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February 12, 1996


Cruise No: MF9604 (FOCI 9602)
Area: Shelikof Strait


March 10, 1996	Depart 	Dutch Harbor 
March 13, 1996	Arrive	Kodiak

Participating organizations:
NOAA Alaska Fisheries Science Center (AFSC)
NOAA Pacific Marine Environmental Laboratory (PMEL)

Cruise Description and Objectives:

The Fisheries-Oceanography Coordinated Investigations (FOCI) program is a joint effort by scientists at PMEL, AFSC, and several academic institutions, to understand the biological and physical processes which cause recruitment variability of commercially valuable fish and shellfish stocks in Alaskan waters. The Bering Sea FOCI program is presently studying the effects of the biotic and abiotic environment on the early life stages of walleye pollock spawned in the eastern Bering Sea. There are two aspects to the study: the acquisition and analysis of timeseries data, and specific research topics to be covered on a cruise by cruise basis.

The main objective of this cruise is to deploy subsurface moorings in Shelikof Strait. If the three moorings at Unimak Pass were not recovered during MF96-01, and if time and weather permits, the moorings at Unimak Pass will be recovered.


1.1. Chief Scientist: Carol DeWitt (PMEL) 526-6808

The Chief Scientist has the authority to revise or alter the technical portion of the instructions as work progresses provided that, after consultation with the Commanding Officer, it is ascertained that the proposed changes will not: (1) jeopardize the safety of personnel or the ship; (2) exceed the overall time allotted for the project; (3) result in undue additional expenses; (4) alter the general intent of these project instructions.

1.2. Participating Scientists:

William Parker	M/USA	NOAA/PMEL
Dennis Benjamin	M/USA	NOAA/NMFS

1.3 Ship Operations Contact:

Mr. Larry Mordock
(206) 553  4764
1801 Fairview Ave. East
Seattle, WA 981023767


It is anticipated that conditions will permit the deployment of five (5) subsurface Shelikof Strait moorings, and, possibly, the recovery of three (3) moorings at Unimak Pass. A continual dialogue between scientific and ship's personnel will be especially important.

To insure fulfillment of all the scientific objectives, the ship will steam at maximum cruising speed whenever time in transit and between stations is greater than one hour. A standard oceanographic watch will be utilized which consists of a winch operator, a scientific staff of two and a Survey Tech on deck. Operations will be conducted 24 hours a day.

2.1. Summary of Activities:

The order of mooring operations will depend on weather and light conditions. Subject to change, at the Chief Scientist's discretion, the mooring operations will proceed as follows: F-95UP-1,2, and 3 recoveries (if not recovered on MF-96-01, and if time and weather permit), F-9618 deployment, F-9616 deployment, F-9601 deployment, F-9602 deployment, and F-9603 deployment. A CTD cast will be taken after each mooring deployment and before each mooring recovery. Table 1 contains a draft copy of the mooring characteristics and deployment positions.

2.2. Moorings

The Shelikof Strait moorings will be loaded onto the Miller Freeman in Seattle. These consist of five (5) subsurface moorings.

A CTD cast will be conducted at each mooring site after deployment and prior to recovery.

2.3. CTD/Water Sample Operations:

PMC's SeaBird 911Plus CTD will be the primary system used. PMC will also provide a back-up Sea-Bird 911Plus CTD system. Both underwater CTD units will be equipped with two thermistors. The PMEL CTD stand, which has been modified for the attachment of a Sea-Tech fluorometer, will be used. CTD data will be acquired on a PMEL computer using SEASOFT software. The capability will be available to display CTD data using the SCS system and monitors will be available. Survey technicians and scientists will keep the "CTD Cast Information/Rosette Log" in addition to the wire usage log. The CTD should descend at a rate of 30 m/min for the first 200 m and 45 m/min below that. The ascent rate should be 50 m/min. The FOCI fluorometer, light meter, and chlorophyll absorbance meter (ChlAM) should be mounted on the rosette for all casts where possible. However, the ChlAM can not exceed 300 m and the fluorometer and light meter cannot exceed 500 m. Water samples will be collected with 10l Niskin bottles. Depth, fluorescence and light levels will be recorded on the "CTD Cast Information/Rosette Log" for all water bottle samples.

CTD Calibration: Salinity comparisons will be conducted on every cast (or as specified by the Chief Scientist). No reversing thermometers will be required. However, the CTD systems will each have two thermistors. A survey technician will run the AutoSal analysis during the cruise and record the readings on an AutoSal log.

2.4 Chlorophyll and Nutrient Samples:

Chlorophyll and nutrient samples will be taken from the 10l Niskin bottles. Sampling depths will occur at the depths where a ChlAM has been deployed on a subsurface mooring. At each sampling depth, three Nisken bottles will be tripped. This may require more than one CTD cast at some sites. The approx. 250 ml chlorophyll samples will be filtered onto GF/F filters, placed in microcentrifuge tubes, labeled, wrapped in aluminum foil and placed in the freezer at 70oC.

2.5. ADCP

ADCP Observations:
The purpose of the Vessel-Mounted Acoustic Doppler Current Profiler (VM-ADCP) is to measure the ocean current velocity continuously over the upper 300 m of the water column, usually in 8 depth increments. Current velocities relative to the earth at this spatial and temporal resolution cannot be measured by other methods: CTD sections, current meter moorings, or drifting buoys.

ADCP data is also used to estimate the abundance and distribution of biological scatterers over the same depth range and in the same depth increments.

ADCP Data Collection:
The ADCP measurement requires three instruments that must work in concert: the ADCP, the ship's gyrocompass and a GPS receiver. The ADCP is connected to a dedicated PC and controlled by RD Instruments' Data Acquisition System (DAS) software kept in DOS directory C:\ADCP248. Separate written instructions detailing the ADCP setup and configuration files are kept in the ADCP notebook in the DataPlot compartment.

The ADCP PC is interfaced to the ship's gyrocompass and to the primary scientific GPS receiver. The GPS shall be configured to send only NMEA-0183 messages GPGGA and GPVTG at the maximum fix update rate for the receiver (usually 1 or 2 second rate).

The ADCP PC logs data from the profiler to SyQuest disks and optionally sends a complete data structure to SCS for logging on that system. This redundancy in data logging is desirable for post-cruise processing flexibility. PMEL supplies the SyQuest disks for FOCI projects. No more than one SyQuest disk will be required for the cruise. At the end of the cruise, a backup of the SyQuest should be made to a unique sub directory of another disk maintained by the ship for this purpose until the original data is certified at PMEL.

Detailed, post-cruise processing of ADCP data is designed to take advantage of a higher quantity of navigation data than is retained by the ADCP acquisition software. Thus, the ship's SCS is relied to log GPS navigation data at maximum available rates. The SCS system shall log output from the best two navigation receivers at all times during a cruise. For the purpose of designating a primary and secondary GPS system, precedence shall be assigned according to the following list of GPS receivers available on the Miller Freeman:

1. Trimble Centurion with encryption key installed and enabled (PPS-GPS)
2. Northstar 941X receiving differential corrections from radiobeacon (DGPS)
3. Trimble Centurion operating without encryption key (SPS-GPS)
4. Northstar 941X without differential corrections (SPS-GPS)
5. Magnavox MX-200 (SPS-GPS)

Changes in the availability of GPS equipment shall be communicated to PMEL to allow the above list to remain current. It is the responsibility of the ship to install and enable the appropriate encryption key for use of a PPS-GPS receiver.

Both primary and secondary GPS receivers shall be configured to output NMEA-0183 messages GPGGA and GPVTG, and SCS shall be configured to log these messages to disk. The SCS SENSOR.DAT file should be configured to enable logging only of the NMEA-0183 format messages. GPGGA and GPVTG derived sensor messages are not desirable for post-processing.

SCS should log the primary GPS data at 1 second intervals, the secondary GPS data at 10 second intervals, gyro data at 2 second intervals, Loran-C data (required only during periods of GPS lapses) at 2 second intervals, and the temperature and input voltage of the ADCP electronics (deck unit) at 60 second intervals. The latter are used for adjusting the acoustic back scattered signal strength to absolute levels and relating the signal to biological scatterers.

ADCP Underway Operations:
The ADCP operates continuously during the entire cruise. At the start of a cruise, the system shall be configured and started according to the provided checklists "Before Leaving Port" and "Underway to Operations Area". The ADCP and its interface to the gyro and navigation must be checked daily by completing the "ADCP Daily Log" and also at the end of the cruise with the ship tied to the pier. The centerboard height affects the depth of sampling. The centerboard shall be lowered as soon as practical upon leaving port and remain lowered throughout the cruise. If it is necessary to raise the centerboard during the cruise, the times of raising and lowering must be logged in the Marine Operations Abstract (MOA).

In case of problems please describe the problem, error message numbers, flashing lights, etc. on the log sheets. Also contact Dan Dougherty (206-526-6844; e-mail DOUGHERTY@PMEL.NOAA.GOV) or Ned Cokelet (206-526-6820; e-mail COKELET@PMEL.NOAA.GOV) at PMEL as soon as possible.

Dedicated ADCP transects should be run at constant heading (not constant course-over-ground) if practicable, thus minimizing gyro lag. However, transects along lines of current-meter moorings should remain on the line with the ship's heading gradually adjusted to accomplish this. Sharp turns should be avoided. The ship's speed should be constant. 12 kts is often satisfactory, but the ship may have to slow down if the ADCP's percent good pings decreases below 75% in the upper 200-250 m due to sea state.

The ADCP should operate in bottom track mode when the water depth is less than about 500 m for more than a few hours. This gives currents better-compensated for transducer misalignment but somewhat lower in statistical significance because the number of pings is reduced. For extended periods in deeper water, an ADCP configuration without bottom tracking should be used.

ADCP Backtrack-L Calibration:
At least one backtrack-L calibration maneuver per cruise should be executed to test the instruments and to calibrate the transducer misalignment angle for which a 0.5ø error can seriously bias the measurements. The "misalignment angle" may change with the ship's trim as well as with remounting the ADCP transducers. The basic idea is to measure the current twice on closely spaced parallel tracks of opposite heading when the ADCP and GPS are working well. The maneuver consists of 4 legs (N, S, E and W headings) connected by simple U-turns forming an L shape. Each leg should be 30 minutes long - the first 10 minutes are to allow the ship and instruments to stabilize on the new heading. The entire calibration should require about 2 1/2 hours with 5 minutes allowed for each turn. The following should be considered:

1. Negligible currents are best, but stronger currents are acceptable as long as they are reasonably uniform and steady. Avoid regions of strong horizontal shear due to topography, flow through passes, eddies and current boundaries. In tidal currents measure when the current is steadiest, often at maximum flood and ebb rather than at slack water.
2. Calibration legs can be done in any order provided opposite-headed legs are sequential.
3. Opposite-headed legs should be parallel and closely spaced, but not retraced. Use U-turns to minimize gyro oscillations. Avoid Williamson and hairpin turns.
4. The ADCP's PC screen should show at least 75%-good pings down to 250 m.
5. The ship should go fast enough to detect a misalignment error (over 5 kts), but slow enough to satisfy condition 4. This depends on sea conditions. 10-12 kts is often satisfactory.
6. Choose a time when GPS is navigating and is expected to remain so over the next 2 hours.

ADCP Absolute Backscatter Calibration:
A test to calibrate the absolute backscatter strength and to determine the background noise level of the ship-ADCP system may be performed once per cruise at the discretion of the Chief Scientist. Specific instructions in such event will be provided by PMEL personnel aboard, and cannot be anticipated in advance of the cruise.

Typically, such a test will be attempted in conditions when weather is relatively calm, and the water depth exceeds 250 m. This test may require that the main power plant, pumps, sonars, and other sources of acoustic and electronic noise be shut down. If conducted in the course of normal operations, the work will require about 1 hour. There may be opportunities for variations of the test any time the ship is at anchor, requiring the cooperation of the ship's officers and engineering watch.

2.6. Radiometer

The ship will be equipped with a radiometer to measure solar energy. The scientists will supply the calibrated instrument, mounting hardware and cable to run to DataPlot. We will need the assistance of the ship's electronics tech and SCS Manager to
correctly install the instrument and make sure that the data are being logged by the SCS.


3.1 Equipment and Capabilities to be Provided by the Ship:

The following systems and their associated support services are essential to the cruise. Sufficient consumables, back-up units, and on-site spares and technical support must be in place to assure that operational interruptions are minimal. All measurement instruments are expected to have current calibrations, and all pertinent calibration information shall be included in the data package.

bulletOceanographic winch with slip rings and 3-conductor cable terminated for CTD.

bulletTwo Sea-Bird SBE 911Plus CTD systems including underwater CTD unit, the rosette, the deck unit, and tape recorder. The PMEL CTD stand, which has been modified for the attachment of a Sea-Tech fluorometer, will be the primary stand used - the ship will provide a back-up CTD stand. The PMC underwater CTD units should have mounts compatible with the PMEL CTD stand. The ship will provide weights for the CTD stand and 2 pingers. (PMEL will provide the dual thermistors.)

bullet10-liter sampling bottles for use with rosette (10).

bulletSpare 10-liter sampling bottles (4).

bulletFor CTD field corrections: IAPSO water and AUTOSAL salinometer.

bulletWire speed indicator and readout.

bulletFor meteorological observations: 2 anemometers (one the R. M. Young system interfaced to the SCS), calibrated air thermometer (wet-and dry-bulb) and a calibrated barometer and/or barograph.

bulletFreezer space for storage of samples (blast and storage freezers).

bulletSimrad EQ-50 echo sounder

bulletJRC JFV-200R color sounder recorder

bulletRDI ADCP with PC-compatible data acquisition computer and SyQuest drives

bulletUse of 386 PC in DataPlot for data analysis

bulletSCS (Shipboard Computer System)

bulletStern platform in place

bulletSafety harnesses for working on quarter deck and fantail.

bulletLaboratory space with exhaust hood, sink, lab tables and storage space.

bulletSea-water hoses and nozzles to wash down CTD.

bulletAdequate deck lighting for night-time operations.

bulletNavigational equipment, including GPS and radar .

3.2 Equipment to be Provided by the Project:

bulletMiscellaneous scientific sampling and processing equipment

bulletScientific ultra-cold freezer

bulletSubsurface moorings (5)

3.3 Ultracold Freezer Requirements:

The scientific ultracold freezer will remain on the ship in operating condition from the beginning of the first FOCI cruise until the ship returns to Seattle and the samples within can be unloaded. Since valuable samples will be in the unit, operation must be continuous without interruption. Therefore, the unit should be hardwired into the ships electrical system or connected with a threaded plug. The unit must be securely fastened to a bulkhead or counter, easily accessible, with a minimum of 4" on each side around the bottom. The location, fastening and wiring should be similar to last
year. In addition, a weight should be taped to the top of the unit to prevent the lid from lifting in heavy seas.

The freezer has an alarm, but the ship's personnel are requested to check the digital temperature display twice daily to insure that the operating temperature is below 60 degrees C. The unit will be locked between cruises, and a key left with the Chief Survey Tech. In the event that the unit fails, the temperature will maintain for about 12 hours if the lid isn't opened. If the unit fails and cannot be fixed on the ship, the scientific blast freezer should be precooled to its minimum (38 degrees C), and all frozen specimens should be transferred to it immediately, without thawing. Kevin Bailey (206/5264243, 4239) must be notified.

A daily record of the temperature (digital readout) on the scientific ultracold freezer will be submitted to K. Bailey (AFSC) upon the ship's return to Seattle.

3.3. Scientific Computer System (SCS)

The ship's Scientific Computer System (SCS) shall operate throughout the cruise, acquiring and logging data from navigation, meteorological, oceanographic, and fisheries sensors.

The SCS data acquisition node will provide project scientists with the capability of monitoring sensor acquisition via text and graphic displays. A data processing node will be available to project scientists throughout the cruise, configured according to the specifications of the FOCI SCS administrators.

Sensor identification, and data acquistion and logging parameters are specified in the system file SENSOR.DAT. This file shall be maintained in a current state by the ship's SCS manager. Specific FOCI requirements for the content of the SENSOR.DAT file shall be provided by the FOCI SCS administrators during MF96-01. Changes to the SENSOR.DAT specifications may be made by the ship's SCS manager on a cruise-by-cruise basis, at the request of the chief scientist. All changes in content of the SENSOR.DAT file shall be communicated to the FOCI SCS administrators.

SCS sensor data logged to disk files shall be organized into several logical groupings according to intended post-cruise processing. These logical groupings will be specified by the FOCI SCS administrators prior to the start of the 1996 field operations season. The ship's SCS manager will assign data elements from newly-installed sensors to the appropriate logical group(s), and inform the FOCI SCS administrators of such changes.

At regular intervals, not to exceed every 5 days, SCS ship's manager will archive data from disk files to 8-mm tape cartridge for delivery to the project representative at the end of the cruise. To ensure compatibility with the laboratory tape drive mechanisms, backup 8-mm tapes shall not be recorded with hardware compression options.

Real-time data will also be logged to QIC tapes to provide additional data security in the event of disk failure; these tapes will be archived by the ship until project data tapes have been received and verified by the laboratories.

The ship's SCS manager will ensure data quality through the administration of standard SCS protocols for data monitoring. If requested by the chief scientist, standard SCS daily quality assurance summaries will be prepared for review.

Additional recording of processed data may be requested of the ship's SCS manager; if so, specific instructions will be found elsewhere in this document. During the cruise, the scientific party may require the assistance of the ship's SCS manager to determine if all sensors are functioning properly and to monitor some of the collected data in real time to make sampling strategy decisions.

The FOCI SCS co-administrators are:
Tiffany Vance: (206)526-6767; e-mail: VANCE@PMEL.NOAA.GOV
Dan Dougherty: (206)526-6844; e-mail: DOUGHERTY@PMEL.NOAA.GOV


4.1. Data Disposition and Responsibilities:

The Chief Scientist is responsible for the disposition, feedback on data quality, and archiving of data and specimens collected on board the ship for the primary project. The Chief Scientist will be considered to be the representative of the AFSC/PMEL Lab Director for purpose of data disposition. A single copy of all data gathered by the vessel will be delivered to the Chief Scientist upon request for forwarding to the Lab Director, who in turn will be responsible for distribution of data to other investigators desiring copies.

4.2. Data requirements

The following data products will be included in the cruise data package:
(a) Marine operations abstracts,
(b) Marine weather observation logs,
(c) PMEL CTD weather observation logs,
(d) Autosalinometer logs,
(e) CTD audio cassettes,
(f) Calibration sheets for all ship's instruments used,
(g) ADCP daily log sheets,
(h) ADCP SyQuest 105 MB disks,
(i) SCS 8 mm backup tapes,
(j) SeaPlot Files, disk and hard copy,
(k) Ultracold freezer temperature daily log, (end of field season),

4.2.1. Marine Observation Log: A Marine Operations Abstract (MOA) form will be maintained by the ship's officers during the cruise. The Chief Scientist and the Commanding Officer or designee will negotiate the details regarding forms required by the project for each operation.

4.2.2. Station Plot: A diskette and hard copy of SeaPlot files should also be maintained for transfer to the Chief Scientist. The requirement for a copy of station plots on a NOAA chart or mylar have been dropped.

4.2.3. Navigation: Observations and reliable fixes shall be plotted and identified by date/time group or equivalent. Fixes shall be evaluated for course and/or speed made good. Primary navigational control shall be provided by GPS satellite, radar range and bearing, and visual fixes.

4.2.4. Synoptic Weather Reports: In accordance with OMO Instruction 3142 dated December 5, 1985 and Amendment 3142B dated August 4, 1986, a weather log of NOAA Form 721A will be maintained by ships personnel, and data will be transmitted via SEAS. The completed logs will be forwarded to NWS port meteorologists.
Complete meteorological observations will be logged on the NOAA Form 7713d at hourly intervals for scientific data purposes.

4.2.5. Scientific Ultracold Freezer Log: A daily record of the temperature (digital readout) on the scientific ultracold freezer will be submitted to K. Bailey (AFSC) upon the ship's return to Seattle.

4.3. Cruise Reports

The Chief Scientist and Commanding Officer will jointly prepare a cruise report for submission to the Director, PMC, as required by NOAA Directives Manual 1717. The Commanding Officer's report will follow formats and reporting requirements prescribed in PMC Oporder 1.3.6.

4.4. Evaluation Report

One Ship Operations Evaluation Report is required for each leg of the primary project only, using the form provided for that purpose.


5.1. Additional Investigations

Any other work done during the cruise period will be subordinate to the main project and performed so as not to interfere with that outlined in these instructions. The Chief Scientist will be responsible for determining the priority of additional work relative to the main project.

5.2. Ancillary Projects:

(a) SEAS Data Collecting and Transmission (PMC OPORDER 1.2.1.)
(b) Marine Mammal Reporting (PMC OPORDER RP1294)
(c) Nautical Charting (PMC OPORDER 1.2.6.)
(d) Bathymetric Trackline (PMC OPORDER 1.2.5.)
(e) Alaska Weather Reporting (PMC OPORDER 1.2.7.)
(f) Sea Turtle Observations (SPPMC295, Sea Turtle Observation Program, 1995)

5.3. Piggyback Projects:

None at this time


6.1. Radio Interference

Some scientific equipment is sensitive to radio frequency interference. If interference occurs, it may be necessary to adjust operations and communications schedules if efforts to electronically isolate the equipment are unsuccessful.

6.2. Planning Meeting

A precruise meeting between the Commanding Officer and the Chief Scientist will be held prior to the start of the cruise. Its purpose is to identify the daytoday requirements of the project in order to best utilize shipboard personnel resources and to identify overtime requirements. A brief meeting of all scientific personnel, the Field Operations Officer, Chief Boatswain, survey department, and other relevant ship's personnel should be held before the vessel reaches the experiment area for the purposes of (1) introducing new scientific personnel to ship's procedures, proper channels, etc.; (2) discussing operating procedures for deploying various pieces of sampling equipment; and (3) coordinating scientific watch assignments.

6.3. Meals

All scientists (passengers) will pay for their meals at a rate of $8.20 per day for two or more meals and $4.10 a day for one meal, in accordance with NOAA Administrative Order 203100, and PMC Directive 8704. The Commanding Officer will furnish NOAA Form 7590, Authorization of Mess Obligation, for the Chief Scientist's and Commanding Officer's signature for all the scientists' meals.

6.3.1. Midnight Lunches: The scientific staff will work 12 hour watches (12 to 12). A microwave oven will be available to reheat meals requested to be set aside for the watch.

6.4. Hazardous Materials

The Chief Scientist shall be responsible for complying with NC Instruction 6280A, Hazardous Waste; policy, guidance, and training, dated February 4, 1991, paragraph 7.g and paragraph 9. By federal law, the ship may not sail without a complete inventory of MSDS, and appropriate neutralizing agents, buffers, and/or absorbents in amounts adequate to address spills of a size equal to the amount aboard.

No hazardous materials will be provided.


7.1. A daily JFT schedule will be maintained between KVJ and the MILLER FREEMAN Monday through Friday. Radio contact will be maintained when possible. A scientific progress report will be sent to AFSC via INMARSAT voice, Fax, or JFT at least once a week.

7.2. Since it is sometimes necessary for the scientific staff to communicate with other research vessels, commercial vessels, and shore based NOAA facilities, the Chief Scientist or designee may request the use of radio transceivers aboard the vessel.

7.3. The Chief Scientist anticipates the need for daily reports on the position of satellitedrifters in the study area and the health of the biophysical moorings. These will be sent either by Fax from PMEL over INMARSAT or over Internet from PMEL to the PMC radio room and forwarded to the ship via JFT route. Important phone numbers are

PMEL/CARD Fax: (206) 5266485
PMEL/ADMIN Fax: (206) 5266815
AFSC/RACE Fax (206) 5266723

Program contacts:
Phyllis Stabeno (PMEL) (206) 5266453
Kevin Bailey (AFSC) (206) 5264243

Important Internet email addresses are
AFSC person:
PMC radio room:

7.4. The MILLER FREEMAN is equipped with INMARSAT, a telephone/teletype satellite communication system. If the scientific staff uses this system, they will be obligated to pay for their calls, which are estimated at $7.70 per minute and data voice rapid fax at $4 per minute for Telex. The Chief Scientist, or designee will have access to, and assistance provided for transmitting and receiving communications through INMARSAT as needed during the cruise.

7.5. The MILLER FREEMAN is equipped with cellular telephone capability. If the scientific staff use this system, they will be obligated to pay for incoming and outgoing calls, which are estimated at $0.90 per minute for airtime, plus any applicable long distance charges charged to the ship's number.


1. Mooring characteristics and locations.

1. Mooring locations

EcoFOCI Project Office
7600 Sand Point Way NE
Seattle, Washington 98115
Comments and information:
  EcoFOCI Coordinator

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