Vibration measurement by pulse differential holographic interferometry

Technique measures structural deformation of materials subjected to wide range of temperatures and other environmental conditions. Effects of convection currents are eliminated by operating a pulsed laser in double pulse mode that exposes hologram twice in quick succession

Applications of holography to vibrations, transient response, and wave propagation

Applications of holography to vibrations, transient response, and wave propagatio

Morphing Ensemble Kalman Filters

A new type of ensemble filter is proposed, which combines an ensemble Kalman filter (EnKF) with the ideas of morphing and registration from image processing. This results in filters suitable for nonlinear problems whose solutions exhibit moving coherent features, such as thin interfaces in wildfire modeling. The ensemble members are represented as the composition of one common state with a spatial transformation, called registration mapping, plus a residual. A fully automatic registration method is used that requires only gridded data, so the features in the model state do not need to be identified by the user. The morphing EnKF operates on a transformed state consisting of the registration mapping and the residual. Essentially, the morphing EnKF uses intermediate states obtained by morphing instead of linear combinations of the states.Comment: 17 pages, 7 figures. Added DDDAS references to the introductio

Scaling the Effects of Ocean Acidification on Coral Growth and Coral-Coral Competition on Coral Community Recovery

Ocean acidification (OA) is negatively affecting calcification in a wide variety of marine organisms. These effects are acute for many tropical scleractinian corals under short-term experimental conditions, but it is unclear how these effects interact with ecological processes, such as competition for space, to impact coral communities over multiple years. This study sought to test the use of individual-based models (IBMs) as a tool to scale up the effects of OA recorded in short-term studies to community-scale impacts, combining data from field surveys and mesocosm experiments to parameterize an IBM of coral community recovery on the fore reef of Moorea, French Polynesia. Focusing on the dominant coral genera from the fore reef, Pocillopora, Acropora, Montipora and Porites, model efficacy first was evaluated through the comparison of simulated and empirical dynamics from 2010-2016, when the reef was recovering from sequential acute disturbances (a crown-of-thorns seastar outbreak followed by a cyclone) that reduced coral cover to ~0% by 2010. The model then was used to evaluate how the effects of OA (1,100-1,200 µatm pCO2) on coral growth and competition among corals affected recovery rates (as assessed by changes in % cover y-1) of each coral population between 2010-2016. The model indicated that recovery rates for the fore reef community was halved by OA over 7 years, with cover increasing at 11% y-1 under ambient conditions and 4.8% y-1 under OA conditions. However, when OA was implemented to affect coral growth and not competition among corals, coral community recovery increased to 7.2% y-1, highlighting mechanisms other than growth suppression (i.e., competition), through which OA can impact recovery. Our study reveals the potential for IBMs to assess the impacts of OA on coral communities at temporal and spatial scales beyond the capabilities of experimental studies, but this potential will not be realized unless empirical analyses address a wider variety of response variables representing ecological, physiological and functional domains

Conspecific aggregations mitigate the effects of ocean acidification on calcification of the coral Pocillopora verrucosa

In densely populated communities, such as coral reefs, organisms can modify the physical and chemical environment for neighbouring individuals.We tested the hypothesis that colony density (12 colonies each placed ∼0.5 cm apart versus ∼8 cm apart) can modulate the physiological response (measured through rates of calcification, photosynthesis and respiration in the light and dark) of the coral Pocillopora verrucosa to partial pressure of CO2 (P) treatments (∼400 μatm and ∼1200 μatm) by altering the seawater flow regimes experienced by colonies placed in aggregations within a flume at a single flow speed. While light calcification decreased 20% under elevated versus ambient P for colonies in low-density aggregations, light calcification of high-density aggregations increased 23% at elevated versus ambient P. As a result, densely aggregated corals maintained calcification rates over 24 h that were comparable to those maintained under ambient P, despite a 45% decrease in dark calcification at elevated versus ambient P. Additionally, densely aggregated corals experienced reduced flow speeds and higher seawater retention times between colonies owing to the formation of eddies. These results support recent indications that neighbouring organisms, such as the conspecific coral colonies in the present example, can create smallscale refugia from the negative effects of ocean acidification

On dimension reduction in Gaussian filters

A priori dimension reduction is a widely adopted technique for reducing the computational complexity of stationary inverse problems. In this setting, the solution of an inverse problem is parameterized by a low-dimensional basis that is often obtained from the truncated Karhunen-Loeve expansion of the prior distribution. For high-dimensional inverse problems equipped with smoothing priors, this technique can lead to drastic reductions in parameter dimension and significant computational savings. In this paper, we extend the concept of a priori dimension reduction to non-stationary inverse problems, in which the goal is to sequentially infer the state of a dynamical system. Our approach proceeds in an offline-online fashion. We first identify a low-dimensional subspace in the state space before solving the inverse problem (the offline phase), using either the method of "snapshots" or regularized covariance estimation. Then this subspace is used to reduce the computational complexity of various filtering algorithms - including the Kalman filter, extended Kalman filter, and ensemble Kalman filter - within a novel subspace-constrained Bayesian prediction-and-update procedure (the online phase). We demonstrate the performance of our new dimension reduction approach on various numerical examples. In some test cases, our approach reduces the dimensionality of the original problem by orders of magnitude and yields up to two orders of magnitude in computational savings

Assessment of Temperature Optimum Signatures of Corals at Both Latitudinal Extremes of the Red Sea

Rising ocean temperatures are pushing reef-building corals beyond their temperature optima (Topt), resulting in reduced physiological performances and increased risk of bleaching. Identifying refugia with thermally resistant corals and understanding their thermal adaptation strategy is therefore urgent to guide conservation actions. The Gulf of Aqaba (GoA, northern Red Sea) is considered a climate refuge, hosting corals that may originate from populations selected for thermal resistance in the warmer waters of the Gulf of Tadjoura (GoT, entrance to the Red Sea and 2000 km south of the GoA). To better understand the thermal adaptation strategy of GoA corals, we compared the temperature optima (Topt) of six common reef-building coral species from the GoA and the GoT by measuring oxygen production and consumption rates as well as photophysiological performance (i.e. chlorophyll fluorescence) in response to a short heat stress. Most species displayed similar Topt between the two locations, highlighting an exceptional continuity in their respective physiological performances across such a large latitudinal range, supporting the GoA refuge theory. Stylophora pistillata showed a significantly lower Topt in the GoA, which may suggest an ongoing population-level selection (i.e. adaptation) to the cooler waters of the GoA and subsequent loss of thermal resistance. Interestingly, all Topt were significantly above the local maximum monthly mean seawater temperatures in the GoA (27.1°C) and close or below in the GoT (30.9°C), indicating that GoA corals, unlike those in the GoT, may survive ocean warming in the next few decades. Finally, Acropora muricata and Porites lobata displayed higher photophysiological performance than most species, which may translate to dominance in local reef communities under future thermal scenarios. Overall, this study is the first to compare the Topt of common reef-building coral species over such a latitudinal range and provides insights into their thermal adaptation in the Red Sea

Fast and Pervasive Transcriptomic Resilience and Acclimation of Extremely Heat-Tolerant Coral Holobionts from the Northern Red Sea

Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (\u3e94%) and algal (\u3e71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean

Variational data assimilation for the initial-value dynamo problem

The secular variation of the geomagnetic field as observed at the Earth's surface results from the complex magnetohydrodynamics taking place in the fluid core of the Earth. One way to analyze this system is to use the data in concert with an underlying dynamical model of the system through the technique of variational data assimilation, in much the same way as is employed in meteorology and oceanography. The aim is to discover an optimal initial condition that leads to a trajectory of the system in agreement with observations. Taking the Earth's core to be an electrically conducting fluid sphere in which convection takes place, we develop the continuous adjoint forms of the magnetohydrodynamic equations that govern the dynamical system together with the corresponding numerical algorithms appropriate for a fully spectral method. These adjoint equations enable a computationally fast iterative improvement of the initial condition that determines the system evolution. The initial condition depends on the three dimensional form of quantities such as the magnetic field in the entire sphere. For the magnetic field, conservation of the divergence-free condition for the adjoint magnetic field requires the introduction of an adjoint pressure term satisfying a zero boundary condition. We thus find that solving the forward and adjoint dynamo system requires different numerical algorithms. In this paper, an efficient algorithm for numerically solving this problem is developed and tested for two illustrative problems in a whole sphere: one is a kinematic problem with prescribed velocity field, and the second is associated with the Hall-effect dynamo, exhibiting considerable nonlinearity. The algorithm exhibits reliable numerical accuracy and stability. Using both the analytical and the numerical techniques of this paper, the adjoint dynamo system can be solved directly with the same order of computational complexity as that required to solve the forward problem. These numerical techniques form a foundation for ultimate application to observations of the geomagnetic field over the time scale of centuries

Empirically Derived Thermal Thresholds of Four Coral Species Along the Red Sea Using a Portable and Standardized Experimental Approach

Global warming is causing an unprecedented loss of species and habitats worldwide. This is particularly apparent for tropical coral reefs, with an increasing number of reefs experiencing mass bleaching and mortality on an annual basis. As such, there is a growing need for a standardized experimental approach to rapidly assess the thermal limits of corals and predict the survival of coral species across reefs and regions. Using a portable experimental system, the Coral Bleaching Automated Stress System (CBASS), we conducted standardized 18 h acute thermal stress assays to quantitively determine the upper thermal limits of four coral species across the length of the Red Sea coastline, from the Gulf of Aqaba (GoA) to Djibouti (~ 2100 km). We measured dark-acclimated photosynthetic efficiency (Fv/Fm), algal symbiont density, chlorophyll a, and visual bleaching intensity following heat stress. Fv/Fm was the most precise response variable assessed, advancing the Fv/Fm effective dose 50 (ED50, i.e., the temperature at which 50% of the initial Fv/Fm is measured) as an empirically derived proxy for thermal tolerance. ED50 thermal thresholds from the central/southern Red Sea and Djibouti populations were consistently higher for Acropora hemprichii, Pocillopora verrucosa, and Stylophora pistillata (0.1–1.8 °C above GoA corals, respectively), in line with prevailing warmer maximum monthly means (MMMs), though were lower than GoA corals relative to site MMMs (1.5–3.0 °C). P. verrucosa had the lowest thresholds overall. Despite coming from the hottest site, thresholds were lowest for Porites lobata in the southern Red Sea, suggesting long-term physiological damage or ongoing recovery from a severe, prior bleaching event. Altogether, the CBASS resolved historical, taxonomic, and possibly recent environmental drivers of variation in coral thermal thresholds, highlighting the potential for a standardized, short-term thermal assay as a universal approach for assessing ecological and evolutionary variation in the upper thermal limits of corals