<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Leichter, J. J.</style></author><author><style face="normal" font="default" size="100%">Stokes, M. D.</style></author><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author><author><style face="normal" font="default" size="100%">Witting, J.</style></author><author><style face="normal" font="default" size="100%">Washburn, L.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The island-scale internal wave climate of Moorea, French Polynesia.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Geophysical Research: Oceans</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">117</style></volume><pages><style face="normal" font="default" size="100%">C06008</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Analysis of five-year records of temperatures and currents collected at Moorea reveal strong internal wave activity at predominantly semi-diurnal frequencies impacting reef slopes at depths ?30 m around the entire island. Temperature changes of 1.5 oC to 3 oC are accompanied by surges of upward and onshore flow and vertical shear in onshore currents. Superimposed on annual temperature changes of approximately 3 oC, internal wave activity is high from Oct–May and markedly lower from Jun–Sep. The offshore pycnocline is broadly distributed with continuous stratification to at least 500 m depth, and a subsurface fluorescence maximum above the strong nutricline at approximately 200 m. Minimum buoyancy periods range from 4.8 to 6 min, with the maximum density gradient occurring at 50 to 60 m depth in summer and deepening to approximately 150 to 200 m in winter. The bottom slope angle around all of Moorea is super-critical relative to the vertical stratification angle suggesting that energy propagating into shallow water is only a portion of total incident internal wave energy. Vertical gradient Richardson numbers indicate dominance by density stability relative to current shear with relatively limited diapycnal mixing. Coherence and lagged cross-correlation of semi-diurnal temperature variation indicate complex patterns of inter-site arrival of internal waves and no clear coherence or lagged correlation relationships among island sides. Semi-diurnal and high frequency internal wave packets likely arrive on Moorea from a combination of local and distant sources and may have important impacts for nutrient and particle fluxes in deep reef environments.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2012-93218</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Collin, A.</style></author><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Towards deeper measurements of tropical reefscape structure using the WorldView-2 spaceborne sensor.</style></title><secondary-title><style face="normal" font="default" size="100%">Remote Sensing</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year></dates><volume><style face="normal" font="default" size="100%">4</style></volume><pages><style face="normal" font="default" size="100%">1425-1447</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Owing to the shallowness of waters, vast areas, and spatial complexity, reefscape mapping requires Digital Depth Models (DDM) at a fine scale but over large areas. Outperforming waterborne surveys limited by shallow water depths and costly airborne campaigns, recently launched satellite sensors, endowed with high spectral and very high spatial capabilities, can adequately address the raised issues. Doubling the number of spectral bands, the innovative eight band WorldView-2 (WV2) imagery is very susceptible to enhance the DDM retrieved from the traditional four band QuickBird-2 (QB2). Based on an efficiently recognized algorithm (ratio transform), resolving for the clear water bathymetry, we compared DDM derived from simulated QB2 with WV2 spectral combinations using acoustic ground-truthing in Moorea (French Polynesia). Three outcomes emerged from this study. Increasing spatial resolution from 2 to 0.5 m led to reduced agreement between modeled and in situ water depths. The analytical atmospheric correction (FLAASH) provided poorer results than those derived without atmospheric correction and empirical dark object correction. The purple, green, yellow and NIR3 (WV2 1st-3rd-4th-8th bands) spectral combination, processed with the atmospheric correction at the 2 m resolution, furnished the most robust consistency with ground-truthing (30 m (r = 0.65)), gaining 10 m of penetration relative to other spaceborne-derived bathymetric retrievals. The integration of the WV2-boosted bathymetry estimation into radiative transfer model holds great promise to frequently monitor the reefscape features at the colony-scale level.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2012-93501</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rosman, J.H.</style></author><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A framework for understanding drag parameterizations for coral reefs</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Geophysical Research</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><volume><style face="normal" font="default" size="100%">116</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In a hydrodynamic sense, a coral reef is a complex array of obstacles that exerts a net drag force on water moving over the reef. This drag is typically parameterized in ocean circulation models using drag coefficients (CD) or roughness length scales (z0); however, published CD for coral reefs span two orders of magnitude, posing a challenge to predictive modeling. Here we examine the reasons for the large range in reported CD and assess the limitations of using CD and z0 to parameterize drag on reefs. Using a formal framework based on the 3D spatially averaged momentum equations, we show that CD and z0 are functions of canopy geometry and velocity profile shape. Using an idealized two layer model, we illustrate that CD can vary by more than an order of magnitude for the same geometry and flow depending on the reference velocity selected and that differences in definition account for much of the range in reported CD values. Roughness length scales z0 are typically used in 3D circulation models to adjust CD for reference height, but this relies on spatially averaged near bottom velocity profiles being logarithmic. Measurements from a shallow backreef indicate that z0 determined from fits to point measurements of velocity profiles can be very different from z0 required to parameterize spatially averaged drag. More sophisticated parameterizations for drag and shear stresses are required to simulate 3D velocity fields over shallow reefs; in the meantime, we urge caution when using published CD and z0 values for coral reefs.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2011-86842</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author><author><style face="normal" font="default" size="100%">Rosman, J.H.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Analysis of bottom-track and compass error in a self-contained acoustic Doppler diver navigation console.</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year></dates><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">1229-1238</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Cobra-Tac (Teledyne RD Instruments) is a self-contained diver navigation system based on acoustic Doppler velocity log (DVL) technology that uses dead reckoning to compute displacements from a known starting point The navigational accuracy of the system was evaluated using a series of field tests with known solutions Initial test data had an obvious directional bias in the navigation measurements. with positional errors as large as 5% of the track length An analysis of this error showed that the DVL speed measurements were extremely accurate and that most of the position error could be explained by heading-dependent compass error Compass error versus heading curves were different depending on whether a given route was mapped in a clockwise or counterclockwise direction. and further testing indicated that this was clue to a combination of local magnetic field anomalies at the test site and instrument tilt A post processing correction procedure. based on a one-cycle compass error model, was derived that significantly improves Cobra-Tac position estimates After correction. position errors were well within manufacturer specifications Further tests using new firmware that permitted in situ underwater compass calibration gave position errors of less than 1% of the track length This level of accuracy should be sufficient for a wide range of scientific applications. Collectively. the test results and analyses indicate that Cobra-Tac can give very accurate navigation results, but the accuracy depends strongly on compass calibration and diver skill with the system</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2010-84613</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author><author><style face="normal" font="default" size="100%">Leichter, J. J.</style></author><author><style face="normal" font="default" size="100%">Monismith, S. G.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Episodic circulation and exchange in a wave-driven coral reef and lagoon system</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">&lt;Go to ISI&gt;://000261355500029</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">53</style></volume><pages><style face="normal" font="default" size="100%">2681-2694</style></pages><isbn><style face="normal" font="default" size="100%">0024-3590</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We examined the role of wave-driven circulation relative to wind and buoyancy forcing in a coral reef-lagoon system. Circulation measurements in Paopao Bay, Moorea, French Polynesia, during austral summer show the importance of waves in driving flows over the reef crest, through the lagoon, and out the reef pass. Tides were comparatively weak, due to proximity to amphidromic points, and exhibited an unusual spring-neap cycle where the major lunar tide modulated the major solar tide, and the overall tidal phase stayed approximately constant. Wind had only a secondary effect compared to surface waves. A simple fluid mass balance indicated rapid flushing of the shallow back reef and export through the reef pass, and a reef capture zone width of similar to 2.3 km. The reef pass circulation dynamics exhibited two-layer baroclinic exchange flow when waves were small, which was suppressed during large wave events. The unusually weak tidal forcing provided an opportunity to more closely investigate wave-driven circulation dynamics. As expected theoretically, there was a wave-driven setup of the free surface across the shallow lagoon, which drove a highly frictional flow, evident by a large drag coefficient C-D approximate to 0.1. Diverging from extant theory, the observed setup varied strongly with significant wave height and period. Overall, the circulation and exchange between this coral reef system and the adjacent open ocean were largely determined by episodic remote-forcing events and differed significantly from periodic tidal-exchange mechanisms.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2008-83494</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rosman, J.H.</style></author><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author><author><style face="normal" font="default" size="100%">Koseff, J. R.</style></author><author><style face="normal" font="default" size="100%">Monismith, S. G.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extracting Reynolds stresses from acoustic Doppler current profiler measurements in wave-dominated environments</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">&lt;Go to ISI&gt;://000253582700010</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">25</style></volume><pages><style face="normal" font="default" size="100%">286-306</style></pages><isbn><style face="normal" font="default" size="100%">0739-0572</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Surface waves introduce velocity correlations that bias and often dominate Reynolds stress estimates made using the traditional variance method for acoustic Doppler current profilers (ADCPs). This analysis shows that the wave bias is the sum of a real wave stress and an error due to instrument tilt, both of which have a large uncertainty. Three alternative extensions to the variance method for calculating Reynolds stress profiles from ADCP measurements in wavy conditions are analyzed. The previously proposed variance fitting method (Variance Fit) is evaluated and two more general methods that use along- and between-beam velocity differencing with adaptive filtering (Vertical AF and Horizontal AF) are derived. The three methods are tested on datasets containing long-period monochromatic swell (Moorea, French Polynesia) and shorter-period mixed swell (Santa Barbara, California). The Variance Fit method leaves a residual wave bias in beam velocity variances, especially for intermediate waves, but gives physically reasonable Reynolds stress estimates because most of the residual wave bias cancels when the variance method is applied. The new Vertical AF method does not produce inherent wave bias in beam velocity variances, but yields comparable Reynolds stresses to the Variance Fit method. The Horizontal AF method performs poorly for all but monochromatic waves. Error remaining after one of the above methods is applied can be attributed to residual wave error, correlation of turbulence between points chosen for differencing, or correlation between waves and turbulence. A simple procedure is provided for determining the minimum bin separation that can be used.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><accession-num><style face="normal" font="default" size="100%">LTER.2008-83506</style></accession-num></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lenihan, H. S.</style></author><author><style face="normal" font="default" size="100%">Adjeroud, M.</style></author><author><style face="normal" font="default" size="100%">Kotchen, M. J.</style></author><author><style face="normal" font="default" size="100%">Hench, J.L.</style></author><author><style face="normal" font="default" size="100%">Nakamura, T.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reef structure regulates small-scale spatial variation in coral bleaching</style></title></titles><keywords><keyword><style  face="normal" font="default" size="100%">MCR</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">&lt;Go to ISI&gt;://000261229600011</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">370</style></volume><pages><style face="normal" font="default" size="100%">127-141</style></pages><isbn><style face="normal" font="default" size="100%">0171-8630</style></isbn><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Coral bleaching is often characterized by high spatial variation across reef systems. Using a field survey and manipulative experiment, we tested whether the physical structure of coral reefs modifies environmental conditions that, in turn, influence spatial variation in bleaching in 3 scleractinian corals, Pocillopora verrucosa, Acropora elseyi, and Porites rus. Corals inhabit mainly the hard-bottom seafloor, or dead or partially dead coral heads ('bommies'). Bommies (0.10 to 3.0 m tall) position corals at different water depths and expose them to differences in light, temperature, hydrodynamics, and sedimentation, factors that can influence patterns of bleaching. We conducted our Study in association with a 14 d warming event that caused bleaching in lagoons of Moorea, French Polynesia. Bleaching in naturally occurring colonies of Pocillopora spp. and Acopora spp. was greater on the seafloor (0 m tall) than on short (0.35 to 0.40 m tall) and tall bommies (1.0 to 1.2 m tall). Bleaching in P. verrucosa and A. elseyi transplanted to reef structures in the experiment generally decreased with increasing reef height (seafloor &gt; short bommies &gt; tall bommies). P. rus did not bleach under any conditions observed. Regression analyses revealed that reef structure controlled current speed and sedimentation at the microhabitat scale (from centimeters to meters), and that these factors regulated bleaching and mortality in P. verrucosa and A. elseyi. Our results imply that the physical structure of shallow water reef habitat influences the performance of coral colonies by modifying environmental stress, and that accounting for this structure is important in managing coral reef systems.</style></abstract><accession-num><style face="normal" font="default" size="100%">LTER.2008-83497</style></accession-num></record></records></xml>