Tsunami observations by coastal ocean radar

When tsunami waves propagate across the open ocean, they are steered by the Coriolis effect and refraction due to gentle gradients in the bathymetry on scales longer than the wavelength. When the wave encounters steep gradients at the edges of continental shelves and at the coast, the wave becomes nonlinear and conservation of momentum produces squirts of surface current at the head of submerged canyons and in coastal bays. High frequency (HF) coastal ocean radar is well conditioned to observe the surface current bursts at the edge of the continental shelf and give a warning of 40 minutes to 2 hours when the shelf is 50 to 200km wide. The period of tsunami waves is invariant over changes in bathymetry and is in the range 2 to 30 minutes. Wavelengths for tsunamis (in 500 to 3000m depth) are in the range 8.5 to over 200 km, and on a shelf where the depth is about 50m (as in the Great Barrier Reef (GBR)) the wavelengths are in the range 2.5 to 30 km. In the use of HF radar technology, there is a trade-off between the precision of surface current speed measurements and time resolution. It is shown that the phased array HF ocean surface radar being deployed in the GBR and operating in a routine way for mapping surface currents, can resolve surface current squirts from tsunamis in the wave period range 20 to 30 minutes and in the wavelength range greater than about 6 km. An advantage in signal-to-noise ratio can be obtained from the prior knowledge of the spatial pattern of the squirts at the edge of the continental shelf, and it is estimated that, with this analysis, the time resolution of the GBR radar may be reduced to about 2.5 minutes, which corresponds to a capability to detect tsunamis at the shelf edge in the period range 5 to 30 minutes. It is estimated that the lower limit of squirt velocity detection at the shelf edge would correspond to a tsunami with water elevation of about 2.5 cm in the open ocean. This means that the GBR HF radar is well conditioned for use as a monitor of small, as well as larger, tsunamis and has the potential to contribute to the understanding of tsunami genesis research

The relentless march of mass coral bleaching: a global perspective of changing heat stress

The global coral bleaching event of 2014-2017 resulted from the latest in a series of heat stress events that have increased in intensity. We assessed global- and basin-scale variations in sea surface temperature-based heat stress products for 1985-2017 to provide the context for how heat stress during 2014-2017 compared with the past 3 decades. Previously, undefined "Heat Stress Year" periods (used to describe interannual variation in heat stress) were identified for the Northern and Southern Hemispheres, in which heat stress peaks during or shortly after the boreal and austral summers, respectively. The proportion of reef pixels experiencing bleaching-level heat stress increased through the record, accelerating during the last decade. This increase in accumulated heat stress at a bleaching level is a result of longer stress events rather than an increase in the peak stress intensity. Thresholds of heat stress extent for the three tropical ocean basins were established to designate "global" events, and a Global Bleaching Index was defined that relates heat stress extent to that observed in 1998. Notably, during the 2014-2017 global bleaching event, more than three times as many reefs were exposed to bleaching-level heat stress as in the 1998 global bleaching

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

Cumulative probability noise analysis in geophysical spectral records

The technique of rank ordering of spectral energy density samples was applied to high frequency (HF) ocean backscatter radar spectra to examine the properties of signal and noise in the record. HF ocean backscatter spectra have characteristic Bragg scatter lines and bands of energy with random phasing, and it is known that spiky noise from sferics and anthropogenic sources contribute to the observed energy density. Rank ordering of the spectral density data revealed three main features: (i) first-order Bragg scattering; (ii) continuum of randomly phased energy; and (iii) the underlying noise floor of the system. It is shown that the technique of rank ordering of spectral amplitude samples provides better insights and an improved algorithm for differentiating between bands of randomly phased sea echoes and system noise. The analysis reveals a constant offset in the spectral energy density data from the Ocean Surface Current Radar (OSCR) HF radar system, which should be removed before algorithms are applied to extract significant wave height information. The rank ordering of spectral energy density samples is a useful tool for differentiating between system noise and wide-band incoherent energy often obtained in a wide range of geophysical remote sensing

Mitigation of coral bleaching on the reef front by wave mixing

Coral bleaching becomes particularly likely when the water becomes stratified, with warm water absorbing solar radiation and sitting in a stable fashion on top of underlying cooler water. The physical conditions that cause vertical mixing of the water column often mitigate coral bleaching. Generally these are thought to be: low current speeds (low turbulent kinetic energy); low wave heights (small degree of micro-breakers and non-linearities); low wind speeds (low stress and shears). In this work we evaluate the mixing along the exposed 'weather edge' of a reef where even small-amplitude waves break and cause vertical mixing. Given that low wind speeds increase the likelihood of bleaching, the waves that might influence the reef-front are generally swell waves produced by the wind at a distant location. The combination of non-linearities in the waves and dispersion mean that the swell is the main contributor to vertical mixing at the reef-front. We adopt linear wave theory to bring the wave across the shelf to the reef front. Within about one wavelength of a steep reef front, the wave becomes non-linear and its surface elevation increases until it breaks. In this breaking zone, wave dynamics do not apply and the physics is best dealt with by momentum and energy considerations. Some of the energy is reflected as a propagating wave; some energy is carried over the reef-top into a lagoon or reef-flat as a momentum bore or a re-generated wave train; and some is converted to turbulence at the reef front. The energy that produces turbulent mixing at the reef front is compared with the potential energy of stratification, and it is found that even small-amplitude waves produce significant mixing. The partitioning of energy depends predominantly on wave height and sea water level. For most reefs, the elevation of the reef top is the level of the Lowest Astronomical Tide and this is used as the datum. The partition indices are presented as functions of Hs/D, where Hs is the significant wave height, and D is the water depth. Other parameters of water depth, wavelength, and width of the reeftop have smaller effects on the energy partition. The calculations show that for small Hs/D values (high tide) the mixing is high. As Hs/D increases towards low tide, more energy is spilled across the reef and less is spent on vertical mixing at the reef front. The application of this work to reef ecology is in identifying sections of a reef that are more resilient to coral bleaching. The results here show that even the smallest of swell produces sufficient vertical mixing to remove stratification and mitigate coral bleaching along the exposed front of a reef. The side of the reef normally exposed to swell will also normally be the windward side where prevailing wind-driven currents are likely to be driven across the reef flat. This means that corals on the reef front are likely to be a prime source of larvae in any recovery process if the reef suffers coral loss by bleaching, crown of thorns or disease

First observed severe mass bleaching in Malaysia, Greater Coral Triangle

[Extract] Malaysia contains approximately 4,000 km2 of reef (Wilkinson 2008) and an estimated 500 hermatypic coral species, which constitutes more than 60% of the worlds described hermatypic coral species (Veron et al. 2009). However, these reefs are exposed to numerous anthropogenic pressures and more than 40% are classified as having a high or very high Integrated Threat Index (Burke et al. 2002). Prior to 2010, severe and widespread coral bleaching had not been observed on Malaysian reefs, including during the 1997/98 global event when bleaching of Malaysian reefs was mild and occurred only in localized patches (Wilkinson 1998; Kushairi 1999)

The use of computational fluid dynamics in predicting the tidal flushing of animal burrows

Numerical hydrodynamic modelling has been used extensively over the last few decades to simulate flow in the ocean, bays and estuaries; however, modelling of much smaller scale phenomena is less common. In this work a commercially available Computational Fluid Dynamics package (FIDAP), normally used for industrial applications, was used to simulate tidally-induced flow in multi-opening animal burrows. U-shaped burrows of varying complexities were modelled to determine the effect of different surface characteristics and burrow geometries on surface water velocities, burrow velocities and burrow flushing times. The turbulent 2D model showed the slope of the surface water was proportional to the square of both the surface and burrow velocities. The effect of placing a root in the surface flow was to reduce the surface water velocity; however, the burrow flow depended upon the root position. For the root location either upstream or downstream of the burrow, the burrow velocity was reduced by 50%. With the root located between the burrow openings the burrow velocity increased by 200%, due to the increase in pressure difference across the burrow openings. A buttress root placed in the flow immediately downstream of the upstream burrow, caused the burrow flushing rate to increase significantly with increasing buttress height. Flushing times for burrows of varying depth were determined computationally by use of a tracer for the burrow water. For a burrow of depth 1·2 m, the flushing times were 5 and 28 min for root location between the burrow openings and downstream of the burrow, respectively. Animal burrows often consist of multiply-connected loops. A second burrow was added to the primary burrow and flushing times were found to be 15 and 38 min, respectively. A burrow system of four connected burrows was modelled which had corresponding flushing times up to 24 and 47 min, respectively. The calculated times are consistent with the hypothesis that a significant flushing of animal burrows occurs within a single tidal event. This preliminary investigation indicates that CFD models may be very useful in studying small scale hydrodynamic phenomena such as flow in animal burrows

The effect of water density variations on the tidal flushing of animal burrows

Animal burrows in mangrove swamps play an important role in the transport of various soluble materials, including salt. Flushing of burrows by inundating tides provides an efficient mechanism for the exchange of these materials. The density increase in the burrow, due to salt diffusion from pore water into the burrow, causes a greater resistance to the flushing. As the salinity difference between surface and burrow waters increases, the burrows no longer flush, and hydrostatic equilibrium exists between the different density waters. A flume experiment was conducted to compare burrow flushing characteristics with theoretical predictions. The results were consistent with a simple analytical theory in predicting whether burrows would flush. When equilibrium was attained, the difference between the interface depths was 10% greater than the theoretical prediction, which was within the experimental error. In addition, a comparison between a two-opening and a three-opening burrow showed that there was no benefit to the flushing capability due to additional openings. Computational fluid dynamic models were undertaken to compare with the experimental and theoretical flushing characteristics. These were also consistent with the flushing prediction theory. When equilibrium was attained, the difference between the interface depths in the model was 33% greater than the theoretical prediction. The computational study with an additional opening supported the experimental evidence that there is no advantage to the flushing. Insight into small-scale processes unable to be accurately observed could be obtained from the models, e.g. oscillations of density interfaces and turbulent scales at the burrow openings. The consistency in prediction of flushing between the theoretical, experimental and computational methods, now allows modelling of more complex burrow structures with great confidence

SATELLITE BATHYMETRY USE IN NUMERICAL MODELS OF OCEAN THERMAL STRESS

Techniques for deriving estimated bathymetry from satellite data are well established; however, use of this product in complex terrains is limited. Accurate bathymetry is essential in the construction of hydrodynamic models and satellite-derived bathymetry is a strong candidate for use in coastal and shallow waters. A case study of Palau is presented which uses satellite-derived bathymetry as input to a hydrodynamic model. Palau underwent widespread coral bleaching during 1998, thought to be due to thermal stress, and existing satellite products observed anomalous increases in temperature. The numerical model is used to evaluate sea surface temperature patterns during such a bleaching event. Comparisons between the model and thermal indicators derived from satellite data are made, and the results used to suggest improvements for satellite monitoring of thermal stress event

Relative dispersion of surface drifters in a barrier reef region

The spreading of two clusters of satellite-tracked surface drifters was quantified by 'relative dispersion' and 'relative diffusivity' (the time derivative of relative dispersion) in two regions of the southern Great Barrier Reef (GBR): a low-density reef matrix of complex topography and a shelf lagoon over flat bathymetry. Although based on a small data set, averaged values of these parameters over a 12 day period with concurrent measurements for the two regions indicated that relative dispersion and diffusivity of drifter pairs were 182 and 52 times greater, respectively, along the reef matrix than found in the lagoon. Relative diffusivities in the southern GBR were anisotropic and varied largely in space and time within the spatial scales of 1-100 km and temporal scales of hours to 16-20 days; they were considerably enhanced by high-frequency tidal processes. Submesoscale processes (<20 km) were important in the southern GBR, particularly in areas with complex topography where secondary circulations around the reefs and regions of steep bathymetry caused abrupt increase in dispersion. Although the dispersion was much higher along the reef matrix, the presence of ring circulations around the islands and wake eddies in the lee of islands can act as trapping mechanisms to keep particles within the reef matrix, retarding the loss to open water areas. This provides an efficient physical mechanism for both enhancing larval connectivity between reefs and, at the same time, trapping larvae when in the vicinity of reefs