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1. The Wire Flyer Towed Profiling System

   https://doi.org/10.1175/JTECH-D-17-0180.1  

   Roman, Chris ; Ullman, David S. ; Hebert, Dave ; Licht, Stephen ( February 2019 , Journal of Atmospheric and Oceanic Technology)

   The Wire Flyer towed vehicle is a new platform able to collect high-resolution water column sections. The vehicle is motivated by a desire to effectively capture spatial structures at the submesoscale. The vehicle fills a niche that is not achieved by other existing towed and repeat profiling systems. The Wire Flyer profiles up and down along a ship-towed cable autonomously using controllable wings for propulsion. At ship speeds between 2 and 5 kt (1.02–2.55 m s⁻¹), the vehicle is able to profile over prescribed depth bands down to 1000 m. The vehicle carries sensors for conductivity, temperature, depth, oxygen, turbidity, chlorophyll, pH, and oxidation reduction potential. During normal operations the vehicle is typically commanded to cover vertical regions between 300 and 400 m in height with profiles that repeat at kilometer spacing. The vertical profiling speed can be user specified up to 150 m min⁻¹. The high-density sampling capability at depths below the upper few hundred meters makes the vehicle distinct from other systems. During operations an acoustic modem is used to communicate with the vehicle to provide status information, data samples, and the ability to modify the sampling pattern. This paper provides an overview of the vehicle system, describesmore »its operation, and presents results from several cruises.

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2. Investigation and Design of a Towable Hydrophone Array for General Ocean Sensing

   https://doi.org/10.1109/OCEANSE.2019.8867239  

   Schinault, Matthew E. ; Penna, Seth M. ; Garcia, Heriberto A. ; Ratilal, Purnima ( June 2019 , IEEE OCEANS 2019 - Marseille)

   An eight-element oil-filled hydrophone array is used to measure the acoustic field in littoral waters. This prototype array was deployed during an experiment between Jeffrey’s Ledge and the Stellwagen Bank region off the coast of Rockport, Massachusetts USA. During the experiment, several humpback whale vocalizations, distant ship tonals and high frequency conventional echosounder pings were recorded. Visual confirmation of humpback moving in bearing relative to the array verifies the directional sensing from array beamforming. During deployment, the array is towed at speeds varying from 4-7 kts in water depths of roughly 100 m with conditions at sea state 2 to 3. This array system consists of a portable winch with array, tow cable and 3 water-resistant boxes housing electronics. This system is deployed and operated by 2 crew members onboard a 13 m commercial fishing vessel during the experiment. Non-acoustic sensor (NAS) information is obtained to provide depth, temperature, and heading data using commercial off the shelf (COTS) components utilizing RS485/232 data communications. Acoustic data sampling was performed at 8 kHz, 30 kHz and 100 kHz with near real-time processing of data and enhanced Signal to Noise Ratio (SNR) from beamforming. The electrical system components are deployed with 3 stackedmore »electronics boxes housing power, data acquisition and data processing components in water resistant compartments. A laptop computer with 8 TB of external storage and an independent Global Positioning System (GPS) antenna is used to run Passive Ocean Acoustic Waveguide Remote Sensing (POAWRS) software providing beamformed spectrogram data and live NAS data with capability of capturing several days of data. The acquisition system consists of Surface Mount Device (SMD) pre-amplifiers with filter to an analog differential pair shipboard COTS acquisition system. Pre-amplifiers are constructed using SMD technology where components are pressure tolerant and potting is not necessary. Potting of connectors, electronics and hydrophones via 3D printed molding techniques will be discussed. Array internal components are manufactured with Thermoplastic Polyurethane (TPU) 3D printed material to dampen array vibrations with forward and aft vibration isolation modules (VIM). Polyurethane foam (PUF) used to scatter breathing waves and dampen contact from wires inside the array without attenuating high frequencies and allowing for significant noise reduction. A single Tygon array section with a length of 7.5 m and diameter of 38 mm contains 8 transducer elements with a spacing of 75 cm (1 kHz design frequency). Pre- amplifiers and NAS modules are affixed using Vectran and steel wire rope positioned by swaged stops along the strength member. The tow cable length is 100 m with a diameter of 22 mm that is potted to a hose adapter to break out 12 braided copper wire twisted pair conductors and terminates the tow cable Vectran braid. This array in its current state of development is a low-cost alternative to obtain quality acoustic data from a towed array system. Used here for observation of whale vocalizations, this type of array also has many applications in military sonar and seismic surveying. Maintenance on the array can be performed without the use of special facilities or equipment for dehosing and conveniently uses castor oil as an environmentally safe pressure compensating and coupling fluid. Array development including selection of transducers, NAS modules, acoustic acquisition system, array materials and method of construction with results from several deployments will be discussed. We also present beamformed spectrograms containing humpback whale downsweep moans and underwater blowing (bubbles) sounds associated with feeding on sand lance (Ammodytes dubius).« less
3. Expedition 367 Preliminary Report: South China Sea Rifted Margin

   https://doi.org/10.14379/iodp.pr.367.2018  

   Sun, Z. ; Stock, J. ; Klaus, A. ( August 2018 , Preliminary report)

   International Ocean Discovery Program Expedition 367 is the first of two consecutive cruises that form the South China Sea Rifted Margin program. Expeditions 367 and 368 share the common key objectives of testing scientific hypotheses of breakup of the northern South China Sea (SCS) margin and comparing its rifting style and history to other nonvolcanic or magma-poor rifted margins. Four primary sites were selected for the overall program: one in the outer margin high (OMH) and three seaward of the OMH on distinct, margin-parallel basement ridges. These ridges are informally labeled A, B, and C within the continent–ocean transition (COT) zone going from the OMH to the steady-state oceanic crust of the SCS. The main scientific objectives include 1. Determining the nature of the basement within critical crustal units across the COT of the SCS that are critical to constrain style of rifting, 2. Constraining the time interval from initial crustal extension and plate rupture to the initial generation of igneous ocean crust, 3. Constraining vertical crustal movements during breakup, and 4. Examining the nature of igneous activity from rifting to seafloor spreading. In addition, sediment cores from the drill sites will provide information on the Cenozoic regional tectonic andmore »environmental development of the Southeast Asia margin. Expedition 367 successfully completed operations at two of the four primary sites (Site U1499 on Ridge A and Site U1500 on Ridge B). At Site U1499, we cored to 1081.8 m in 22.1 days, with 52% recovery, and then logged downhole data from 655 to 1020 m. In 31 days at Site U1500, we penetrated to 1529 m, cored a total of 1012.8 m with 37% recovery, and collected log data from 842 to 1133 m. At each site we drilled to reach the depth of the main seismic reflector (acoustic basement), which prior to the expedition had been interpreted to be crystalline basement. Our objective was to determine which lithospheric layer constitutes the basement of the COT and whether there was middle or lower continental crust or subcontinental lithospheric mantle exhumed in the COT before the final lithospheric breakup. At Site U1499, coring ~200 m into the acoustic basement sampled sedimentary rocks, including early Miocene chalks underlain by pre-Miocene polymict breccias and poorly cemented gravels composed of sandstone pebbles and cobbles. Preliminary structural and lithologic analysis suggested that the gravels might be early synrift to prerift sediment. At Site U1500, the main seismic reflector corresponds to the top of a basalt sequence at ~1379.1 m. We cored 149.90 m into this volcanic package, recovering 114.92 m (77%) of sparsely to moderately plagioclase-phyric basalt comprising numerous lava flows including pillow lavas with glass, chilled margins, altered veins, hyaloclastites, and minor sediment. Preliminary geochemical analyses show that the basalt is tholeiitic. We speculate that the basalt might belong to the very early stage of magmatism prior to steady-state seafloor spreading (known as an “embryonic ocean” regime). Sampling of the Pleistocene to lower Miocene sedimentary section at Sites U1499 and U1500 was not continuous for two reasons. First, there was extremely poor recovery within substantial intervals interpreted to be poorly lithified sands. Second, we chose to drill down without coring in some sections at Site U1500 to ensure sufficient time to achieve this site’s high-priority deep objectives. Nevertheless, the upper Miocene basin sequence, consisting of interbedded claystone, siltstone, and sandstone, is continuous on seismic reflection profiles, and can be correlated between the two sites using both seismic reflectors and biostratigraphy. Together with results from other holes previously drilled in the SCS, these samples will help to constrain changes in paleoceanographic conditions during the Miocene in this part of the SCS basin.« less
4. Mariana Convergent Margin and South Chamorro Seamount

   https://doi.org/10.14379/iodp.proc.366.2018  

   Fryer, P. ; Wheat, C.G. ; Williams, T. ( February 2018 , Proceedings of the International Ocean Discovery Program)

   Geologic processes at convergent plate margins control geochemical cycling, seismicity, and deep biosphere activity in subduction zones and suprasubduction zone lithosphere. International Ocean Discovery Program Expedition 366 was designed to address the nature of these processes in the shallow to intermediate depth of the Mariana subduction channel. Although no technology is available to permit direct sampling of the subduction channel of an intraoceanic convergent margin at depths up to 19 km, the Mariana forearc region (between the trench and the active volcanic arc) provides a means to access materials from this zone. Active conduits, resulting from fractures in the forearc, are prompted by along- and across-strike extension that allows slab-derived fluids and materials to ascend to the seafloor along associated faults, resulting in the formation of serpentinite mud volcanoes. Serpentinite mud volcanoes of the Mariana forearc are the largest mud volcanoes on Earth. Their positions adjacent to or atop fault scarps on the forearc are likely related to the regional extension and vertical tectonic deformation in the forearc. Serpentinite mudflows at these volcanoes include serpentinized forearc mantle clasts, crustal and subducted Pacific plate materials, a matrix of serpentinite muds, and deep-sourced formation fluid. Mud volcanism on the Mariana forearc occursmore »within 100 km of the trench, representing a range of depths and temperatures to the downgoing plate and the subduction channel. These processes have likely been active for tens of millions of years at the Mariana forearc and for billions of years on Earth. At least 19 active serpentinite mud volcanoes have been located in the Mariana forearc. Two of these mud volcanoes are Conical and South Chamorro Seamounts, which are the farthest from the Mariana Trench at 86 and 78 km, respectively. Both seamounts were cored during Ocean Drilling Program Legs 125 and 195, respectively. Data from these two seamounts represent deeper, warmer examples of the continuum of slab-derived materials as the Pacific plate subducts, providing a snapshot of how slab subduction affects fluid release, the composition of ascending fluids, mantle hydration, and the metamorphic paragenesis of subducted oceanic lithosphere. Data from the study of these two mud volcanoes constrain the pressure, temperature, and composition of fluids and materials within the subduction channel at depths of up to 19 km. Understanding such processes is necessary for elucidating factors that control seismicity in convergent margins, tectonic and magma genesis processes in the volcanic arc and backarc areas, fluid and material fluxes, and the nature and variability of environmental conditions that impact subseafloor microbial communities. Expedition 366 focused on data collection from cores recovered from three serpentinite mud volcanoes that define a continuum of subduction-channel processes to compare with results from drilling at the two previously cored serpentinite mud volcanoes and with previously collected gravity, piston, and remotely operated vehicle push cores across the trench-proximal forearc. Three serpentinite mud volcanoes (Yinazao, Fantangisña, and Asùt Tesoro) were chosen at distances 55 to 72 km from the Mariana Trench. Cores were recovered from active sites of eruption on their summit regions and on the flanks where ancient flows are overlain by more recent ones. Recovered materials show the effects of dynamic processes that are active at these sites, bringing a range of materials to the seafloor, including materials from the crust of the Pacific plate, most notably subducted seamounts (even corals). Most of the recovered material consists of serpentinite mud containing lithic clasts, which are derived from the underlying forearc crust and mantle and the subducting Pacific plate. A thin cover of pelagic sediment was recovered at many Expedition 366 sites, and at Site U1498 we cored through distal serpentinite mudflows and into the underlying pelagic sediment and volcanic ash deposits. Recovered serpentinized ultramafic rocks and mudflow matrix materials are largely uniform in major element composition, spanning a limited range in SiO2, MgO, and Fe2O3 compositions. However, variation in trace element composition reflects interstitial water composition, which differs as a function of the temperature and pressure of the underlying subduction channel. Dissolved gases H2, CH4, and C2H6 are highest at the site farthest from the trench, which also has the most active fluid discharge of the Expedition 366 serpentinite mud volcanoes. These dissolved gases and their active discharge from depth likely support active microbial communities, which were the focus of in-depth subsampling and preservation for shore-based analytical and culturing procedures. The effects of fluid discharge were also registered in the porosity and gamma ray attenuation density data indicated by higher than expected values at some of the summit sites. These higher values are consistent with overpressured fluids that slow compaction of serpentinite mud deposits. In contrast, flank sites have significantly greater decreases in porosity with depth, suggesting that processes in addition to compaction are required to achieve the observed data. Thermal measurements reveal higher heat flow values on the flanks (~31 mW/m2) than on the summits (~17 mW/m2) of the seamounts. The new 2G Enterprises superconducting rock magnetometer (liquid helium free) revealed relatively high values of both magnetization and bulk magnetic susceptibility of discrete samples related to ultramafic rocks, particularly dunite. Magnetite, a product of serpentinization, and authigenic carbonates were observed in the mudflow matrix materials. In addition to coring operations, Expedition 366 focused on the deployment and remediation of borehole casings for future observatories and set the framework for in situ experimentation. Borehole work commenced at South Chamorro Seamount, where the original-style CORK was partially removed. Work then continued at each of the three summit sites following coring operations. Cased boreholes with at least three joints of screened casing were deployed, and a plug of cement was placed at the bottom of each hole. Water samples were collected from two of the three boreholes, revealing significant inputs of formation fluids. This suggests that each of the boreholes tapped a hydrologic zone, making these boreholes suitable for experimentation with the future deployment of a CORK-Lite.« less
5. Recent Advances in the Temple University Digital Pathology Corpus

   https://doi.org/10.1109/SPMB47826.2019.9037859  

   Hunt, I. ; Husain, S. ; Simon, J. ; Obeid, I. ; Picone, J. ( December 2019 , IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad ; Picone, Joseph ; Selesnick, Ivan (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing a large open source database of high-resolution digital pathology images known as the Temple University Digital Pathology Corpus (TUDP) [1]. Our long-term goal is to release one million images. We expect to release the first 100,000 image corpus by December 2020. The data is being acquired at the Department of Pathology at Temple University Hospital (TUH) using a Leica Biosystems Aperio AT2 scanner [2] and consists entirely of clinical pathology images. More information about the data and the project can be found in Shawki et al. [3]. We currently have a National Science Foundation (NSF) planning grant [4] to explore how best the community can leverage this resource. One goal of this poster presentation is to stimulate community-wide discussions about this project and determine how this valuable resource can best meet the needs of the public. The computing infrastructure required to support this database is extensive [5] and includes two HIPAA-secure computer networks, dual petabyte file servers, and Aperio’s eSlide Manager (eSM) software [6]. We currently have digitized over 50,000 slides from 2,846 patients and 2,942 clinical cases. There is an average of 12.4 slides per patient and 10.5 slides per casemore »with one report per case. The data is organized by tissue type as shown below: Filenames: tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_0a001_00123456_lvl0001_s000.svs tudp/v1.0.0/svs/gastro/000001/00123456/2015_03_05/0s15_12345/0s15_12345_00123456.docx Explanation: tudp: root directory of the corpus v1.0.0: version number of the release svs: the image data type gastro: the type of tissue 000001: six-digit sequence number used to control directory complexity 00123456: 8-digit patient MRN 2015_03_05: the date the specimen was captured 0s15_12345: the clinical case name 0s15_12345_0a001_00123456_lvl0001_s000.svs: the actual image filename consisting of a repeat of the case name, a site code (e.g., 0a001), the type and depth of the cut (e.g., lvl0001) and a token number (e.g., s000) 0s15_12345_00123456.docx: the filename for the corresponding case report We currently recognize fifteen tissue types in the first installment of the corpus. The raw image data is stored in Aperio’s “.svs” format, which is a multi-layered compressed JPEG format [3,7]. Pathology reports containing a summary of how a pathologist interpreted the slide are also provided in a flat text file format. A more complete summary of the demographics of this pilot corpus will be presented at the conference. Another goal of this poster presentation is to share our experiences with the larger community since many of these details have not been adequately documented in scientific publications. There are quite a few obstacles in collecting this data that have slowed down the process and need to be discussed publicly. Our backlog of slides dates back to 1997, meaning there are a lot that need to be sifted through and discarded for peeling or cracking. Additionally, during scanning a slide can get stuck, stalling a scan session for hours, resulting in a significant loss of productivity. Over the past two years, we have accumulated significant experience with how to scan a diverse inventory of slides using the Aperio AT2 high-volume scanner. We have been working closely with the vendor to resolve many problems associated with the use of this scanner for research purposes. This scanning project began in January of 2018 when the scanner was first installed. The scanning process was slow at first since there was a learning curve with how the scanner worked and how to obtain samples from the hospital. From its start date until May of 2019 ~20,000 slides we scanned. In the past 6 months from May to November we have tripled that number and how hold ~60,000 slides in our database. This dramatic increase in productivity was due to additional undergraduate staff members and an emphasis on efficient workflow. The Aperio AT2 scans 400 slides a day, requiring at least eight hours of scan time. The efficiency of these scans can vary greatly. When our team first started, approximately 5% of slides failed the scanning process due to focal point errors. We have been able to reduce that to 1% through a variety of means: (1) best practices regarding daily and monthly recalibrations, (2) tweaking the software such as the tissue finder parameter settings, and (3) experience with how to clean and prep slides so they scan properly. Nevertheless, this is not a completely automated process, making it very difficult to reach our production targets. With a staff of three undergraduate workers spending a total of 30 hours per week, we find it difficult to scan more than 2,000 slides per week using a single scanner (400 slides per night x 5 nights per week). The main limitation in achieving this level of production is the lack of a completely automated scanning process, it takes a couple of hours to sort, clean and load slides. We have streamlined all other aspects of the workflow required to database the scanned slides so that there are no additional bottlenecks. To bridge the gap between hospital operations and research, we are using Aperio’s eSM software. Our goal is to provide pathologists access to high quality digital images of their patients’ slides. eSM is a secure website that holds the images with their metadata labels, patient report, and path to where the image is located on our file server. Although eSM includes significant infrastructure to import slides into the database using barcodes, TUH does not currently support barcode use. Therefore, we manage the data using a mixture of Python scripts and manual import functions available in eSM. The database and associated tools are based on proprietary formats developed by Aperio, making this another important point of community-wide discussion on how best to disseminate such information. Our near-term goal for the TUDP Corpus is to release 100,000 slides by December 2020. We hope to continue data collection over the next decade until we reach one million slides. We are creating two pilot corpora using the first 50,000 slides we have collected. The first corpus consists of 500 slides with a marker stain and another 500 without it. This set was designed to let people debug their basic deep learning processing flow on these high-resolution images. We discuss our preliminary experiments on this corpus and the challenges in processing these high-resolution images using deep learning in [3]. We are able to achieve a mean sensitivity of 99.0% for slides with pen marks, and 98.9% for slides without marks, using a multistage deep learning algorithm. While this dataset was very useful in initial debugging, we are in the midst of creating a new, more challenging pilot corpus using actual tissue samples annotated by experts. The task will be to detect ductal carcinoma (DCIS) or invasive breast cancer tissue. There will be approximately 1,000 images per class in this corpus. Based on the number of features annotated, we can train on a two class problem of DCIS or benign, or increase the difficulty by increasing the classes to include DCIS, benign, stroma, pink tissue, non-neoplastic etc. Those interested in the corpus or in participating in community-wide discussions should join our listserv, nedc_tuh_dpath@googlegroups.com, to be kept informed of the latest developments in this project. You can learn more from our project website: https://www.isip.piconepress.com/projects/nsf_dpath.« less