scholarly journals Portraying Gradients of Structural Complexity in Coral Reefs Using Fine-Scale Depth Profiles

2021 ◽  
Vol 8 ◽  
Author(s):  
Lauriane Ribas-Deulofeu ◽  
Pierre-Alexandre Château ◽  
Vianney Denis ◽  
Chaolun Allen Chen

Structural complexity is an important feature to understand reef resilience abilities, through its role in mediating predator-prey interactions, regulating competition, and promoting recruitment. Most of the current methods used to measure reef structural complexity fail to quantify the contributions of fine and coarse scales of rugosity simultaneously, while other methods require heavy data computation. In this study, we propose estimating reef structural complexity based on high-resolution depth profiles to quantify the contributions of both fine and coarse rugosities. We adapted the root mean square of the deviation from the assessed surface profile (Rq) with polynomials. The efficiency of the proposed method was tested on nine theoretical cases and 50 in situ transects from South Taiwan, and compared to both the chain method and the visual rugosity index commonly employed to characterize reef structural complexity. The Rq indices proposed as rugosity estimators in this study consider multiple levels of reef rugosity, which the chain method and the visual rugosity index fail to apprehend. Furthermore, relationships were found between Rq scores and specific functional groups in the benthic community. Indeed, the fine scale rugosity of the South Taiwan reefs mainly comes from biotic components such as hard corals, while their coarse scale rugosity is essentially provided by the topographic variations that reflect the geological context of the reefs. This approach allows identifying the component of the rugosity that could be managed and which could, ultimately, improve strategies designed for conservation.

2019 ◽  
Author(s):  
Clara Fannjiang ◽  
T. Aran Mooney ◽  
Seth Cones ◽  
David Mann ◽  
K. Alex Shorter ◽  
...  

AbstractZooplankton occupy critical roles in marine ecosystems, yet their fine-scale behavior remains poorly understood due to the difficulty of studying individualsin situ. Here we combine biologging with supervised machine learning (ML) to demonstrate a pipeline for studyingin situbehavior of larger zooplankton such as jellyfish. We deployed the ITAG, a biologging package with high-resolution motion sensors designed for soft-bodied invertebrates, on 8Chrysaora fuscescensin Monterey Bay, using the tether method for retrieval. Using simultaneous video footage of the tagged jellyfish, we develop ML methods to 1) identify periods of tag data corrupted by the tether method, which may have compromised prior research findings, and 2) classify jellyfish behaviors. Our tools yield characterizations of fine-scale jellyfish activity and orientation over long durations, and provide evidence that developing behavioral classifiers onin siturather than laboratory data is essential.Summary StatementHigh-resolution motion sensors paired with supervised machine learning can be used to infer fine-scalein situbehavior of zooplankton for long durations.


2017 ◽  
Author(s):  
Pierre Marrec ◽  
Andrea M. Doglioli ◽  
Gérald Grégori ◽  
Mathilde Dugenne ◽  
Alice Della Penna ◽  
...  

Abstract. Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted in fall 2015 in which, a fine-scale structure in the North Western Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll-a and nutrients concentrations) with ADCP current velocity. We also deployed a new model of CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of surface phytoplankton community structure of surface waters with a spatial resolution of few km and a hourly temporal resolution. For the first time with this type of AFCM we were able to resolve Prochlorococcus and Synechococcus picocyanobacteria. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated to a 1-m vertical resolution pumping system deployed during fixed stations. The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters, characterized by an increase in Chl-a concentration. Prochlorococcus, pico- and nano-eukaryotes were more abundant in cold core waters while Synechococcus dominated in warm boundary waters. Nanoeukaryote were the main contributors (> 50 %) in terms of pigment content (FLR) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in-situ growth rate and apparent net primary production for Prochlorococcus (μ = 0.21 d−1, NPP = 0.11 mgC m−3 d−1) and Synechococcus (μ = 0.72 d−1, NPP = 2.68 mgC m−3 d−1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in-situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.


2018 ◽  
Vol 22 (15) ◽  
pp. 1-19 ◽  
Author(s):  
Xiaolei Fu ◽  
Lifeng Luo ◽  
Ming Pan ◽  
Zhongbo Yu ◽  
Ying Tang ◽  
...  

Abstract Better quantification of the spatiotemporal distribution of soil moisture across different spatial scales contributes significantly to the understanding of land surface processes on the Earth as an integrated system. While observational data for root-zone soil moisture (RZSM) often have sparse spatial coverage, model-simulated soil moisture may provide a useful alternative. TOPMODEL-Based Land Surface–Atmosphere Transfer Scheme (TOPLATS) has been widely studied and actively modified in recent years, while a detailed regional application with evaluation currently is still lacking. Thus, TOPLATS was used to generate high-resolution (30 arc s) RZSM based on coarse-scale (0.125°) forcing data over part of the Arkansas–Red River basin. First, the simulated RZSM was resampled to coarse scale to compare with the results of Mosaic, Noah, and VIC from NLDAS. Second, TOPLATS performance was assessed based on the spatial absolute difference among the models. The comparison shows that TOPLATS performance is similar to VIC, but different from Mosaic and Noah. Last, the simulated RZSM was compared with in situ observations of 16 stations in the study area. The results suggest that the simulated spatial distribution of RZSM is largely consistent with the distribution of topographic index (TI) in most instances, as topography was traditionally considered a major, but not the only, factor in horizontal redistribution of soil moisture. In addition, the finer-resolution RZSM can reflect the in situ soil moisture change at most local sites to a certain degree. The evaluation confirms that TOPLATS is a useful tool to estimate high-resolution soil moisture and has great potential to provide regional soil moisture estimates.


Author(s):  
Ping Lu ◽  
David J. Smith

Surface profile imaging at resolutions of better than 2Å is highly suitable for studies of surface structures and reactions. In the case of semiconductor materials, the main challenge is to prepare surfaces free of any contamination. The technique has previously been used to study surface reconstructions of Si and CdTe. In our previous observations, clean surfaces of CdTe were obtained by careful control of the incident electron beam within a JEM-4000EX high resolution electron microscope with a pressure of 10-7 torr. In the present study, observations of reconstructions and dynamic phenomena on CdTe surfaces were carried out with a Phillips-430ST, modified for Ultra-High Vacuum in the vicinity of the specimen and equipped with an in situ heating facility. The base vacuum in the region of the sample could usually reach ∼3×l0-9 torr after baking the microscope column at ∼120°C for 36 hours. The CdTe specimen was prepared by cutting a large single crystal into 3mm discs in a [110] direction, then mechanically polishing to a thickness of ∼20 microns, and finally ion milling to perforation.When viewed along a [110] projection, the CdTe sample was found to be dominated by clean or nearly clean (111) and (110) surfaces(with amorphous materials less than 5Å) whilst the (001) surface was usually very short and rough. A completely clean surface was obtained by in situ annealing of the crystal to about 200°. The (110) surface was then found to be reconstructed with a very characteristic chevron appearance in the manner described previously. Long and flat CdTe(OOl) surfaces were obtained by insitu annealing of the crystal at ∼510°C at which temperature edges of the crystal started to gradually sublime. Characterization of the surface structure was then possible when the crystal was cooled back down to temperatures below about 300°C. It was found that the (001) surface had a (2×1) reconstruction at temperatures below about 200°C which transformed reversibly into a (3×1) reconstruction over the approximate temperature range of 200°C<T<300°C. Figures la and lb show the (2×1) and (3×1) reconstructed (001) surfaces, viewed along the [110] projection, which were recorded at temperatures of 140°C and 240°C respectively. Structural models for the (2×1) and (3×1) reconstructions, obtained directly on the basis of the experimental images, are shown in Figs.2a and 2b respectively. The (2×1) reconstruction involves a 1/2 monolayer of Cd vacancies and a very large inward contraction of the remaining Cd surface atoms, which then displace the second layer of Te atoms as indicated. This model is similar to that proposed by Chadi for the Ga-rich (2×1) reconstructed GaAs(100) surface. The (3×1) reconstruction involves both the formation of surface dimers and the presence of vacancies at the surface. Every third atomic-pair is missing along the [1,-1,0] direction, and the remaining two atom pairs at the surface form the surface dimer. Although the (3×1) reconstruction has a larger number of electrons in dangling bonds, a surface with vacancies can be relaxed to reduce the strain energy due to the surface dimers. The directions of the atomic displacements away from the ideal dimer positions are indicated in the figure. Relatively large atomic displacements for several layers into the bulk are clearly visible in experimental images, as seen in Fig.lb. Further details of the surface reconstructions can be found elsewhere.


2013 ◽  
Vol 16 (04) ◽  
pp. 353-368 ◽  
Author(s):  
A.. Dehghan Khalili ◽  
J.-Y.. -Y. Arns ◽  
F.. Hussain ◽  
Y.. Cinar ◽  
W.V.. V. Pinczewski ◽  
...  

Summary High-resolution X-ray-computed-tomography (CT) images are increasingly used to numerically derive petrophysical properties of interest at the pore scale—in particular, effective permeability. Current micro-X-ray-CT facilities typically offer a resolution of a few microns per voxel, resulting in a field of view of approximately 5 mm3 for a 2,0482 charge-coupled device. At this scale, the resolution is normally sufficient to resolve pore-space connectivity and calculate transport properties directly. For samples exhibiting heterogeneity above the field of view of such a single high-resolution tomogram with resolved pore space, a second low-resolution tomogram can provide a larger-scale porosity map. This low-resolution X-ray-CT image provides the correlation structure of porosity at an intermediate scale, for which high-resolution permeability calculations can be carried out, forming the basis for upscaling methods dealing with correlated heterogeneity. In this study, we characterize spatial heterogeneity by use of overlapping registered X-ray-CT images derived at different resolutions spanning orders of magnitude in length scales. A 38-mm-diameter carbonate core is studied in detail and imaged at low resolution—and at high resolution by taking four 5-mm-diameter subsets, one of which is imaged by use of full-length helical scanning. Fine-scale permeability transforms are derived by use of direct porosity/permeability relationships, random sampling of the porosity/permeability scatter plot as a function of porosity, and structural correlations combined with stochastic simulation. A range of these methods is applied at the coarse scale. We compare various upscaling methods, including renormalization theory, with direct solutions by use of a Laplace solver and report error bounds. Finally, we compare with experimental measurements of permeability at both the small-plug and the full-plug scale. We find that both numerically and experimentally for the carbonate sample considered, which displays nonconnecting vugs and intrafossil pores, permeability increases with scale. Although numerical and experimental results agree at the larger scale, the digital core-analysis results underestimate experimentally measured permeability at the smaller scale. Upscaling techniques that use basic averaging techniques fail to provide truthful vertical permeability at the fine scale because of large permeability contrasts. At this scale, the most accurate upscaling technique uses Darcy's law. At the coarse scale, an accurate permeability estimate with error bounds is feasible if spatial correlations are considered. All upscaling techniques work satisfactorily at this scale. A key part of the study is the establishment of porosity transforms between high-resolution and low-resolution images to arrive at a calibrated porosity map to constrain permeability estimates for the whole core.


SPE Journal ◽  
2016 ◽  
Vol 21 (06) ◽  
pp. 2112-2127 ◽  
Author(s):  
Faruk O. Alpak ◽  
Jeroen C. Vink

Summary Numerical modeling of the in-situ conversion process (ICP) is a challenging endeavor involving thermal multiphase flow, compositional pressure/volume/temperature (PVT) behavior, and chemical reactions that convert solid kerogen into light hydrocarbons and are tightly coupled to temperature propagation. Our investigations of grid-resolution effects on the accuracy and performance of ICP simulations demonstrated that ICP-simulation outcomes (e.g., oil/gas production rates and cumulative volumes) may exhibit relatively large errors on coarse grids, where “coarse” means a gridblock size of more than 3 to 5 m. On the other hand, coarse-scale models are attractive because they deliver favorable computational performance, especially for optimization and uncertainty quantification workflows that demand a large number of simulations. Furthermore, field-scale models become unmanageably large if gridblock sizes of 3 to 5 m or less have to be used. Therefore, there is a clear business need to accelerate the ICP simulations with minimal compromise of accuracy. We developed a novel multiscale-modeling method for ICP that reduces numerical-modeling errors and approximates the fine-scale simulation results on relatively coarse grids. The method uses a two-scale adaptive local-global solution technique. One global coarse-scale and multiple local fine-scale near-heater models are timestepped in a sequentially coupled fashion. At a given global timestep, the global-model solution provides accurate boundary conditions to the local near-heater models. These boundary conditions account for the global characteristics of the thermal-reactive flow and transport phenomena. In turn, fine-scale information about heater responses is upscaled from the local models, and used in the global coarse-scale model. These flow-based effective properties correct the thermal-reactive flow and transport in the global model either explicitly, by updating relevant coarse-grid properties for the next timestep, or implicitly, by repeatedly updating the properties through a convergent iterative scheme. Upon convergence, global coarse-scale and local fine-scale solutions are compatible with each other. We demonstrate the much-improved accuracy and efficiency delivered by the multiscale method by use of a 2D cross-section pattern-scale ICP simulation problem. The following conclusions are reached through numerical testing: (1) The multiscale method significantly improves the accuracy of the simulation results over conventionally upscaled models. The method is particularly effective in correcting the global coarse-scale model through the use of the fine-scale information about heater temperatures to regulate the heat-injection rate into the formation more accurately. The effective coarse-grid properties computed by the multiscale method at every timestep also enhance the accuracy of the ICP simulations, as demonstrated in a dedicated test case, in which a constant heat-injection rate is enforced across models of all investigated resolutions. (2) Multiscale ICP models result in accelerated simulations with a speed-up of four to 16 times with respect to fine-scale models “out of the box” without any special optimization effort. (3) Our multiscale method delivers high-resolution solutions in the vicinity of the heaters at a reduced computational cost. These fine-scale solutions can be used to better understand the evolution of the fluids and solids (e.g., kerogen conversion and coke deposition) in the vicinity of the heaters (several-feet-long spatial scale). Simultaneously, with the fine-scale near-heater solutions, the local-global coupled multiscale model provides key commercial ICP performance indicators at the pattern scale (several-hundred-feet-long spatial scale) such as production functions.


2020 ◽  
Vol 6 (20) ◽  
pp. eaay5487 ◽  
Author(s):  
Mikkel Brydegaard ◽  
Samuel Jansson ◽  
Elin Malmqvist ◽  
Yeromin P. Mlacha ◽  
Alem Gebru ◽  
...  

Yearly, a quarter billion people are infected and a half a million killed by the mosquito-borne disease malaria. Lack of real-time observational tools for continuously assessing the unperturbed mosquito flight activity in situ limits progress toward improved vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect adjacent to a Tanzanian village. We evaluated one-third million insect observations during five nights, four days, and one annular solar eclipse. We demonstrate in situ lidar classification of several insect families and their sexes based on their modulation signatures. We were able to compare the fine-scale spatiotemporal activity patterns of malaria vectors during ordinary days and an eclipse to disentangle phototactic activity patterns from the circadian mechanism. We observed an increased insect activity during the eclipse attributable to mosquitoes. These unprecedented findings demonstrate how lidar-based monitoring of distinct mosquito activities could advance our understanding of vector ecology.


2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pavel P Kuksa ◽  
Alexandre Amlie-Wolf ◽  
Yih-Chii Hwang ◽  
Otto Valladares ◽  
Brian D Gregory ◽  
...  

Abstract Most regulatory chromatin interactions are mediated by various transcription factors (TFs) and involve physically interacting elements such as enhancers, insulators or promoters. To map these elements and interactions at a fine scale, we developed HIPPIE2 that analyzes raw reads from high-throughput chromosome conformation (Hi-C) experiments to identify precise loci of DNA physically interacting regions (PIRs). Unlike standard genome binning approaches (e.g. 10-kb to 1-Mb bins), HIPPIE2 dynamically infers the physical locations of PIRs using the distribution of restriction sites to increase analysis precision and resolution. We applied HIPPIE2 to in situ Hi-C datasets across six human cell lines (GM12878, IMR90, K562, HMEC, HUVEC, NHEK) with matched ENCODE/Roadmap functional genomic data. HIPPIE2 detected 1042 738 distinct PIRs, with high resolution (average PIR length of 1006 bp) and high reproducibility (92.3% in GM12878). PIRs are enriched for epigenetic marks (H3K27ac, H3K4me1) and open chromatin, suggesting active regulatory roles. HIPPIE2 identified 2.8 million significant PIR–PIR interactions, 27.2% of which were enriched for TF binding sites. 50 608 interactions were enhancer–promoter interactions and were enriched for 33 TFs, including known DNA looping/long-range mediators. These findings demonstrate that the novel dynamic approach of HIPPIE2 (https://bitbucket.com/wanglab-upenn/HIPPIE2) enables the characterization of chromatin and regulatory interactions with high resolution and reproducibility.


2012 ◽  
Vol 29 (6) ◽  
pp. 867-879 ◽  
Author(s):  
Bruno Buongiorno Nardelli

Abstract A novel technique for the high-resolution interpolation of in situ sea surface salinity (SSS) observations is developed and tested. The method is based on an optimal interpolation (OI) algorithm that includes satellite sea surface temperature (SST) in the covariance estimation. The covariance function parameters (i.e., spatial, temporal, and thermal decorrelation scales) and the noise-to-signal ratio are determined empirically, by minimizing the root-mean-square error and mean error with respect to fully independent validation datasets. Both in situ observations and simulated data extracted from a numerical model output are used to run these tests. Different filters are applied to sea surface temperature data in order to remove the large-scale variability associated with air–sea interaction, because a high correlation between SST and SSS is expected only at small scales. In the tests performed on in situ observations, the lowest errors are obtained by selecting covariance decorrelation scales of 400 km, 6 days, and 2.75°C, respectively, a noise-to-signal ratio of 0.01 and filtering the scales longer than 1000 km in the SST time series. This results in a root-mean-square error of ~0.11 g kg−1 and a mean error of ~0.01 g kg−1, that is, reducing the errors by ~25% and ~60%, respectively, with respect to the first guess.


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