Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology

AbstractExtreme disturbances such as hurricanes can cause reductions in coral cover and three-dimensional (3D) structural complexity of coral reefs. We examined changes in structural complexity utilizing 3D reconstruction of a coral-reef site before and after Hurricane Walaka passed through Lalo of the Northwestern Hawaiian Islands. This event resulted in complete destruction of the coral-reef habitat, with dramatic changes in benthic cover from pre-hurricane tabulate coral to post-hurricane rubble. Rugosity and mean slope decreased after the hurricane, while structural complexity, captured by vector ruggedness measure (VRM), showed resolution-specific responses. This metric captured the structural complexity of rubble at a high raster resolution of 1 cm and that of tabulate coral at lower resolutions, resulting in decreases in mean VRM values at 2- and 4-cm resolutions but an increase at 1-cm resolution. Variability in profile and planform curvature was reduced after the hurricane due to a disappearance of extreme curvature values created by the tabulate coral after the hurricane. This study highlights the varying responses of habitat complexity metrics to the complete destruction of a coral reef and provides us with insights into how choices of habitat complexity metrics can affect quantitative assessments of 3D habitat structure.

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Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models

Remote Sensing ◽

10.3390/rs12172676 ◽

2020 ◽

Vol 12 (17) ◽

pp. 2676 ◽

Cited By ~ 1

Author(s):

Atsuko Fukunaga ◽

John H. R. Burns

Keyword(s):

Coral Reef ◽

Digital Elevation Models ◽

Three Dimensional ◽

Structural Complexity ◽

3D Models ◽

3D Reconstructions ◽

3D Mesh ◽

Coral Colony ◽

Digital Elevation ◽

Mesh Models

Underwater photogrammetry has been increasingly used in coral-reef research in recent years. Habitat metrics extracted from resulting three-dimensional (3D) reconstructions can be used to examine associations between the structural complexity of the reef habitats and the distribution of reef organisms. We created simulated 3D models of bare surface structures and 3D reconstructions of coral morphologies to investigate the behavior of various habitat metrics that were extracted from both Digital Elevation Models (DEMs) and 3D mesh models. Analyzing the resulting values provided us with important insights into how these metrics would compare with one another in the characterization of coral-reef habitats. Surface complexity (i.e., reef rugosity), fractal dimension extracted from DEMs and vector dispersion obtained from 3D mesh models exhibited consistent patterns in the ranking of structural complexity among the simulated bare surfaces and coral morphologies. The vector ruggedness measure obtained from DEMs at three different resolutions of 1, 2, and 4 cm effectively captured differences in the structural complexity among different coral morphologies. Profile curvature and planform curvature, on the other hand, were better suited to capture the structural complexity derived from surface topography such as walls and overhanging ledges. Our results indicate that habitat metrics extracted from DEMs are generally suitable when characterizing a relatively large plot of a coral reef captured from an overhead planar angle, while the 3D metric of vector dispersion is suitable when characterizing a coral colony or a relatively small plot methodically captured from various angles.

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COMPARISON OF COMMERCIAL STRUCTURE-FROM-MOTION PHOTOGRAMMETY SOFTWARE USED FOR UNDERWATER THREE-DIMENSIONAL MODELING OF CORAL REEF ENVIRONMENTS

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-2-w3-127-2017 ◽

2017 ◽

Vol XLII-2/W3 ◽

pp. 127-131 ◽

Cited By ~ 15

Author(s):

J. H. R. Burns ◽

D. Delparte

Keyword(s):

Coral Reef ◽

Structural Characteristics ◽

Spatial Scales ◽

3D Structure ◽

Light Availability ◽

Three Dimensional ◽

Structural Complexity ◽

Physical Structure ◽

Natural Environments ◽

Ecological Processes

Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

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Coral reef structural complexity

AccessScience ◽

10.1036/1097-8542.161575 ◽

2018 ◽

Keyword(s):

Coral Reef ◽

Structural Complexity

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Human iPSC-Based Modeling of Central Nerve System Disorders for Drug Discovery

International Journal of Molecular Sciences ◽

10.3390/ijms22031203 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1203

Author(s):

Lu Qian ◽

Julia TCW

Keyword(s):

Drug Discovery ◽

Disease Modeling ◽

Three Dimensional ◽

Structural Complexity ◽

Induced Pluripotent Stem Cell ◽

Cell Types ◽

Central Nerve System ◽

Human Ipscs ◽

Nerve System

A high-throughput drug screen identifies potentially promising therapeutics for clinical trials. However, limitations that persist in current disease modeling with limited physiological relevancy of human patients skew drug responses, hamper translation of clinical efficacy, and contribute to high clinical attritions. The emergence of induced pluripotent stem cell (iPSC) technology revolutionizes the paradigm of drug discovery. In particular, iPSC-based three-dimensional (3D) tissue engineering that appears as a promising vehicle of in vitro disease modeling provides more sophisticated tissue architectures and micro-environmental cues than a traditional two-dimensional (2D) culture. Here we discuss 3D based organoids/spheroids that construct the advanced modeling with evolved structural complexity, which propels drug discovery by exhibiting more human specific and diverse pathologies that are not perceived in 2D or animal models. We will then focus on various central nerve system (CNS) disease modeling using human iPSCs, leading to uncovering disease pathogenesis that guides the development of therapeutic strategies. Finally, we will address new opportunities of iPSC-assisted drug discovery with multi-disciplinary approaches from bioengineering to Omics technology. Despite technological challenges, iPSC-derived cytoarchitectures through interactions of diverse cell types mimic patients’ CNS and serve as a platform for therapeutic development and personalized precision medicine.

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Using virtual reality to estimate aesthetic values of coral reefs

Royal Society Open Science ◽

10.1098/rsos.172226 ◽

2018 ◽

Vol 5 (4) ◽

pp. 172226 ◽

Cited By ~ 5

Author(s):

Julie Vercelloni ◽

Sam Clifford ◽

M. Julian Caley ◽

Alan R. Pearse ◽

Ross Brown ◽

...

Keyword(s):

Coral Reef ◽

Coral Reefs ◽

Structural Complexity ◽

Natural Environments ◽

Natural Ecosystems ◽

Aesthetic Value ◽

Natural Systems ◽

Holistic Conservation ◽

Past Experiences ◽

Aesthetic Values

Aesthetic value, or beauty, is important to the relationship between humans and natural environments and is, therefore, a fundamental socio-economic attribute of conservation alongside other ecosystem services. However, beauty is difficult to quantify and is not estimated well using traditional approaches to monitoring coral-reef aesthetics. To improve the estimation of ecosystem aesthetic values, we developed and implemented a novel framework used to quantify features of coral-reef aesthetics based on people's perceptions of beauty. Three observer groups with different experience to reef environments (Marine Scientist, Experienced Diver and Citizen) were virtually immersed in Australian's Great Barrier Reef (GBR) using 360° images. Perceptions of beauty and observations were used to assess the importance of eight potential attributes of reef-aesthetic value. Among these, heterogeneity, defined by structural complexity and colour diversity, was positively associated with coral-reef-aesthetic values. There were no group-level differences in the way the observer groups perceived reef aesthetics suggesting that past experiences with coral reefs do not necessarily influence the perception of beauty by the observer. The framework developed here provides a generic tool to help identify indicators of aesthetic value applicable to a wide variety of natural systems. The ability to estimate aesthetic values robustly adds an important dimension to the holistic conservation of the GBR, coral reefs worldwide and other natural ecosystems.

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The role of hydrological transience in peatland pattern formation

Earth Surface Dynamics ◽

10.5194/esurf-1-29-2013 ◽

2013 ◽

Vol 1 (1) ◽

pp. 29-43 ◽

Cited By ~ 9

Author(s):

P. J. Morris ◽

A. J. Baird ◽

L. R. Belyea

Keyword(s):

Steady State ◽

Hydraulic Properties ◽

Three Dimensional ◽

Structural Complexity ◽

Plant Litter ◽

Future Climate Change ◽

Litter Production ◽

Landscape Models ◽

Water Tables

Abstract. The sloping flanks of peatlands are commonly patterned with non-random, contour-parallel stripes of distinct micro-habitats such as hummocks, lawns and hollows. Patterning seems to be governed by feedbacks among peatland hydrological processes, plant micro-succession, plant litter production and peat decomposition. An improved understanding of peatland patterning may provide important insights into broader aspects of the long-term development of peatlands and their likely response to future climate change. We recreated a cellular simulation model from the literature, as well as three subtle variants of the model, to explore the controls on peatland patterning. Our models each consist of three submodels, which simulate: peatland water tables in a gridded landscape, micro-habitat dynamics in response to water-table depths, and changes in peat hydraulic properties. We found that the strength and nature of simulated patterning was highly dependent on the degree to which water tables had reached a steady state in response to hydrological inputs. Contrary to previous studies, we found that under a true steady state the models predict largely unpatterned landscapes that cycle rapidly between contrasting dry and wet states, dominated by hummocks and hollows, respectively. Realistic patterning only developed when simulated water tables were still transient. Literal interpretation of the degree of hydrological transience required for patterning suggests that the model should be discarded; however, the transient water tables appear to have inadvertently replicated an ecological memory effect that may be important to peatland patterning. Recently buried peat layers may remain hydrologically active despite no longer reflecting current vegetation patterns, thereby highlighting the potential importance of three-dimensional structural complexity in peatlands to understanding the two-dimensional surface-patterning phenomenon. The models were highly sensitive to the assumed values of peat hydraulic properties, which we take to indicate that the models are missing an important negative feedback between peat decomposition and changes in peat hydraulic properties. Understanding peatland patterning likely requires the unification of cellular landscape models such as ours with cohort-based models of long-term peatland development.

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The Ryanodine Receptor/Calcium Release Channel and its Interaction Partners

Microscopy and Microanalysis ◽

10.1017/s143192760002496x ◽

1998 ◽

Vol 4 (S2) ◽

pp. 968-969

Author(s):

Terry Wagenknecht ◽

Montserrat Samso

Keyword(s):

Calcium Release ◽

Striated Muscle ◽

Ryanodine Receptors ◽

Three Dimensional ◽

Structural Complexity ◽

Body Representation ◽

Calcium Release Channel ◽

Release Channel ◽

Fk506 Binding Protein ◽

Dimensional Reconstruction

Ryanodine receptors (RyRs) function as the major intracellular calcium release channels in striated muscle, where they also play a central role in excitation-contraction (e-c) coupling, the signal transduction process by which neuron-induced depolarization of the muscle plasma membrane leads to release of Ca from the sarcoplasmic reticulum. Structurally, RyRs are the largest ion channels known, being composed of 4 identical large subunits (565 kDa). In situ, RyRs interact with numerous proteins that are essential for e-c coupling or regulation thereof. Some of these ligands include calmodulin, a 12-kDa FK506-binding protein (FKBP, an immunophi1 in), calsequestrin, triadin, and the dihydropyridine receptor (DHPR).Detergent-solubilized, purified RyRs appear to retain their native structure as assessed by electron cryo-microscopy, and are amenable to three-dimensional reconstruction by single-particle image processing techniques. In Fig. 1, a solid-body representation of the reconstructed skeletal muscle RyR shows the structural complexity that is revealed at moderate resolutions (3-4 nm).

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Using 3D photogrammetry from ROV video to quantify cold-water coral reef structural complexity and investigate its influence on biodiversity and community assemblage

Coral Reefs ◽

10.1007/s00338-019-01827-3 ◽

2019 ◽

Vol 38 (5) ◽

pp. 1007-1021 ◽

Cited By ~ 14

Author(s):

David M. Price ◽

Katleen Robert ◽

Alexander Callaway ◽

Claudio Lo lacono ◽

Rob A. Hall ◽

...

Keyword(s):

Coral Reef ◽

Cold Water ◽

Structural Complexity ◽

Community Assemblage ◽

3D Photogrammetry ◽

Water Coral

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Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions

Remote Sensing ◽

10.3390/rs12061011 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1011 ◽

Cited By ~ 2

Author(s):

Atsuko Fukunaga ◽

John H. R. Burns ◽

Kailey H. Pascoe ◽

Randall K. Kosaki

Keyword(s):

Fractal Dimension ◽

Coral Reefs ◽

Habitat Structure ◽

Coral Cover ◽

Three Dimensional ◽

Structural Complexity ◽

Coralline Algae ◽

Crustose Coralline Algae ◽

Surface Areas ◽

Abundance And Diversity

Quantifying the three-dimensional (3D) habitat structure of coral reefs is an important aspect of coral reef monitoring, as habitat architecture affects the abundance and diversity of reef organisms. Here, we used photogrammetric techniques to generate 3D reconstructions of coral reefs and examined relationships between benthic cover and various habitat metrics obtained at six different resolutions of raster cells, ranging from 1 to 32 cm. For metrics of 3D structural complexity, fractal dimension, which utilizes information on 3D surface areas obtained at different resolutions, and vector ruggedness measure (VRM) obtained at 1-, 2- or 4-cm resolution correlated well with benthic cover, with a relatively large amount of variability in these metrics being explained by the proportions of corals and crustose coralline algae. Curvature measures were, on the other hand, correlated with branching and mounding coral cover when obtained at 1-cm resolution, but the amount of variability explained by benthic cover was generally very low when obtained at all other resolutions. These results show that either fractal dimension or VRM obtained at 1-, 2- or 4-cm resolution, along with curvature obtained at 1-cm resolution, can effectively capture the 3D habitat structure provided by specific benthic organisms.

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