The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef

Ecological processes on coral reefs commonly have limited spatial and temporal scales and may not be recorded in their long-term geological history. The widespread degradation of Caribbean coral reefs over the last 40 years therefore provides an opportunity to assess the impact of more significant ecological changes on the geological and geomorphic structure of reefs. Here, we document the changing ecology of communities in a coral reef seascape within the context of its geomorphic zonation. By comparing basic ecological indices between historical and modern data we show that in 35 years the reef-front zone was transformed from a complex coral assemblage with a three-dimensional structure, to a size-homogenized and flattened one that is quasi indistinguishable from the adjacent non-accretional coral-ground zone. Today coral assemblages at Punta Maroma are characterized by the dominance of opportunistic species which are either tolerant to adverse environmental conditions, including sedimentation, or are known to be the first scleractinian species to recruit on disturbed reefs, implying they reflect a post-hurricane stage of adjustment. Despite an increase in similarity in ecological indices, the reef-front and coral-ground geomorphic zones still retain significant differences in coral assemblages and benthic habitat and are not homogeneous. The partial convergence of coral assemblages certainly has important consequences for the ecology and geological viability of the reef and its role in coastal protection, but environmental physical drivers continue to exert a fundamental role in the character and zonation of benthic communities of this reef seascape.

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High-resolution three-dimensional probes of biomaterials and their interfaces

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2011.0253 ◽

2012 ◽

Vol 370 (1963) ◽

pp. 1337-1351 ◽

Cited By ~ 19

Author(s):

Kathryn Grandfield ◽

Anders Palmquist ◽

Håkan Engqvist

Keyword(s):

High Resolution ◽

Electron Tomography ◽

Three Dimensional ◽

Controlled Drug Release ◽

Biological Tissues ◽

Dimensional Structure ◽

Bone Interface ◽

Biomaterial Interfaces ◽

Titania Coating

Interfacial relationships between biomaterials and tissues strongly influence the success of implant materials and their long-term functionality. Owing to the inhomogeneity of biological tissues at an interface, in particular bone tissue, two-dimensional images often lack detail on the interfacial morphological complexity. Furthermore, the increasing use of nanotechnology in the design and production of biomaterials demands characterization techniques on a similar length scale. Electron tomography (ET) can meet these challenges by enabling high-resolution three-dimensional imaging of biomaterial interfaces. In this article, we review the fundamentals of ET and highlight its recent applications in probing the three-dimensional structure of bioceramics and their interfaces, with particular focus on the hydroxyapatite–bone interface, titanium dioxide–bone interface and a mesoporous titania coating for controlled drug release.

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The SCALEX Campaign: Scale-Crossing Land Surface and Boundary Layer Processes in the TERENO-preAlpine Observatory

Bulletin of the American Meteorological Society ◽

10.1175/bams-d-15-00277.1 ◽

2017 ◽

Vol 98 (6) ◽

pp. 1217-1234 ◽

Cited By ~ 29

Author(s):

B. Wolf ◽

C. Chwala ◽

B. Fersch ◽

J. Garvelmann ◽

W. Junkermann ◽

...

Keyword(s):

Land Surface ◽

Three Dimensional ◽

Observational Research ◽

Spatial And Temporal Scales ◽

Soil Variables ◽

Boundary Layer Processes ◽

Long Time ◽

Modelling Studies ◽

June July

Abstract ScaleX is a collaborative measurement campaign, collocated with a long-term environmental observatory of the German Terrestrial Environmental Observatories (TERENO) network in the mountainous terrain of the Bavarian Prealps, Germany. The aims of both TERENO and ScaleX include the measurement and modeling of land surface–atmosphere interactions of energy, water, and greenhouse gases. ScaleX is motivated by the recognition that long-term intensive observational research over years or decades must be based on well-proven, mostly automated measurement systems, concentrated in a small number of locations. In contrast, short-term intensive campaigns offer the opportunity to assess spatial distributions and gradients by concentrated instrument deployments, and by mobile sensors (ground and/or airborne) to obtain transects and three-dimensional patterns of atmospheric, surface, or soil variables and processes. Moreover, intensive campaigns are ideal proving grounds for innovative instruments, methods, and techniques to measure quantities that cannot (yet) be automated or deployed over long time periods. ScaleX is distinctive in its design, which combines the benefits of a long-term environmental-monitoring approach (TERENO) with the versatility and innovative power of a series of intensive campaigns, to bridge across a wide span of spatial and temporal scales. This contribution presents the concept and first data products of ScaleX-2015, which occurred in June–July 2015. The second installment of ScaleX took place in summer 2016 and periodic further ScaleX campaigns are planned throughout the lifetime of TERENO. This paper calls for collaboration in future ScaleX campaigns or to use our data in modelling studies. It is also an invitation to emulate the ScaleX concept at other long-term observatories.

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INVESTIGATIONS ON MESOPHOTIC CORAL ECOSYSTEMS IN CUBA (1970-1973) AND MEXICO (1983-1984)

CICIMAR Oceánides ◽

10.37543/oceanides.v33i2.230 ◽

2018 ◽

Vol 33 (2) ◽

pp. 27

Author(s):

Vassil Zlatarski

Keyword(s):

Coral Reefs ◽

Species Complex ◽

Three Dimensional ◽

Published Data ◽

Two Dimensional ◽

Mesophotic Coral Ecosystems ◽

Trends Analysis ◽

Collaborative Efforts ◽

Existing Data

After a pioneering study of Jamaican coral reefs, the Cuban archipelago was the second to be surveyed by SCUBA for scleractinian corals and reef life to a depth of 90m, sampling all phenotypes. Regrettably, the published data on the mesophotic coral ecosystems (MCEs) of Cuba, collected 1970 to 1973, have been ignored. This is also true for the published data on the MCEs of the Mexican Yucatán Peninsula, collected 1983 to 1984. These two investigations described immense areas exhibiting a rich continuum of coral life, from shallow reefs into MCEs without scleractinian faunal break, and no depth-specialists species complex. Instead, a morphological changeover of three-dimensional corallum into two-dimensional corallum was observed and documented. The existing data on the Cuban and Mexican MCEs (now 45 and 34 years old, respectively) present a unique opportunity for long-term status and ecosystem trends analysis. MCEs require terminological clarification from collaborative efforts to effectively use the globally available data.Investigaciones sobre ecosistemas coralinos mesofóticos en Cuba (1970-1973) y México (1983-1984)RESUMEN. Después de un estudio pionero en arrecifes de Jamaica sobre corales escleratinios y vida arrecifal, el archipiélago cubano fue el segundo que se estudió mediante buceo SCUBA a profundidades de hasta 90m, incluyendo muestras de todos los fenotipos. Infortunadamente, los datos publicados sobre ecosistemas coralinos mesofóticos (ECM), recabados entre 1970 y 1973 han sido soslayados, al igual que los datos publicados sobre los ECM de la Península de Yucatán, México, recabados entre 1983 y 1984. Ambas investigaciones describen áreas inmensas que exhiben un rico continuo de vida coralina, desde arrecifes someros hasta ECM sin ruptura en la fauna escleratinia y sin complejos de especies especialistas de profundidad. En vez de esto, se observó y documentó un reemplazamiento de formas tridimensionales de corales por formas bidimensionales. La información existente sobre ECM cubanos y mexicanos con antigüedades de 45 y 34 años, respectivamente ofrecen una oportunidad única para realizar análisis sobre estatus a largo plazo y tendencias de ecosistema. Los ECM requieren aclaración terminológica de esfuerzos de colaboración para utilizar efectivamente los datos disponibles globalmente.

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Stability of temperatures from TIMED/SABER v1.07 (2002–2009) and Aura/MLS v2.2 (2004–2009) compared with OH(6-2) temperatures observed at Davis Station, Antarctica

Atmospheric Chemistry and Physics Discussions ◽

10.5194/acpd-10-21547-2010 ◽

2010 ◽

Vol 10 (9) ◽

pp. 21547-21565 ◽

Cited By ~ 1

Author(s):

W. J. R. French ◽

F. J. Mulligan

Keyword(s):

Cold Bias ◽

Spatial And Temporal Scales ◽

Ground Station ◽

Volume Emission ◽

The Difference ◽

Miss Distance ◽

Hydroxyl Layer ◽

The Impact ◽

Long Term Studies

Abstract. Temperature profiles from two satellite instruments – TIMED/SABER and Aura/MLS – have been used to calculate hydroxyl-layer equivalent temperatures for comparison with values measured from OH(6-2) emission lines observed by a ground-based spectrometer located at Davis Station, Antarctica (68° S, 78° E). The profile selection criteria – <500 km from the ground station and solar zenith angles >97° – yielded a total of 2359 SABER profiles over 8 years (2002–2009) and 7407 MLS profiles over 5.5 years (2004–2009). The availability of simultaneous OH volume emission rate (VER) profiles from the SABER (OH-B channel) enabled an assessment of the impact of several different weighting functions in the calculation of OH-equivalent temperatures. The maximum difference between all derived hydroxyl layer equivalent temperatures was less than 3 K. Restricting the miss-distance and miss-time criteria showed little effect on the bias, suggesting that the OH layer is relatively uniform over the spatial and temporal scales considered. However, a significant trend was found in the bias between SABER and Davis OH of ~0.7 K/year over the 8-year period with SABER becoming warmer compared with the Davis OH temperatures. In contrast, Aura MLS exhibited a cold bias of 9.9 ± 0.4 K compared with Davis OH, but importantly, the bias remained constant over the 2004–2009 year period examined. The difference in bias behaviour of the two satellites has significant implications for multi-annual and long-term studies using their data.

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Guanxi, Trust, and Long-Term Orientation in Chinese Business Markets

Journal of International Marketing ◽

10.1509/jimk.13.2.28.64860 ◽

2005 ◽

Vol 13 (2) ◽

pp. 28-56 ◽

Cited By ~ 243

Author(s):

Don Y. Lee ◽

Philip L. Dawes

Keyword(s):

Hong Kong ◽

Interpersonal Relationships ◽

Chinese Culture ◽

Three Dimensional ◽

Business Markets ◽

Latent Construct ◽

Chinese Business ◽

The Government ◽

The Impact

This research focuses on buying firms’ trust in a supplier's salesperson and posits that this type of trust is determined by characteristics of the salesperson, the interpersonal relationships between a salesperson and the buying firm's boundary personnel, and characteristics of personal interactions between these two parties. More important, the authors discuss the concept of interpersonal relationships in the context of Chinese culture and model it as a three-dimensional latent construct, which, in some literature, is called guanxi. A key aspect of this research is that the authors investigate the impact of each dimension of guanxi on salesperson trust separately. Moreover, the authors consider the buying firm's trust in the supplying firm and its long-term orientation toward the supplier the consequences of salesperson trust. To test the model, the authors use data collected from 128 buying organizations in Hong Kong. The sampled firms are from both the government and private sectors.

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Dynamic modelling framework to track sediment provenance and solve lakes in long-term landscape evolution models

10.5194/egusphere-egu21-9392 ◽

2021 ◽

Author(s):

Boris Gailleton ◽

Luca Malatesta ◽

Jean Braun ◽

Guillaume Cordonnier

Keyword(s):

Landscape Evolution ◽

Dynamic Modelling ◽

Signal Propagation ◽

Sediment Provenance ◽

Topological Order ◽

Time Step ◽

Spatial And Temporal Scales ◽

Modelling Framework ◽

The Impact

Many laws have been developed to describe the different aspects of landscape evolution at large spatial and temporal scales. Natural landscapes have heterogeneous properties (lithologies, climates, tectonics, etc.) that are associated with multiple coexisting processes. In turn, this can demand different mathematical expressions to model landscape evolution as a function of time and or space. Landscape Evolution Models are mostly designed to facilitate the combination of different landscape-wide laws in a plug-and-play way and many frameworks are being developed in this aim. However, most current frameworks cannot capture important landscape processes such as lake dynamics and full sediment tracing because they are optimized for speed and handle fluxes separately. Several processes require information from more than the immediate neighboring cells within a time step and demand an integrated knowledge from the entire upstream trajectory. Lakes for example require knowledge of all upstream water and sediment fluxes to be filled. These can only be known if all the laws controlling those have been processed. Tackling these situation with a grid logic requires substantial amount of numerical refactoring from existing models.We present an alternative method to tackle landscape evolution modelling in heterogeneous landscapes with a framework inspired from Lagrangian and cellular automaton methods. Our framework only relies on the assumption that upstream nodes needs to be processed before the downstream ones, including lakes with outlets, in order to process all selected governing equations on a pixel-to-pixel basis. This way, we ensure that the true content of sediment and water fluxes can be known and tracked at any points. We first utilise graph theory to (i) find the most comprehensive path to reroute water through depressions and (ii) determine a generic multiple flow topological order (any node is processed after all potential upstream ones). Particles that register and track all fluxes simultaneously can then "roll" on the landscape and merge between each other while interacting with the grid.This formulation makes possible a number of generic features. (i) The laws can be dynamically adapted to the environment (e.g. switching from single to multiple flow function of water content, adapting erodibility function of the sediment composition and quantity), (ii) Depressions can be explicitly managed, filled (or not) and separated from the rest of the landscape (e.g. sedimentation or evaporation in lakes) as a function function of inputted fluxes and parameters, (iii) full provenance, transport time, and deposition tracking as the particle can always keep in memory where the fluxes are from and in what proportions. In this contribution, we demonstrate the impact the importance of considering these additional elements in landscape evolution. In particular, lake dynamic can significantly impact the long-term signal propagation from source to sink.

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Hepatocyte Aggregate Culture Technique for Bioreactors in Hybrid Liver Support Systems

The International Journal of Artificial Organs ◽

10.1177/039139889301601210 ◽

1993 ◽

Vol 16 (12) ◽

pp. 843-846 ◽

Cited By ~ 29

Author(s):

J.C. Gerlach ◽

K. Klöppel ◽

C. MÜller ◽

N. Schnoy ◽

M.D. Smith ◽

...

Keyword(s):

High Performance ◽

Large Scale ◽

Support Systems ◽

Three Dimensional ◽

Culture Technique ◽

Dimensional Structure ◽

Cell Aggregates ◽

Liver Support ◽

Aggregate Culture

Utilizing a modified culture technique for hepatocytes, a high performance suspension culture is possible in which hepatocytes spontaneously form cell aggregates. The aggregates of 20-100 cells have been histologically confirmed to hold a three-dimensional structure, they show a long-term external metabolism and a survival time comparable with standard adhesion cultures. This technique has several advantages in the construction of large scale bioreactors for hybrid liver support systems.

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Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Amino Acids ◽

10.1007/s00726-019-02787-2 ◽

2019 ◽

Vol 51 (10-12) ◽

pp. 1409-1431 ◽

Cited By ~ 5

Author(s):

Luigi Grassi ◽

Chiara Cabrele

Keyword(s):

Small Molecules ◽

Three Dimensional ◽

Drug Market ◽

Structure And Function ◽

Dimensional Structure ◽

Chemical Modifications ◽

Small Molecule Drugs ◽

And Function ◽

The Impact

Abstract Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

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A systematic study of proto-neutron star convection in three-dimensional core-collapse supernova simulations

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/staa261 ◽

2020 ◽

Vol 492 (4) ◽

pp. 5764-5779 ◽

Cited By ~ 9

Author(s):

Hiroki Nagakura ◽

Adam Burrows ◽

David Radice ◽

David Vartanyan

Keyword(s):

Neutron Star ◽

Systematic Study ◽

Three Dimensional ◽

Three Dimensions ◽

Core Collapse ◽

Core Collapse Supernova ◽

Tau Neutrinos ◽

The Impact ◽

Proto Neutron Star

ABSTRACT This paper presents the first systematic study of proto-neutron star (PNS) convection in three dimensions (3D) based on our latest numerical fornax models of core-collapse supernova (CCSN). We confirm that PNS convection commonly occurs, and then quantify the basic physical characteristics of the convection. By virtue of the large number of long-term models, the diversity of PNS convective behaviour emerges. We find that the vigour of PNS convection is not correlated with CCSN dynamics at large radii, but rather with the mass of PNS − heavier masses are associated with stronger PNS convection. We find that PNS convection boosts the luminosities of νμ, ντ, $\bar{\nu }_{\mu }$, and $\bar{\nu }_{\tau }$ neutrinos, while the impact on other species is complex due to a competition of factors. Finally, we assess the consequent impact on CCSN dynamics and the potential for PNS convection to generate pulsar magnetic fields.

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SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

Bioinformatics ◽

10.1093/bioinformatics/btaa159 ◽

2020 ◽

Vol 36 (11) ◽

pp. 3372-3378

Author(s):

Alexander Gress ◽

Olga V Kalinina

Keyword(s):

Protein Function ◽

Structural Information ◽

Solvent Accessibility ◽

Three Dimensional ◽

Structural Data ◽

Supplementary Information ◽

Dimensional Structure ◽

Relative Solvent Accessibility ◽

Precise Measure ◽

The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

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