On the error statistics of Viterbi decoding and the performance of concatenated codes

Computer simulation results are presented on the performance of convolutional codes of constraint lengths 7 and 10 concatenated with the (255, 223) Reed-Solomon code (a proposed NASA standard). These results indicate that as much as 0.8 dB can be gained by concatenating this Reed-Solomon code with a (10, 1/3) convolutional code, instead of the (7, 1/2) code currently used by the DSN. A mathematical model of Viterbi decoder burst-error statistics is developed and is validated through additional computer simulations

Potential flow artifacts associated with benthic experimental gear: Deep-sea mudbox examples

In response to the growing recognition of the potential effects of near-bed hydrodynamics on various benthic processes, flume studies were conducted to document fine-scale flow patterns over several types of mudboxes that have been used to study colonization by deep-sea organisms. Mudboxes are typically filled with natural sediments or sediment treatments and placed in the field to observe how timing, larval supply and sediment composition may affect larval settlement. This study addresses potential hydrodynamic biases of mudbox structures as obstructions to the near-bed flow. Detailed velocity profiles were made over two types of “free vehicle” mudboxes that could be deployed and recovered from a surface vessel. One of these (“Old Free Vehicle”) was not designed with regard for potential hydrodynamic biases whereas the other (“New Free Vehicle”) was designed specifically to minimize flow disturbances and maintain a realistic boundary-layer flow over the mudbox sediments. Flume velocity profiles also were made over two smaller mudboxes designed to be deployed by a submersible, one (“Flush Sediment Tray”) which was designed to be placed flush with the ocean bottom, thus minimizing flow disturbance, and another (“Raised Mudbox”) which was not. Flume simulations indicated that the Old Free Vehicle and the Raised Mudbox cause considerable disturbance to the near-bed flow regime; flows over the mudbox sediment surface differed markedly from those predicted for the natural seabed and those observed over the flume bed in the absence of the mudboxes. Flow accelerations, growing secondary boundary layers and eddy formation were observed over these mudbox sediments, and vertical velocity profiles varied considerably in the along-channel direction. The alternative mudbox designs (New Free Vehicle and Flush Sediment Tray) were largely successful in reducing or eliminating these flow artifacts. Boundary-layer flows over both the New Free Vehicle and the Flush Sediment Tray were much more uniform, and velocity profiles over the sediment surfaces were very similar to those in the empty flume channel and those predicted for a natural deep-sea habitat. In addition, there was no evidence of eddy formation and other major flow disturbances. These flume studies underscore the benefit of considering potential hydrodynamic effects in designing benthic experimental sampling gear to reduce potential flow disturbances that may bias data collections and confound data interpretation

Shoaling of nonlinear internal waves in Massachusetts Bay

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C08031, doi:10.1029/2008JC004726.The shoaling of the nonlinear internal tide in Massachusetts Bay is studied with a fully nonlinear and nonhydrostatic model. The results are compared with current and temperature observations obtained during the August 1998 Massachusetts Bay Internal Wave Experiment and observations from a shorter experiment which took place in September 2001. The model shows how the approaching nonlinear undular bore interacts strongly with a shoaling bottom, offshore of where KdV theory predicts polarity switching should occur. It is shown that the shoaling process is dominated by nonlinearity, and the model results are interpreted with the aid of a two-layer nonlinear but hydrostatic model. After interacting with the shoaling bottom, the undular bore emerges on the shallow shelf inshore of the 30-m isobath as a nonlinear internal tide with a range of possible shapes, all of which are found in the available observational record.A. Scotti began this project as a Postdoctoral Scholar at the Woods Hole Oceanographic Institution, with support from the Johnson Foundation and the USGS. Further support was provided to Scotti by the Office of Naval Research under grants N00014-01-1-0172, N00014-03-1-0553, and N00014-05-1-0361, and by NSF under grant OCE 07-29636. R. Beardsley was supported by ONR under grants N00014-98-1- 0059, N00014-00-1-0210, and the Smith Chair in Coastal Physical Oceanography. J. Pineda was supported by ONR under grants N00014-01-1-0172, and by a WHOIOcean Life Institute Fellowship

Near-bottom circulation and dispersion of sediment containing Alexandrium fundyense cysts in the Gulf of Maine during 2010–2011

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 96–111, doi:10.1016/j.dsr2.2013.11.003.The life cycle of Alexandrium fundyense in the Gulf of Maine includes a dormant cyst stage that spends the winter predominantly in the bottom sediment. Wave-current bottom stress caused by storms and tides induces resuspension of cyst-containing sediment during winter and spring. Resuspended sediment could be transported by water flow to different locations in the Gulf and the redistribution of sediment containing A. fundyense cysts could alter the spatial and temporal manifestation of its spring bloom. The present study evaluates model near-bottom flow during storms, when sediment resuspension and redistribution are most likely to occur, between October and May when A. fundyense cells are predominantly in cyst form. Simulated water column sediment (mud) concentrations from representative locations of the Gulf are used to initialize particle tracking simulations for the period October 2010–May 2011. Particles are tracked in full three-dimensional model solutions including a sinking velocity characteristic of cyst and aggregated mud settling (0.1 mm s−1). Although most of the material was redeposited near the source areas, small percentages of total resuspended sediment from some locations in the western (~4%) and eastern (2%) Maine shelf and the Bay of Fundy (1%) traveled distances longer than 100 km before resettling. The redistribution changed seasonally and was sensitive to the prescribed sinking rate. Estimates of the amount of cysts redistributed with the sediment were small compared to the inventory of cysts in the upper few centimeters of sediment but could potentially have more relevance immediately after deposition.Research support to all authors, except DJM and VAS, was provided by U.S. Geological Survey. DJM gratefully acknowledges financial support of the National Oceanic and Atmospheric Administration (Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation Grant OCE-1314642 and National Institute of Environmental Health Sciences Grant 1P01ES021923-01. VAS was supported by the North East Consortium Grant NA05NMF4721057

Investigating the importance of sediment resuspension in Alexandrium fundyense cyst population dynamics in the Gulf of Maine

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 79–95, doi:10.1016/j.dsr2.2013.10.011.Cysts of Alexandrium fundyense, a dinoflagellate that causes toxic algal blooms in the Gulf of Maine, spend the winter as dormant cells in the upper layer of bottom sediment or the bottom nepheloid layer and germinate in spring to initiate new blooms. Erosion measurements were made on sediment cores collected at seven stations in the Gulf of Maine in the autumn of 2011 to explore if resuspension (by waves and currents) could change the distribution of over-wintering cysts from patterns observed in the previous autumn; or if resuspension could contribute cysts to the water column during spring when cysts are viable. The mass of sediment eroded from the core surface at 0.4 Pa ranged from 0.05 kg m−2 near Grand Manan Island, to 0.35 kg m−2 in northern Wilkinson Basin. The depth of sediment eroded ranged from about 0.05 mm at a station with sandy sediment at 70 m water depth on the western Maine shelf, to about 1.2 mm in clayey–silt sediment at 250 m water depth in northern Wilkinson Basin. The sediment erodibility measurements were used in a sediment-transport model forced with modeled waves and currents for the period October 1, 2010 to May 31, 2011 to predict resuspension and bed erosion. The simulated spatial distribution and variation of bottom shear stress was controlled by the strength of the semi-diurnal tidal currents, which decrease from east to west along the Maine coast, and oscillatory wave-induced currents, which are strongest in shallow water. Simulations showed occasional sediment resuspension along the central and western Maine coast associated with storms, steady resuspension on the eastern Maine shelf and in the Bay of Fundy associated with tidal currents, no resuspension in northern Wilkinson Basin, and very small resuspension in western Jordan Basin. The sediment response in the model depended primarily on the profile of sediment erodibility, strength and time history of bottom stress, consolidation time scale, and the current in the water column. Based on analysis of wave data from offshore buoys from 1996 to 2012, the number of wave events inducing a bottom shear stress large enough to resuspend sediment at 80 m ranged from 0 to 2 in spring (April and May) and 0 to 10 in winter (October through March). Wave-induced resuspension is unlikely in water greater than about 100 m deep. The observations and model results suggest that a millimeter or so of sediment and associated cysts may be mobilized in both winter and spring, and that the frequency of resuspension will vary interannually. Depending on cyst concentration in the sediment and the vertical distribution in the water column, these events could result in a concentration in the water column of at least 104 cysts m−3. In some years, resuspension events could episodically introduce cysts into the water column in spring, where germination is likely to be facilitated at the time of bloom formation. An assessment of the quantitative effects of cyst resuspension on bloom dynamics in any particular year requires more detailed investigation.Research support to Donald M. Anderson and Bruce A. Keafer provided through the Woods Hole Center for Oceans and Human Health; National Science Foundation Grants OCE-0430724 and OCE-0911031; and National Institute of Environmental Health Sciences Grant 1-P50-ES012742-01; the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and A09NOS4780193; the MERHAB Grant program through NOAA Grant NA11NOS4780025; and the PCMHAB Grant program through NOAA Grant NA11NOS4780023. Research support to all other authors was provided by U.S. Geological Survey

Characterizing wave- and current- induced bottom shear stress : U.S. middle Atlantic continental shelf

This paper is not subject to U.S. copyright. The definitive version was published in Continental Shelf Research 52 (2013): 73-86, doi:10.1016/j.csr.2012.10.012.Waves and currents create bottom shear stress, a force at the seabed that influences sediment texture distribution, micro-topography, habitat, and anthropogenic use. This paper presents a methodology for assessing the magnitude, variability, and driving mechanisms of bottom stress and resultant sediment mobility on regional scales using numerical model output. The analysis was applied to the Middle Atlantic Bight (MAB), off the U.S. East Coast, and identified a tidally-dominated shallow region with relatively high stress southeast of Massachusetts over Nantucket Shoals, where sediment mobility thresholds are exceeded over 50% of the time; a coastal band extending offshore to about 30 m water depth dominated by waves, where mobility occurs more than 20% of the time; and a quiescent low stress region southeast of Long Island, approximately coincident with an area of fine-grained sediments called the “Mud Patch”. The regional high in stress and mobility over Nantucket Shoals supports the hypothesis that fine grain sediment winnowed away in this region maintains the Mud Patch to the southwest. The analysis identified waves as the driving mechanism for stress throughout most of the MAB, excluding Nantucket Shoals and sheltered coastal bays where tides dominate; however, the relative dominance of low-frequency events varied regionally, and increased southward toward Cape Hatteras. The correlation between wave stress and local wind stress was lowest in the central MAB, indicating a relatively high contribution of swell to bottom stress in this area, rather than locally generated waves. Accurate prediction of the wave energy spectrum was critical to produce good estimates of bottom shear stress, which was sensitive to energy in the long period waves.P.S. Dalyander was supported by the U.S. Geological Survey Mendenhall Research Fellowship Program

Carbon Budget of Tidal Wetlands, Estuaries, and Shelf Waters of Eastern North America

Carbon cycling in the coastal zone affects global carbon budgets and is critical for understanding the urgent issues of hypoxia, acidification, and tidal wetland loss. However, there are no regional carbon budgets spanning the three main ecosystems in coastal waters: tidal wetlands, estuaries, and shelf waters. Here we construct such a budget for eastern North America using historical data, empirical models, remote sensing algorithms, and process‐based models. Considering the net fluxes of total carbon at the domain boundaries, 59 ± 12% (± 2 standard errors) of the carbon entering is from rivers and 41 ± 12% is from the atmosphere, while 80 ± 9% of the carbon leaving is exported to the open ocean and 20 ± 9% is buried. Net lateral carbon transfers between the three main ecosystem types are comparable to fluxes at the domain boundaries. Each ecosystem type contributes substantially to exchange with the atmosphere, with CO2 uptake split evenly between tidal wetlands and shelf waters, and estuarine CO2 outgassing offsetting half of the uptake. Similarly, burial is about equal in tidal wetlands and shelf waters, while estuaries play a smaller but still substantial role. The importance of tidal wetlands and estuaries in the overall budget is remarkable given that they, respectively, make up only 2.4 and 8.9% of the study domain area. This study shows that coastal carbon budgets should explicitly include tidal wetlands, estuaries, shelf waters, and the linkages between them; ignoring any of them may produce a biased picture of coastal carbon cycling

Alexandrium fundyense cysts in the Gulf of Maine : long-term time series of abundance and distribution, and linkages to past and future blooms

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 6-26, doi:10.1016/j.dsr2.2013.10.002.Here we document Alexandrium fundyense cyst abundance and distribution patterns over nine years (1997 and 2004-2011) in the coastal waters of the Gulf of Maine (GOM) and identify linkages between those patterns and several metrics of the severity or magnitude of blooms occurring before and after each autumn cyst survey. We also explore the relative utility of two measures of cyst abundance and demonstrate that GOM cyst counts can be normalized to sediment volume, revealing meaningful patterns equivalent to those determined with dry weight normalization.Cyst concentrations were highly variable spatially. Two distinct 1 seedbeds (defined here as accumulation zones with > 300 cysts cm-3) are evident, one in the Bay of Fundy (BOF) and one in mid-coast Maine. Overall, seedbed locations remained relatively constant through time, but their area varied 3-4 fold, and total cyst abundance more than 10 fold among years. A major expansion of the mid-coast Maine seedbed occurred in 2009 following an unusually intense A. fundyense bloom with visible red-water conditions, but that feature disappeared by late 2010. The regional system thus has only two seedbeds with the bathymetry, sediment characteristics, currents, biology, and environmental conditions necessary to persist for decades or longer. Strong positive correlations were confirmed between the abundance of cysts in both the 0-1 and the 0-3 cm layers of sediments in autumn and geographic measures of the extent of the bloom that occurred the next year (i.e., cysts → blooms), such as the length of coastline closed due to shellfish toxicity or the southernmost latitude of shellfish closures. In general, these metrics of bloom geographic extent did not correlate with the number of cysts in sediments following the blooms (blooms → cysts). There are, however, significant positive correlations between 0-3 cm cyst abundances and metrics of the preceding bloom that are indicative of bloom intensity or vegetative cell abundance (e.g., cumulative shellfish toxicity, duration of detectable toxicity in shellfish, and bloom termination date). These data suggest that it may be possible to use cyst abundance to empirically forecast the geographic extent of the forthcoming bloom and, conversely, to use other metrics from bloom and toxicity events to forecast the size of the subsequent cyst population as the inoculum for the next year’s bloom. This is an important step towards understanding the excystment/encystment cycle in A. fundyense bloom dynamics while also augmenting our predictive capability for this HAB-forming species in the GOM.Research support provided by the ECOHAB Grant program through NOAA Grants NA06NOS4780245 and NA09NOS4780193, and through the Woods Hole Center for Oceans and Human Health, National 1 Science Foundation (NSF) Grants OCE-0430724, OCE-0911031, and OCE-1314642; and National Institute of Environmental Health Sciences (NIEHS) Grants 1-P50-ES012742-01 and 1-P01-ES021923-01, and funding through the states of ME, NH, and MA. We are also grateful for event response funding provided for many of the cruises. Funding for J.L. Martin was provided by Fisheries and Oceans Canada

Generation and propagation of nonlinear internal waves in Massachusetts Bay

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): C10001, doi:10.1029/2007JC004313.During the summer, nonlinear internal waves (NLIWs) are commonly observed propagating in Massachusetts Bay. The topography of the area is unique in the sense that the generation area (over Stellwagen Bank) is only 25 km away from the shoaling area, and thus it represents an excellent natural laboratory to study the life cycle of NLIWs. To assist in the interpretation of the data collected during the 1998 Massachusetts Bay Internal Wave Experiment (MBIWE98), a fully nonlinear and nonhydrostatic model covering the generation/shoaling region was developed, to investigate the response of the system to the range of background and driving conditions observed. Simplified models were also used to elucidate the role of nonlinearity and dispersion in shaping the NLIW field. This paper concentrates on the generation process and the subsequent evolution in the basin. The model was found to reproduce well the range of propagation characteristics observed (arrival time, propagation speed, amplitude), and provided a coherent framework to interpret the observations. Comparison with a fully nonlinear hydrostatic model shows that during the generation and initial evolution of the waves as they move away from Stellwagen Bank, dispersive effects play a negligible role. Thus the problem can be well understood considering the geometry of the characteristics along which the Riemann invariants of the hydrostatic problem propagate. Dispersion plays a role only during the evolution of the undular bore in the middle of Stellwagen Basin. The consequences for modeling NLIWs within hydrostatic models are briefly discussed at the end.A. Scotti began this project as a Postdoctoral Scholar at theWoods Hole Oceanographic Institution, with support from the Johnson Foundation and the USGS. Further support was provided to Scotti by the Office of Naval Research under grants N00014-01-1-0172, N00014- 03-1-0553, and N00014-05-1-0361, and to Beardsley under grants N00014- 98-1-0059, N00014-00-1-0210, and the Smith Chair in Coastal Physical Oceanography

A modified beam-to-earth transformation to measure short-wavelength internal waves with an acoustic Doppler current profiler

Author Posting. © American Meteorological Society 2005. 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 22 (2005): 583–591, doi:10.1175/JTECH1731.1.The algorithm used to transform velocity signals from beam coordinates to earth coordinates in an acoustic Doppler current profiler (ADCP) relies on the assumption that the currents are uniform over the horizontal distance separating the beams. This condition may be violated by (nonlinear) internal waves, which can have wavelengths as small as 100–200 m. In this case, the standard algorithm combines velocities measured at different phases of a wave and produces horizontal velocities that increasingly differ from true velocities with distance from the ADCP. Observations made in Massachusetts Bay show that currents measured with a bottom-mounted upward-looking ADCP during periods when short-wavelength internal waves are present differ significantly from currents measured by point current meters, except very close to the instrument. These periods are flagged with high error velocities by the standard ADCP algorithm. In this paper measurements from the four spatially diverging beams and the backscatter intensity signal are used to calculate the propagation direction and celerity of the internal waves. Once this information is known, a modified beam-to-earth transformation that combines appropriately lagged beam measurements can be used to obtain current estimates in earth coordinates that compare well with pointwise measurements.A. Scotti was partially supported by ONR Grants N00014-03-1-0553 and N00014-01-1- 0172, B. Butman and P. Alexander by the U.S. Geological Survey, and R. Beardsley by the WHOI Smith Chair and ONR Grant N00014-98-1-0210. S. Anderson received partial support from ONR (Grant N00014-97- 1-0158). The Massachusetts Bay Internal Wave Experiment was jointly supported by ONR and USGS