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50 results for “Pattern formation”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Data for "Ferrofluidic aqueous two-phase system with ultralow interfacial tension and micro-pattern formation"
<p>This dataset contains the raw data used for the publication "Ferrofluidic Aqueous Two-Phase System with Ultralow Interfacial Tension, Instabilities and Pattern Formation"</p>
Pattern formation in skyrmionic materials with anisotropic environments
<p>Magnetic Skyrmions have attracted broad attention during recent years because they are regarded as promising candidates as bits of information in novel data storage devices. A broad range of theoretical and experimental investigations have been conducted with the consideration of axisymmetric Skyrmions in isotropic environments. However, one naturally observes a huge variety of anisotropic behavior inmany experimentally relevant materials. In the present work, we investigate the influence of anisotropic environments onto the formation and behavior of the noncollinear spin states of skyrmionic materials by means of Monte Carlo calculations. We find skyrmionic textures which are far from having an axisymmetric shape. Furthermore, we show the possibility to employ periodic modulations of the environment to create skyrmionic tracks.</p>
Turbulence pattern files used for star cluster formation in the Phantom smoothed particle hydrodynamics and magnetohydrodynamics code
<p>** these files are automatically downloaded by Phantom on running the code **</p> <p>The files here are sample cubes containing turbulent driving patterns for the velocity field (vx, vy and vz) used to initiate star cluster formation simulations in the Phantom smoothed particle hydrodynamics and magnetohydrodynamics code</p> <p>These can be used to set up initial conditions for a set of simulations similar to those shown in <a href="http://adsabs.harvard.edu/abs/2003MNRAS.339..577B">Bate, Bonnell & Bromm (2003)</a>. The files here are not the original driving patterns used in the BBB03 simulations, but have the same structure, and give a default driving pattern that can be used without having to re-generate the files. A similar set of files was used for the simulations published in <a href="https://ui.adsabs.harvard.edu/abs/2017MNRAS.465..105L">Liptai et al. (2017)</a>.</p> <p>The files were generated with a piece of code written by Volker Bromm, which was originally part of Matthew Bate's sphNG simulation code.</p> <p>For details of how to read these files, see the Phantom source code (<a href="https://github.com/danieljprice/phantom/blob/master/src/setup/velfield_fromcubes.f90">src/setup/velfield_fromcubes.f90</a>)</p>
Self-organized pattern formation increases local diversity in metacommunities: code and data
<p>Code and data to reproduce the results published in the article "Self-organized pattern formation increases local diversity in metacommunities" (Ecology Letters, https://doi.org/10.1111/ele.13880).</p>
Behavioral strategies and the spatial pattern formation of nesting
<p>This dataset contains data from a combined field and simulation study regarding spatial pattern formation of nesting, described in the paper: "Batsleer, F., Maes, D., Bonte, D. (2021) Behavioral strategies and the spatial pattern formation of nesting. The American Naturalist".</p> <p>The study investigates the relative importance of environmental and behavioral mechanisms in nest aggregations of the ground-nesting digger wasp <em>Bembix rostrata</em>. A field study was combined with an individual-based model that simulated the possible behaviors of spatial organisation of nesting.</p> <p>In the first analysis, a microhabitat model was built based on the location of the nests from a capture-mark-recapture study (CMR) and environmental variables NDVI (vegetation) and insolation (sun irradiance), derived from detailed remote sensing data from a drone flight.</p> <p>In the second analysis, an IBM was built that combined three possible mechanisms of nest choice to simulate the emerging spatial and network patterns found in the field. This was done by combining an environmental cue (based on the microhabitat model) and two relevant behavioral mechanisms related to local site fidelity and conspecific attraction. Strengths and combinations of the mechanisms could vary. Simulations were compared to the field data to find which combinations and strengths of mechanisms can best explain the emerging spatial and network patterns.</p> <p>The main results are that 1) the observed pattern in nature is best predicted by the simultaneous effect of a weak environmental cue and strong behavioral mechanisms. 2) individuals differ in their combination of mechanisms used and will either use local site fidelity (personal information) or conspecific attraction (inadvertent social information), but not both simultaneously. 3) We demonstrate that the nest pattern formation of a central place foraging insect cannot be considered as the sum of environmental and behavioral mechanisms.</p>
Plant Community Formation and Species Distribution Patterns in relation to environmental variables in Endiras Natural Forest, Fogera District, South Gondar Zone, Ethiopia
<p>We need to deposit the data for the manuscript entitled plant community formation and species distribution patterns in relation to environmental variables in Endiras forest, Fogera District, South Gondar Zone, Ethiopia so as to be cited easily </p>
Dissecting glial scar formation by spatial point pattern and topological data analysis
<p>These data were generated by the Laboratory of Neurovascular Interactions (https://elalilab.com/) at University Laval (Quebec, Canada), and reported in "Dissecting glial scar formation by spatial point pattern and topological data analysis". </p> <p>Please refer to the Open Science Framework (OSF) repository (https://osf.io/3vg8j/) or GitHub (https://github.com/elalilab/GlialScar_PPA-TDA_2022) to see the processing pipeline.</p> <p><strong>AUTHORS</strong><br> Manrique-Castano, Daniel; Bhaskar, Dhananjay; ElAli, Ayman</p> <p><strong>KEYWORDS</strong><br> Stroke, cerebral ischemia, brain injury, glial scar, reactive astrocytes, reactive microglia, </p> <p><br> <strong>1. STUDY DESCRIPTION </strong> <br> This research provides a quantitative analysis of reactive glia and glial scar formation in a mouse model of cerebral ischemia. The dataset in this repository consists of raw widefield microscopy images from healthy and ischemic animals. </p> <p><strong>2. EXPERIMENTAL CONDITIONS</strong><br> Six-month-old C57BL/6 mice were subjected to 30 minutes of cerebral ischemia by middle cerebral artery occlusion (MCAO). Brains were harvested at 5, 15, and 30 days post-ischemia (DPI) (see 10.5281/zenodo.3559570). 5 sham animals were included as controls. The full protocol for brain harvesting is available at 10.17504/protocols.io.4r3l27q5pg1y/v1. Brain sections were stained with NeuN, Gfap, and Iba1 antibodies to detect neurons and reactive glia after injury. Full protocol available at 10.17504/protocols.io.yxmvmk94og3p/v1 <br> <br> <strong>3. FILE DESCRIPTION</strong></p> <p><strong>- GT5X_Gfap_Iba1_NeuN.rar: </strong>Contain widefield (5x magnification) .tif images grouped by animals (5-7 images per animal; see research article for further details). The images were taken with the following parameters.</p> <p>Objective: Fluar 5x/0.25 M27<br> Scaling per pixel: 1.300 x 1.300 µm<br> Bit depth: 16 bit </p> <p>Stainings:<br> Neun Channel AF647; Excitation 653; Emission 668; Exposure 3 s<br> IBA1 Channel AFCy3; Excitation 458; Emission 561; Exposure 4 s<br> GFAP Channel AF488; Excitation 493; Emission 517; Exposure 1 s<br> DAPI Channel AF405; Excitation 353; Emission 465; Exposure 50 ms</p> <p>We used a FIJI script to pre-process the original .czi files. The script is shared in the GitHub repository under the name GT_Exp2_5x_GenerateTiffs.jim.</p> <p><strong>- GT10X_Gfap_Iba1_NeuN.rar:</strong> Contain a single widefield (10x magnification) .tif image per animal at the level of the MCA territory (see research article for further details). The images were taken with the following parameters.</p> <p>Objective: ECM paln-NeoFluar 10x/0.30 M27<br> Scaling per pixel: 0.45 x 0.45 µm<br> Bit depth: 16 bit </p> <p>Stainings:<br> Neun Channel AF647; Excitation 653; Emission 668; Exposure 200 ms<br> IBA1 Channel AFCy3; Excitation 458; Emission 561; Exposure 250 ms<br> GFAP Channel AF488; Excitation 493; Emission 517; Exposure 100 ms<br> DAPI Channel AF405; Excitation 353; Emission 465; Exposure 10 ms</p> <p><br> We used a FIJI script to pre-process the original .czi files. The script is shared in the GitHub repository under the name GT_Exp2_10x_GenerateTiffs.jim.<br> <br> For 5x and 10x images, the following naming strings apply:</p> <p>GT5x: Research project identifier indicating the magnification<br> M01(n): Animal ID<br> 5D(n): Days post-ischemia. 0D refers to healthy (naive) animals. <br> Scene1(n): Bregma level. Scene 1 corresponds to the most anterior area sampled, while Scene 6 or 7 is the most posterior.</p> <p><strong>- PointPatterns_10x.rds: </strong>2D point patterns of GFAP, IBA1, and NeuN generated by the r-package <em>spatstat</em>. The observation window comprises a horizontal ROI from the ventricular area to the outer border of the dorsolateral cerebral cortex. The point patterns were generated from the files and coordinates contained in the <strong>QupathProjects_10x.rar</strong> file in this repository. To reproduce the generation of point patterns please refer to the associated GitHub repository (https://github.com/elalilab/Stroke_GlialScar_PPA-TDA). </p> <p><strong>- PointPatterns_5x.rds: </strong>2D point patterns of GFAP, IBA1, and NeuN generated by the r-package <em>spatstat</em>. The observation window comprises the ischemic hemisphere. The point patterns were generated from the files and coordinates contained in the <strong>QupathProjects_5x.rar</strong> file in this repository. To reproduce the generation of point patterns please refer to the associated GitHub repository (https://github.com/elalilab/Stroke_GlialScar_PPA-TDA). </p> <p><strong>- QupathProjects_5x.rar: </strong>QuPath project folder for 5x images (GT5X_Gfap_Iba1_NeuN.rar). Each subfolder (per animal) contains the necessary files to import annotations (alignment to the Allen Brain Atlas) generated by ABBA (https://biop.github.io/ijp-imagetoatlas/). Please see the research article for further details. </p> <p><strong>**NOTE** </strong>Gfap, Iba1, and NeuN folders contain raw .tsv data originated by QuPath (cell counting). These folders are read in the R processing pipeline to extract the coordinates of each cell. Please make sure the whole folder is in the R working directory. The file "project.qpproj" in each folder opens the QuPath project in QuPath and reads the classifiers and data folders. Each folder also contains "_Alignement.json" and "_Registration_json" files generated during the alignment and annotation procedures in ABBA. However, when the route of the source images is changed, the plugin does not allow rerouting, and the files are of no practical use. The issue has been reported to the ABBA Github repository. </p> <p><strong>- QupathProjects_10x.rar:</strong> QuPath project folder for 10x images (GT5X_Gfap_Iba1_NeuN.rar). The folder contains the necessary files to import annotations (Alignment to the Allen Brain Atlas) generated by ABBA (https://biop.github.io/ijp-imagetoatlas/). Please see the research article for further details. </p> <p><strong>**NOTE** </strong>Gfap, Iba1, NeuN, and DAPI folders contain raw .tsv data originated by QuPath (cell counting). These folders are read in the R processing pipeline to extract the coordinates of each cell. Please make sure the whole folder is in the R working directory. The file "project.qpproj" opens the QuPath project in QuPath and reads the classifiers and data folders. </p>
Behavioral strategies and the spatial pattern formation of nesting
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Data from: Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colon Province, Panama
Extant members of the neogastropod family Conidae (cone snails) are renowned for their often dazzling shell coloration patterns and venomous feeding habits. Many cone snail species have also been described from the fossil record, but to date have been little used to understand the evolutionary history of extant clades. The cone snail fauna of the Miocene Gatun Formation of Colón Province, Panama is especially important for understanding the temporal and biogeographic history of tropical American Conidae. Intensive, focused collecting from an exposure of the lower Gatun Formation (deposited ca. 11-10 Ma) resulted in the discovery of nearly 900 specimens of Conidae. Remarkably, many of these well-preserved specimens exhibit revealed coloration patterns when exposed to ultraviolet light. The fluorescing coloration patterns were used in conjunction with other features of shell morphology to differentiate species and, in most cases, evaluate their potential relationships to members of the extant tropical American fauna. Nine species are fully described from this locality, one of which is recognized as new: Conus (Stephanoconus) woodringi n. sp. At least one, and perhaps more, Conidae species are also present at the study locality. The diversity of this Conidae fauna is considered moderate relative to other recently analyzed tropical American fossil assemblages. The phylogenetic diversity of the assemblage, however, is noteworthy: six of the ten species can be confidently assigned to six different clades of extant Conidae, providing potentially useful calibration points for future phylogenetic studies.
Plant community formation and species distribution pattern in relation to environmental variables in Endiras Natural Forest, northwest Ethiopia
<p><span>The study was conducted in Endiras Forest, Northwest Ethiopia, so as to evaluate the effects of environmental variables on the patterns of plant community formation. A systematic random sampling technique was used to collect vegetation data from 56 (20 m x 20 m) plots laid at 100 m intervals on ten transects. In each plot, the species encountered and its percent cover abundance were recorded, which was later transformed into a modified Braun-Blanquet scale. The composite soil samples collected from 15 cm x 15 cm subplots were examined for 13 soil parameters. Communities were determined using cluster analysis. The Shannon-Wiener index was employed to quantify species diversity. The relationships between species and environmental variables were evaluated using Canonical Correspondence Analysis (CCA). Seventy three woody plant species, distributed in 38 families, were documented. Fabaceae was found to be the most species-rich family (21.9%). Five communities were generated from the cluster analyses that vary in diversity. Nine environmental variables were found to be significant in determining patterns of community formation (Pr< 0.05). Organic matter, pH, and altitude, highly correlated with CCA axis 1, are largely shaped the species distribution patterns. Various patterns of community formation demonstrate the need to design different conservation measures.</span></p>
Plant community formation and species distribution pattern in relation to environmental variables in Endiras Natural Forest, northwest Ethiopia
<p><span>The study was conducted in Endiras Forest, Northwest Ethiopia, so as to evaluate the effects of environmental variables on the patterns of plant community formation. A systematic random sampling technique was used to collect vegetation data from 56 (20 m x 20 m) plots laid at 100 m intervals on ten transects. In each plot, the species encountered and its percent cover abundance were recorded. The composite soil samples collected from 15 cm x 15 cm subplots were examined for 13 soil parameters. Communities were determined using cluster analysis. The Shannon-Wiener index was employed to quantify species diversity. The relationships between species and environmental variables were evaluated using CCA. Seventy three woody plant species, distributed in 38 families, were documented. Fabaceae was found to be the most species-rich family (21.9%). Five communities were generated from the cluster analysis. Nine environmental variables were found to be significant in determining patterns of community formation (Pr< 0.05). Organic matter, pH, and altitude are largely shaped the species distribution patterns. Various patterns of community formation demonstrate the need to design different conservation measures.</span></p>
Data supplement for PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models"
<p>Here, we provide <em>Mathematica</em> files that provide the details of the weakly nonlinear analysis employed in the PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models" submitted by Tobias Frohoff-Hülsmann.</p> <p> </p>
Supplementary Movies – Pattern formation by bacteria-phage interactions
<p>Supplementary movies of the manuscript "Pattern formation by bacteria-phage interactions".</p>
Data from: Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colon Province, Panama
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A long tail of truth and beauty: a simple rule of pattern formation explains symmetry, complexity and beauty in the peacock's tail
<p><span>Darwin's theory of sexual selection by female choice has become a standard explanation for exaggerated sexually dimorphic traits, such as the peacock's (<i>Pavo cristatus</i>) long tail. Eyespot beauty-based female choice requires genetic variation in female preference and the number of eyespots, as well as a genetic correlation between the two. However, little genetic variation has been documented in either of these traits in natural and feral peacock populations. We examined the anatomical plan underlying feather development and discovered that eyespot feather follicles originate in alternating rows of 10/11, which uniquely determines the train's feather complexity, bilateral symmetry, and eyespot arrangement and beauty. This pattern precludes intrinsic variation in eyespot number, resulting in a fixed number of total eyespots in fully mature individuals. Since number of eyespots and tail length are independent traits and function of the age of the animal, the only variation available in these trats is also function of age. We propose an alternate, male drive, hypothesis in which females choose males based on their overall dominance (size, vigour, call, courting), and beauty of the train may (or may not) be a factor in female choice but it cannot affect the train length. This hypothesis can explain all known results. </span></p>
Global warming pattern formation: the role of ocean heat uptake
<p>Datasets for the paper:</p> <p>Hu, S., Xie, S.-P., and Kang, S. M. (2021) Global warming pattern formation: the role of ocean heat uptake. Journal of Climate. Resubmitted after minor revision.</p>
The Data For Spatial Variations of Stellar Elemental Abundances in FIRE Simulations of Milky Way-Mass Galaxies: Patterns Today Mostly Reflect Those at Formation
<p>Spatial patterns of stellar elemental abundances encode rich information about a galaxy’s formation<br>history. We analyze the radial, vertical, and azimuthal variations of metals in stars, both today and at<br>formation, in the FIRE-2 cosmological simulations of Milky Way-mass galaxies, and we compare<br>with the Milky Way. Overall, spatial variations of stellar metallicities show only modest differences between formation and today; spatial variations today primarily reflect the conditions of stars at birth, with spatial redistribution of stars after birth contributing secondarily. </p> <p> </p> <p>This data abides by CC-BY.</p>
Tidal channel formation in a rapidly invaded micro-tidal marsh: the role of dynamic vegetation pattern and concurrent channel deepening
<p>The channel formation during the spartina alterniflora invasion influenced by vegetation pattern dynamic and concurrent channel deepening.</p>
A long tail of truth and beauty: a simple rule of pattern formation explains symmetry, complexity and beauty in the peacock’s tail
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.