The kinematics and dynamics of the New England continental shelf and shelf/slope front.

Thesis. 1977. Ph.D.--Massachusetts Institute of Technology. Dept. of Meteorology.Microfiche copy available in Archives and Science.Vita.Bibliography : p. 194-197.Ph.D

AXIS—an Autonomous Expendable Instrument System

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Atmospheric and Oceanic Technology 34 (2017): 2673-2682, doi:10.1175/JTECH-D-17-0054.1.Expendable bathythermographs (XBT) to profile upper-ocean temperatures from vessels in motion have been in use for some 50 years now. Developed originally for navy use, they were soon adapted by oceanographers to map out upper-ocean thermal structure and its space–-time variability from both research vessels and merchant marine vessels in regular traffic. These activities continue today. This paper describes a new technology—the Autonomous Expendable Instrument System (AXIS)—that has been developed to provide the capability to deploy XBT probes on a predefined schedule, or adaptively in response to specific events without the presence of an observer on board. AXIS is a completely self-contained system that can hold up to 12 expendable probes [XBTs, XCTDs, expendable sound velocimeter (XSV)] in any combination. A single-board Linux computer keeps track of what probes are available, takes commands from ashore via Iridium satellite on what deployment schedule to follow, and records and forwards the probe data immediately with a time stamp and the GPS position. This paper provides a brief overview of its operation, capabilities, and some examples of how it is improving coverage along two lines in the Atlantic.Initial development of AXIS mechanical design elements wasmade possible by awards from the Cecil H. and Ida M. Green Technology Innovation Fund and the Sealark Foundation to the team of Dave Fratantoni, Keith von der Heydt (WHOI), and Terry Hammar (WHOI). Construction of the first full AXIS prototype was supported by a technology grant from the National Science Foundation (OCE-0926853) and the second one through an NSF-funded (OCE-1061185) subcontract from the University of Rhode Island.2018-06-2

Oleander is more than a flower twenty-five years of oceanography aboard a merchant vessel

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rossby, T., Flagg, C. N., Donohue, K., Fontana, S., Curry, R., Andres, M., & Forsyth, J. Oleander is more than a flower twenty-five years of oceanography aboard a merchant vessel. Oceanography, 32(3), (2019): 126-137, doi:10.5670/oceanog.2019.319.Since late fall 1992, CMV Oleander III has been measuring upper ocean currents during its weekly trips between Bermuda and Port Elizabeth, New Jersey, by means of an acoustic Doppler current profiler installed in its hull. The overarching objective of this effort has been to monitor transport in the Gulf Stream and surrounding waters. With 25 years of observation in hand, we note that the Gulf Stream exhibits significant year-to-year variations but no evident long-term trend in transport. We show how these data have enabled studies of oceanic variability over a very wide range of scales, from a few kilometers to the full 1,000 km length of its route. We report that the large interannual variations in temperature on the continental shelf are negatively correlated with flow from the Labrador Sea, but that variability in the strength of this flow cannot account for a longer-term warming trend observed on the shelf. Acoustic backscatter data offer a rich trove of information on biomass activities over a wide range of spatial and temporal scales. A peek at the future illustrates how the new and newly equipped Oleander will be able to profile currents to greater depths and thereby contribute to monitoring the strength of the meridional overturning circulation.First and foremost we extend our heartfelt thanks to the Bermuda Container Line/Neptune Group Management Ltd for permission to operate an acoustic Doppler current profiler on board CMV Oleander III, a 150 kHz ADCP between 1992 and 2004, and a 75 kHz ADCP between 2005 and 2018. Their interest and support is gratefully acknowledged. Cor Teeuwen, our initial contact in Holland while the ship was still under construction, played an important role in facilitating the original ADCP installation. His evident interest to make this concept work has stimulated similar activities on other commercial vessels. The interest and willingness of the shipping industry to be supportive of science has been a very positive experience for all of us who have ventured in this direction. Initial funding came from NOAA and the Office of Naval Research. Since 1999, the National Science Foundation has supported the project through funding to the University of Rhode Island and Stony Brook University, and now also to the Bermuda Institute of Ocean Sciences (BIOS), which will be taking over the Oleander operation. NSF is also funding the current transition to the new CMV Oleander. In the early years, G. Schwartze and E. Gottlieb were very helpful with technical support for the project. This included frequent visits to the ship before we had the capability to transfer the data through the Ethernet. We thank Jules Hummon and Eric Firing for adapting the UNOLS-wide UHDAS ADCP operating system to the merchant marine environment. We thank E. Williams and P. Ortner at the Rosenstiel School of Marine and Atmospheric Science, University of Miami, for making the 38 kHz ADCP data from Explorer of the Seas available to us. We also want to thank the NOAA Ship Of Opportunity Program for continued interest in and support of XBT operations along the Oleander section. That support started over 40 years ago and is now stronger than ever. All ADCP data from 1992 through 2018 have been archived at the Joint Archive for Shipboard ADCP (JASADCP), established at the University of Hawaii by NOAA’s National Centers for Environmental Information (NCEI). Averaged yearly data sets can be downloaded in ASCII text or NetCDF formats (http://ilikai.soest.hawaii.edu/​sadcp/main_inv.html). We thank Patrick Caldwell, JASADCP’s manager, for his assistance. All ADCP and XBT data can be obtained at the Stony Brook website: http://po.msrc.sunysb.edu/Oleander/. The URL to the project website is http://oleander.bios.edu—an updated data portal and products will soon be accessible here. An ERDDAP server for Oleander data (in the process of being configured) is at this address: http://erddap.​oleander.​bios.edu:​8080/​erddap/. The following link to BIOS lists over 40 publications that have used the ADCP data one way or another: http://oleander.bios.edu/publications/. We thank the two reviewers for their many interesting and helpful comments and suggestions

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The kinematics and dynamics of the New England continental shelf and shelf/slope front

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution April 1977A 37 day long field program was carried out in March 1974 on the New England continental shelf break to study the current and hydrographic structure and variability on the shelf and in the shelf/slope front. A second experiment was conducted in the shelf break region for one week in January 1975 to study frontal exchange processes. The mean currents during the March 1974 experiment all had a westward alongshore component, increasing in magnitude progressing offshore from ~5 cm/sec to a maximum at the nearshore edge of the shelf/slope front of between 10 and 20 cm/ sec, and decreasing in magnitude with depth. The current structure was such that the velocity vector rotated clockwise with depth in the shelf waters inside the front. The mean alongshore transport of shelf water was on the order of 0.4 Sverdrups through a cross-shelf transect south of Block Island. About 30% of the transport occurred in the wedge-shaped region offshore of the 100 m isobath and inshore of the front. Comparison of the observed mean currents with those predicted by the steady frictional boundary layer model of Csanady (1976) indicates that the model captures most of the essential features of the shelf circulation. The low frequency currents contain approximately 30% of the total current variance. An empirical orthogonal modal analysis indicates that for low frequency alongshore motions the whole shelf together with the water above the front moves as a unit and that the on- offshore currents are characterized by opposing flows at surface and bottom. The alongshore wind stress component is the dominant forcing term for these low frequency motions and for the subsurface pressure field as well. For motion with periods longer than 33 hours, the time derivative term in the cross-shelf momentum balance is comparable with the Coriolis term while the advective terms are 2 to 10 times smaller, on the average. The semi-diurnal tide is barotropic over the shelf with current magnitudes that increase almost by a factor of two between the shelf break and the inshore mooring 70 km shoreward. At the shelf break one-dimensional continuity gives the correct relation between the surface tide and the semi-diurnal currents. The semi-diurnal tide is clockwise polarized. The diurnal tide is baroclinic, increasing somewhat toward the bottom, is less clockwise polarized than the semi-diurnal, and has tidal ellipses aligned with the isobaths. The diurnal tidal energy decreases toward shore. Inertial energy in the frontal zone is equal to the semi-diurnal tidal energy near the surface. The inertial energy decreases with depth and is an order of magnitude smaller further on the shelf. The inertial oscillations are shown to be highly correlated with the wind stress record, arising and decaying on a time scale of 3 to 4 days. The inertial oscillations are shown to be preferentially forced by wind stress events that have a large amount of clockwise energy at near inertial periods. The frontal zone is shown to be in near geostrophic balance with an anticipated vertical shear across the front of the order of 5 to 8 cm/sec. Thus, there is a wedge-shaped region of velocity deficit that is confined directly under the front and above ~200 m. Outside of this region the velocity is alongshore to the west. Low frequency motion of the front is shown to exist on time scales from 3 to 10 days although the complete nature of the motions is not known. An oscillation of the front about its mid-depth position at periods of 3 1/2 to 4 days was caused initially by an eastward wind stress event forcing the front offshore near surface and onshore along the bottom. This was accompanied by large temperature oscillations near the bottom at midshelf and current oscillations confined to those current meters near the front. The internal wave band is most energetic in the center of the front, is about half as energetic above the front where it is subject to variations associated with the wind stress, and is smaller and nearly constant below the front. The internal wave energy decreases shoreward reflecting the decreasing stratification shoreward of the wintertime hydrography. Linear internal wave theory seems to break down in the conditions of the frontal zone. A stability analysis of the front to small perturbations is carried out by extending the model of Margules frontal stability of Orlanski (1968) to include the steep bottom topography of the shelf break region. The study covers the parameter range pertinent to the New England continental shelf break region and indicates that the front is indeed unstable; however, the associated growth rates are so slow that baroclinic instability does not seem to be a viable explanation for the observed frontal motions. Application of the theory to the nearly flat topography of the shelf itself shows that the front would be at least 20 times more unstable there suggesting that the front would migrate offshore to the shelf break region until a stable equilibrium was established between frictional dissipation and the instabilities.Funds for 'the field program and the data analysis of the New England Shelf Dynamics Experiment have been provided by the National Science Foundation through grants GA-4l075 and DES 74-03001