Three-dimensional kernel utilization distributions improve estimates of space use in aquatic animals

Tracking data have previously been used to define animal movement patterns through two-dimensional (2D) kernel utilization distributions and separate analysis of vertical locations. Here we describe the use of three-dimensional (3D) kernel utilization distributions to estimate the volumetric space use of individuals based on tracking data and to estimate the overlap in activity space between individuals. Data from European eels ( Anguilla anguilla ) from Norwegian coastal waters were used to compare the information conveyed by 2D and 3D activity space estimates and the utility of this approach for aquatic species. The use of 3D kernels produced detailed representations of space use in A. anguilla that permitted examination of depth use in a geographic context. Comparison of 2D and 3D home ranges showed that 2D analyses overestimated the amount of overlap between individuals by 13%–20%, because individuals sometimes occurred in the same location but used different depths. Hence, the 3D approach provided more comprehensive representations of animal movement in three dimensions while producing a metric that can be used for testing hypotheses relating to scientific descriptions of activity space, habitat use, and movement parameters.

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The home-range concept: are traditional estimators still relevant with modern telemetry technology?

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2010.0093 ◽

2010 ◽

Vol 365 (1550) ◽

pp. 2221-2231 ◽

Cited By ~ 268

Author(s):

John G. Kie ◽

Jason Matthiopoulos ◽

John Fieberg ◽

Roger A. Powell ◽

Francesca Cagnacci ◽

...

Keyword(s):

Home Range ◽

New Technologies ◽

Animal Movement ◽

Space Use ◽

Ease Of Use ◽

Home Ranges ◽

Data Intensive ◽

Use Patterns ◽

Location Data ◽

Utilization Distributions

Recent advances in animal tracking and telemetry technology have allowed the collection of location data at an ever-increasing rate and accuracy, and these advances have been accompanied by the development of new methods of data analysis for portraying space use, home ranges and utilization distributions. New statistical approaches include data-intensive techniques such as kriging and nonlinear generalized regression models for habitat use. In addition, mechanistic home-range models, derived from models of animal movement behaviour, promise to offer new insights into how home ranges emerge as the result of specific patterns of movements by individuals in response to their environment. Traditional methods such as kernel density estimators are likely to remain popular because of their ease of use. Large datasets make it possible to apply these methods over relatively short periods of time such as weeks or months, and these estimates may be analysed using mixed effects models, offering another approach to studying temporal variation in space-use patterns. Although new technologies open new avenues in ecological research, our knowledge of why animals use space in the ways we observe will only advance by researchers using these new technologies and asking new and innovative questions about the empirical patterns they observe.

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General Method for Extending Discrete Global Grid Systems to Three Dimensions

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi9040233 ◽

2020 ◽

Vol 9 (4) ◽

pp. 233 ◽

Cited By ~ 1

Author(s):

Benjamin Ulmer ◽

John Hall ◽

Faramarz Samavati

Keyword(s):

Three Dimensional ◽

Use Cases ◽

Three Dimensions ◽

Grid Systems ◽

3D Data ◽

Third Dimension ◽

2D And 3D ◽

Polyhedral Projection ◽

Global Grid ◽

General Method

Geospatial sensors are generating increasing amounts of three-dimensional (3D) data. While Discrete Global Grid Systems (DGGS) are a useful tool for integrating geospatial data, they provide no native support for 3D data. Several different 3D global grids have been proposed; however, these approaches are not consistent with state-of-the-art DGGSs. In this paper, we propose a general method that can extend any DGGS to the third dimension to operate as a 3D DGGS. This extension is done carefully to ensure any valid DGGS can be supported, including all refinement factors and non-congruent refinement. We define encoding, decoding, and indexing operations in a way that splits responsibility between the surface DGGS and the 3D component, which allows for easy transference of data between the 2D and 3D versions of a DGGS. As a part of this, we use radial mapping functions that serve a similar purpose as polyhedral projection in a conventional DGGS. We validate our method by creating three different 3D DGGSs tailored for three specific use cases. These use cases demonstrate our ability to quickly generate 3D global grids while achieving desired properties such as support for large ranges of altitudes, volume preservation between cells, and custom cell aspect ratio.

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Gold Exploration in Two and Three Dimensions: Improved and Correlative Insights from Microscopy and X-Ray Computed Tomography

Minerals ◽

10.3390/min10050476 ◽

2020 ◽

Vol 10 (5) ◽

pp. 476

Author(s):

Joshua Chisambi ◽

Bjorn von der Heyden ◽

Muofhe Tshibalanganda ◽

Stephan Le Roux

Keyword(s):

Computed Tomography ◽

Spatial Distribution ◽

Gold Mineralization ◽

Three Dimensional ◽

Three Dimensions ◽

Low Grade ◽

X Ray ◽

3D Space ◽

X Ray Computed ◽

2D And 3D

In this contribution, we highlight a correlative approach in which three-dimensional structural/positional data are combined with two dimensional chemical and mineralogical data to understand a complex orogenic gold mineralization system; we use the Kirk Range (southern Malawi) as a case study. Three dimensional structures and semi-quantitative mineral distributions were evaluated using X-ray Computed Tomography (XCT) and this was augmented with textural, mineralogical and chemical imaging using Scanning Electron Microscopy (SEM) and optical microscopy as well as fire assay. Our results detail the utility of the correlative approach both for quantifying gold concentrations in core samples (which is often nuggety and may thus be misrepresented by quarter- or half-core assays), and for understanding the spatial distribution of gold and associated structures and microstructures in 3D space. This approach overlays complementary datasets from 2D and 3D analytical protocols, thereby allowing a better and more comprehensive understanding on the distribution and structures controlling gold mineralization. Combining 3D XCT analyses with conventional 2D microscopies derive the full value out of a given exploration drilling program and it provides an excellent tool for understanding gold mineralization. Understanding the spatial distribution of gold and associated structures and microstructures in 3D space holds vast potential for exploration practitioners, especially if the correlative approach can be automated and if the resultant spatially-constrained microstructural information can be fed directly into commercially available geological modelling software. The extra layers of information provided by using correlative 2D and 3D microscopies offer an exciting new tool to enhance and optimize mineral exploration workflows, given that modern exploration efforts are targeting increasingly complex and low-grade ore deposits.

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Semblance of heterogeneity in collective cell migration

10.1101/122374 ◽

2017 ◽

Author(s):

Linus J. Schumacher ◽

Philip K. Maini ◽

Ruth E. Baker

Keyword(s):

Cell Migration ◽

Cell Population ◽

Cell Tracking ◽

Animal Movement ◽

Population Heterogeneity ◽

Three Dimensions ◽

Biological Research ◽

Collective Cell Migration ◽

List Type ◽

Tracking Data

AbstractCell population heterogeneity is increasingly a focus of inquiry in biological research. For example, cell migration studies have investigated the heterogeneity of invasiveness and taxis in development, wound healing, and cancer. However, relatively little effort has been devoted to explore when heterogeneity is mechanistically relevant and how to reliably measure it. Statistical methods from the animal movement literature offer the potential to analyse heterogeneity in collections of cell tracking data. A popular measure of heterogeneity, which we use here as an example, is the distribution of delays in directional cross-correlation. Employing a suitably generic, yet minimal, model of collective cell movement in three dimensions, we show how using such measures to quantify heterogeneity in tracking data can result in the inference of heterogeneity where there is none. Our study highlights a potential pitfall in the statistical analysis of cell population heterogeneity, and we argue this can be mitigated by the appropriate choice of null models.Highlightsgroups of identical cells appear heterogeneous due to limited sampling and experimental repeatabilityheterogeneity bias increases with attraction/repulsion between cellsmovement in confined environments decreases apparent heterogeneityhypothetical applications in neural crest and in vitro cancer systemsIn BriefWe use a mathematical model to show how cell populations can appear heterogeneous in their migratory characteristics, even though they are made up of identically-behaving individual cells. This has important consequences for the study of collective cell migration in areas such as embryo development or cancer invasion.

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Phase diagrams of one-, two-, and three-dimensional quantum spin systems

Quantum Information and Computation ◽

10.26421/qic16.9-10-9 ◽

2016 ◽

Vol 16 (9&10) ◽

pp. 885-899

Author(s):

Briiissuurs Braiorr-Orrs ◽

Michael Weyrauch ◽

Mykhailo V. Rakov

Keyword(s):

Three Dimensional ◽

Transverse Field ◽

Quantum Spin ◽

Three Dimensions ◽

Quantum Spin Systems ◽

Bipartite Entanglement ◽

Spatial Dimensions ◽

Characteristic Features ◽

Quantum Spin Models ◽

2D And 3D

We study the bipartite entanglement per bond to determine characteristic features of the phase diagram of various quantum spin models in different spatial dimensions. The bipartite entanglement is obtained from a tensor network representation of the ground state wave-function. Three spin-1/2 models (Ising, XY, XXZ, all in a transverse field) are investigated. Infinite imaginary-time evolution (iTEBD in 1D, ‘simple update’ in 2D and 3D) is used to determine the ground states of these models. The phase structure of the models is discussed for all three dimensions.

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Three-dimensional simulations of non-resonant streaming instability and particle acceleration near non-relativistic astrophysical shocks

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/stz2624 ◽

2019 ◽

Vol 490 (1) ◽

pp. 1156-1165 ◽

Cited By ~ 4

Author(s):

Allard Jan van Marle ◽

Fabien Casse ◽

Alexandre Marcowith

Keyword(s):

Magnetic Field ◽

Particle Acceleration ◽

Three Dimensional ◽

3D Models ◽

Three Dimensions ◽

Spectral Energy ◽

Growth Speed ◽

Field Amplification ◽

Streaming Instability ◽

2D And 3D

ABSTRACT We use particle-in-magnetohydrodynamics-cells to model particle acceleration and magnetic field amplification in a high-Mach, parallel shock in three dimensions and compare the result to 2D models. This allows us to determine whether 2D simulations can be relied upon to yield accurate results in terms of particle acceleration, magnetic field amplification, and the growth rate of instabilities. Our simulations show that the behaviour of the gas and the evolution of the instabilities are qualitatively similar for both the 2D and 3D models, with only minor quantitative differences that relate primarily to the growth speed of the instabilities. The main difference between 2D and 3D models can be found in the spectral energy distributions (SEDs) of the non-thermal particles. The 2D simulations prove to be more efficient, accelerating a larger fraction of the particles and achieving higher velocities. We conclude that, while 2D models are sufficient to investigate the instabilities in the gas, their results have to be treated with some caution when predicting the expected SED of a given shock.

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Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry

F1000Research ◽

10.12688/f1000research.6661.1 ◽

2015 ◽

Vol 4 ◽

pp. 168 ◽

Cited By ~ 1

Author(s):

Ye Hu ◽

Norbert Furtmann ◽

Dagmar Stumpfe ◽

Jürgen Bajorath

Keyword(s):

Knowledge Base ◽

Three Dimensional ◽

Three Dimensions ◽

Binding Modes ◽

Activity Data ◽

Systematic Analysis ◽

Comprehensive Knowledge ◽

Or Groups ◽

2D And 3D ◽

Activity Cliffs

Activity cliffs are formed by pairs or groups of structurally similar or analogous active compounds with large differences in potency. They can be defined in two or three dimensions by comparing graph-based molecular representations or compound binding modes, respectively. Through systematic analysis of publicly available compound activity data and ligand-target X-ray structures we have in a series of studies determined all currently available two- and three-dimensional activity cliffs (2D- and 3D-cliffs, respectively). Furthermore, we have systematically searched for 2D extensions of 3D-cliffs. Herein, we specify different categories of activity cliffs we have explored and introduce an open access data deposition in ZENODO (doi: 10.5281/zenodo.18490) that makes the entire knowledge base of current activity cliffs freely available in an organized form.

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convergent-beam diffraction from surfaces

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100125208 ◽

1987 ◽

Vol 45 ◽

pp. 30-33

Author(s):

J. A. Eades ◽

A. E. Smith ◽

D. F. Lynch

Keyword(s):

Reciprocal Lattice ◽

Three Dimensional ◽

Grazing Incidence ◽

Three Dimensions ◽

Plane Figure ◽

Transmission Electron ◽

Convergent Beam ◽

Beam Patterns ◽

Beam Diffraction

It is quite simple (in the transmission electron microscope) to obtain convergent-beam patterns from the surface of a bulk crystal. The beam is focussed onto the surface at near grazing incidence (figure 1) and if the surface is flat the appropriate pattern is obtained in the diffraction plane (figure 2). Such patterns are potentially valuable for the characterization of surfaces just as normal convergent-beam patterns are valuable for the characterization of crystals.There are, however, several important ways in which reflection diffraction from surfaces differs from the more familiar electron diffraction in transmission.GeometryIn reflection diffraction, because of the surface, it is not possible to describe the specimen as periodic in three dimensions, nor is it possible to associate diffraction with a conventional three-dimensional reciprocal lattice.

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Extension of the Spatial PDI Model to Three Dimensions

Perceptual and Motor Skills ◽

10.2466/pms.1997.84.1.176 ◽

1997 ◽

Vol 84 (1) ◽

pp. 176-178

Author(s):

Frank O'Brien

Keyword(s):

Population Density ◽

Dimensional Space ◽

Finite Lattice ◽

Three Dimensional ◽

Upper Bounds ◽

Three Dimensions ◽

Lower And Upper Bounds ◽

Density Index ◽

Three Dimensional Space

The author's population density index ( PDI) model is extended to three-dimensional distributions. A derived formula is presented that allows for the calculation of the lower and upper bounds of density in three-dimensional space for any finite lattice.

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Homogeneous 2D and 3D alignment of cardiomyocyte in dilated cardiomyopathy revealed by intravital heart imaging

Scientific Reports ◽

10.1038/s41598-021-94100-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kiyoshi Masuyama ◽

Tomoaki Higo ◽

Jong-Kook Lee ◽

Ryohei Matsuura ◽

Ian Jones ◽

...

Keyword(s):

Heart Failure ◽

Dilated Cardiomyopathy ◽

Cardiac Dysfunction ◽

Three Dimensional ◽

Single Layer ◽

Specific Pattern ◽

Two Dimensional ◽

Heart Imaging ◽

Novel Method ◽

2D And 3D

AbstractIn contrast to hypertrophic cardiomyopathy, there has been reported no specific pattern of cardiomyocyte array in dilated cardiomyopathy (DCM), partially because lack of alignment assessment in a three-dimensional (3D) manner. Here we have established a novel method to evaluate cardiomyocyte alignment in 3D using intravital heart imaging and demonstrated homogeneous alignment in DCM mice. Whilst cardiomyocytes of control mice changed their alignment by every layer in 3D and position twistedly even in a single layer, termed myocyte twist, cardiomyocytes of DCM mice aligned homogeneously both in two-dimensional (2D) and in 3D and lost myocyte twist. Manipulation of cultured cardiomyocyte toward homogeneously aligned increased their contractility, suggesting that homogeneous alignment in DCM mice is due to a sort of alignment remodelling as a way to compensate cardiac dysfunction. Our findings provide the first intravital evidence of cardiomyocyte alignment and will bring new insights into understanding the mechanism of heart failure.

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