On the interpretation of energy and energy fluxes of nonlinear internal waves : an example from Massachusetts Bay

Author Posting. © Cambridge University Press, 2006. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 561 (2006):103–112, doi:10.1017/S0022112006000991A self-consistent formalism to estimate baroclinic energy densities and fluxes resulting from the propagation of internal waves of arbitrary amplitude is derived using the concept of available potential energy. The method can be applied to numerical, laboratory or field data.MBIWE98 was supported by the US Geological Survey and the Office of Naval Research. A.S. received support from the Office of Naval Research (N00014-05-1-0361), R.B. from the Walter A. and Hope Noyes Smith Chair on Coastal Oceanography and B.B. from the US Geological Survey

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

Storm-driven sediment transport in Massachusetts Bay

This paper is not subject to U.S. copyright. The definitive version was published in Continental Shelf Research 28 (2008): 257-282, doi:10.1016/j.csr.2007.08.008.Massachusetts Bay is a semi-enclosed embayment in the western Gulf of Maine about 50 km wide and 100 km long. Bottom sediment resuspension is controlled predominately by storm-induced surface waves and transport by the tidal- and wind-driven circulation. Because the Bay is open to the northeast, winds from the northeast (‘Northeasters’) generate the largest surface waves and are thus the most effective in resuspending sediments. The three-dimensional oceanographic circulation model Regional Ocean Modeling System (ROMS) is used to explore the resuspension, transport, and deposition of sediment caused by Northeasters. The model transports multiple sediment classes and tracks the evolution of a multilevel sediment bed. The surficial sediment characteristics of the bed are coupled to one of several bottom-boundary layer modules that calculate enhanced bottom roughness due to wave–current interaction. The wave field is calculated from the model Simulating WAves Nearshore (SWAN). Two idealized simulations were carried out to explore the effects of Northeasters on the transport and fate of sediments. In one simulation, an initially spatially uniform bed of mixed sediments exposed to a series of Northeasters evolved to a pattern similar to the existing surficial sediment distribution. A second set of simulations explored sediment-transport pathways caused by storms with winds from the northeast quadrant by simulating release of sediment at selected locations. Storms with winds from the north cause transport southward along the western shore of Massachusetts Bay, while storms with winds from the east and southeast drive northerly nearshore flow. The simulations show that Northeasters can effectively transport sediments from Boston Harbor and the area offshore of the harbor to the southeast into Cape Cod Bay and offshore into Stellwagen Basin. This transport pattern is consistent with Boston Harbor as the source of silver found in the surficial sediments of Cape Cod Bay and Stellwagen Basin.We gratefully acknowledge support from the USGS Mendenhall Post-Doctoral Research Program for John C. Warner

Surface circulation in Block Island Sound and adjacent coastal and shelf regions : a FVCOM-CODAR comparison

© The Author(s), 2016. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Progress in Oceanography 143 (2016): 26-45, doi:10.1016/j.pocean.2016.02.005.CODAR-derived surface currents in Block Island Sound over the period of June 2000 through September 2008 were compared to currents computed using the Northeast Coastal Ocean Forecast System (NECOFS). The measurement uncertainty of CODAR-derived currents, estimated using statistics of a screened nine-year time series of hourly-averaged flow field, ranged from 3-7 cm/s in speed and 4°-14° in direction. The CODAR-derived and model-computed kinetic energy spectrum densities were in good agreement at subtidal frequencies, but the NECOFS-derived currents were larger by about 28% at semi-diurnal and diurnal tidal frequencies. The short-term (hourly to daily) current variability was dominated by the semidiurnal tides (predominantly the M2 tide), which on average accounted for ~87% of the total kinetic energy. The diurnal tidal and subtidal variability accounted for ~4% and ~9% of the total kinetic energy, respectively. The monthly-averaged difference between the CODAR-derived and model-computed velocities over the study area was 6 cm/s or less in speed and 28° or less in direction over the study period. An EOF analysis for the low-frequency vertically-averaged model current field showed that the water transport in the Block Island Sound region was dominated by modes 1 and 2, which accounted for 89% and 7% of the total variance, respectively. Mode 1 represented a relatively stationary spatial and temporal flow pattern with a magnitude that varied with season. Mode 2 was characterized mainly by a secondary cross-shelf flow and a relatively strong along-shelf flow. Process-oriented model experiments indicated that the relatively stationary flow pattern found in mode 1 was a result of tidal rectification and its magnitude changed with seasonal stratification. Correlation analysis between the flow and wind stress suggested that the cross-shelf water transport and its temporal variability in mode 2 were highly correlated to the surface wind forcing. The mode 2 derived onshore and offshore water transport, and was consistent with wind-driven Ekman theory. The along-shelf water transport over the outer shelf, where a large portion of the water flowed from upstream Nantucket Shoals, was not highly correlated to the surface wind stress.This work was supported by the NSF grants OCE-1332207 and OCE-1332666, MIT Sea Grant College Program through grant 2012-R/RC-127, and the NOAA NERACOOS program funds for NECOFS. Operational funding for the CODAR systems used in this study was provided by the Mid-Atlantic Regional Association Coastal Ocean Observing System. The development of the Global-FVCOM system has been supported by NSF grants OCE-1203393. C. Chen’s contribution was also supported by the International Center for Marine Studies at Shanghai Ocean University through the “Shanghai Universities First-class Disciplines Project”.2017-03-0

Neonatal-onset multisystem inflammatory disease responsive to interleukin-1 beta inhibition

BACKGROUND:Neonatal-onset multisystem inflammatory disease is characterized by fever, urticarial rash, aseptic meningitis, deforming arthropathy, hearing loss, and mental retardation. Many patients have mutations in the cold-induced autoinflammatory syndrome 1 (CIAS1) gene, encoding cryopyrin, a protein that regulates inflammation.METHODS:We selected 18 patients with neonatal-onset multisystem inflammatory disease (12 with identifiable CIAS1 mutations) to receive anakinra, an interleukin-1-receptor antagonist (1 to 2 mg per kilogram of body weight per day subcutaneously). In 11 patients, anakinra was withdrawn at three months until a flare occurred. The primary end points included changes in scores in a daily diary of symptoms, serum levels of amyloid A and C-reactive protein, and the erythrocyte sedimentation rate from baseline to month 3 and from month 3 until a disease flare.RESULTS:All 18 patients had a rapid response to anakinra, with disappearance of rash. Diary scores improved (P<0.001) and serum amyloid A (from a median of 174 mg to 8 mg per liter), C-reactive protein (from a median of 5.29 mg to 0.34 mg per deciliter), and the erythrocyte sedimentation rate decreased at month 3 (all P<0.001), and remained low at month 6. Magnetic resonance imaging showed improvement in cochlear and leptomeningeal lesions as compared with baseline. Withdrawal of anakinra uniformly resulted in relapse within days; retreatment led to rapid improvement. There were no drug-related serious adverse events.CONCLUSIONS:Daily injections of anakinra markedly improved clinical and laboratory manifestations in patients with neonatal-onset multisystem inflammatory disease, with or without CIAS1 mutations

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

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

AquaSat: A Data Set to Enable Remote Sensing of Water Quality for Inland Waters

Satellite estimates of inland water quality have the potential to vastly expand our ability to observe and monitor the dynamics of large water bodies. For almost 50 years, we have been able to remotely sense key water quality constituents like total suspended sediment, dissolved organic carbon, chlorophyll a, and Secchi disk depth. Nonetheless, remote sensing of water quality is poorly integrated into inland water sciences, in part due to a lack of publicly available training data and a perception that remote estimates are unreliable. Remote sensing models of water quality can be improved by training and validation on larger data sets of coincident field and satellite observations, here called matchups. To facilitate model development and deeper integration of remote sensing into inland water science, we have built AquaSat, the largest such matchup data set ever assembled. AquaSat contains more than 600,000 matchups, covering 1984–2019, of ground-based total suspended sediment, dissolved organic carbon, chlorophyll a, and SDDSecchi disk depth measurements paired with spectral reflectance from Landsat 5, 7, and 8 collected within ±1 day of each other. To build AquaSat, we developed open source tools in R and Python and applied them to existing public data sets covering the contiguous United States, including the Water Quality Portal, LAGOS-NE, and the Landsat archive. In addition to publishing the data set, we are also publishing our full code architecture to facilitate expanding and improving AquaSat. We anticipate that this work will help make remote sensing of inland water accessible to more hydrologists, ecologists, and limnologists while facilitating novel data-driven approaches to monitoring and understanding critical water resources at large spatiotemporal scales

Summer CO2 evasion from streams and rivers in the Kolyma River basin, north-east Siberia

Inland water systems are generally supersaturated in carbon dioxide (CO2) and are increasingly recognized as playing an important role in the global carbon cycle. The Arctic may be particularly important in this respect, given the abundance of inland waters and carbon contained in Arctic soils; however, a lack of trace gas measurements from small streams in the Arctic currently limits this understanding.We investigated the spatial variability of CO2 evasion during the summer low-flow period from streams and rivers in the northern portion of the Kolyma River basin in north-eastern Siberia. To this end, partial pressure of carbon dioxide (pCO2) and gas exchange velocities (k) were measured at a diverse set of streams and rivers to calculate CO2 evasion fluxes. We combined these CO2 evasion estimates with satellite remote sensing and geographic information system techniques to calculate total areal CO2 emissions. Our results show that small streams are substantial sources of atmospheric CO2 owing to high pCO2 and k, despite being a small portion of total inland water surface area. In contrast, large rivers were generally near equilibrium with atmospheric CO2. Extrapolating our findings across the Panteleikha-Ambolikha sub-watersheds demonstrated that small streams play a major role in CO2 evasion, accounting for 86% of the total summer CO2 emissions from inland waters within these two sub-watersheds. Further expansion of these regional CO2 emission estimates across time and space will be critical to accurately quantify and understand the role of Arctic streams and rivers in the global carbon budget

Changes in Plasma von Willebrand Factor and Cellular Fibronectin in MRI-Defined Traumatic Microvascular Injury

The neuropathology of traumatic brain injury (TB) is diverse, including primary injury to neurons, axons, glial cells, vascular structures, and secondary processes, such as edema and inflammation that vary between individual patients. Traumatic microvascular injury is an important endophenotype of TBI-related injury. We studied patients who sustained a TBI requiring ER evaluation and had an MRI performed within 48 h of injury. We classified patients into 3 groups based on their MRI findings: (1) those that had evidence of traumatic microvascular injury on susceptibility or diffusion weighted MRI sequences without frank hemorrhage [Traumatic Vascular Injury (TVI) group; 20 subjects]. (2) those who had evidence of intraparenchymal, subdural, epidural, or subarachnoid hemorrhage [Traumatic Hemorrhage (TH) group; 26 subjects], and (3) those who had no traumatic injuries detected by MRI [MRI-negative group; 30 subjects]. We then measured plasma protein biomarkers of vascular injury [von Willebrand Factor (vWF) or cellular fibronectin (cFn)] and axonal injury (phosphorylated neurofilament heavy chain; pNF-H). We found that the TVI group was characterized by decreased expression of plasma vWF (p < 0.05 compared to MRI-negative group; p < 0.00001 compared to TH group) <= 48 h after injury. cFN was no different between groups <= 48 h after injury, but was increased in the TVI group compared to the MRI-negative (p < 0.00001) and TH (p < 0.00001) groups when measured <= 48 h from injury. pNF-H was increased in both the TH and TVI groups compared to the MRI-negative group <= 48 h from injury. When we used the MRI grouping and molecular biomarkers in a model to predict Glasgow Outcome Scale-Extended (GOS-E) score at 30-90 days, we found that inclusion of the imaging data and biomarkers substantially improved the ability to predict a good outcome over clinical information alone. These data indicate that there is a distinct, vascular-predominant endophenotype in a subset of patients who sustain a TBI and that these injuries are characterized by a specific biomarker profile. Further work to will be needed to determine whether these biomarkers can be useful as predictive and pharmacodynamic biomarkers for vascular-directed therapies after TBI