Mammal Observation Form

R/V JOIDES Resolution

Record the use of seismic sources while surveying or performing a VSP.
Indicate start time, stop time and any changes. (Times are in GMT)
Expedition: 339 Observer: Forward Mate on Watch, Aft, Tech on Watch

339 VSP # 2Site: U1387C

N 036 48.3139 W 007 43.1277
Water Depth 578 meters Exclusion Zone 1850 meters

Integrated Ocean Drilling Program

Log of Seismic Source Use During a Seismic Survey
Used in Conjunction with the Marine Mammal Observation Form

R/V JOIDES Resolution

Record the use of seismic sources while surveying or performing a VSP.
Indicate start time, stop time and any changes. (Times are in GMT)
Expedition: 339 Observer: Forward Mate on Watch, Aft, Tech on Watch

339 VSP # 3Site: U1389C

N 036 25.5183 W 007 16.6907
Water Depth 682 meters Exclusion Zone 1850 meters