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24 results for “point patterns”
Point-count bird censusing: long-term monitoring of bird abundance and diversity along the Salt River in the greater Phoenix metropolitan area, ongoing since 2013 (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-cap/641/6. The abstract below was extracted from the Level 0 data package and is included for context:
Moss point transect data for the Kuparuk River near Toolik Field Station, Alaska 1993-current. (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-arc/10317/8. The abstract below was extracted from the Level 0 data package and is included for context: This file contains the consolidated data for percent cover of dominant bryophytes and other easily identifiable macro-algae in the experimental reaches of the Kuparuk River beginning in 1993 and updated annually. In some years percent cover was recorded more than one time per season. In all years percent cover was recorded in riffle habitats and in some (early) years percent cover was recorded for pool habitats. Moss point transects have been done on the Kuparuk since 1993. The Arctic is one of the most rapidly warming regions on Earth. Responses to this warming involve acceleration of processes common to other ecosystems around the world (e.g., shifts in plant community composition) and changes to processes unique to the Arctic (e.g., carbon loss from permafrost thaw). The objectives of the Arctic Long-Term Ecological Research (LTER) Project for 2017-2023 are to use the concepts of biogeochemical and community “openness” and “connectivity” to understand the responses of arctic terrestrial and freshwater ecosystems to climate change and disturbance. These objectives will be met through continued long-term monitoring of changes in undisturbed terrestrial, stream, and lake ecosystems in the vicinity of Toolik Lake, Alaska, observations of the recovery of these ecosystems from natural and imposed disturbances, maintenance of existing long-term experiments, and initiation of new experimental manipulations. Based on these data, carbon and nutrient budgets and indices of species composition will be compiled for each component of the arctic landscape to compare the biogeochemistry an
PIE LTER surveys of salt marsh breeding birds using point counts in Rowley and Newbury, Massachusetts (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-pie/175/8. The abstract below was extracted from the Level 0 data package and is included for context: This data set contains the results of point count surveys of breeding birds in the salt marshes of the Plum Island Estuary. Surveys have been carried out each year in June beginning in 2004 and are ongoing. Currently six circles of 100 m radius are being surveyed. Three of the circles are in plots that had been regularly hayed and three in unhayed plots. Currently only one of the plots is regularly hayed. 85 species recorded as of 2020. Most frequently encountered are Agelaius phoeniceus, Ammospiza caudacuta, Tringa semipalmata. The Plum Island Ecosystems (PIE) LTER is developing a predictive understanding of the response of a linked watershed-marsh-estuarine system in northeastern Massachusetts to rapid environmental change. Over the last 30 years, surface sea water temperatures in the adjacent Gulf of Maine have risen at 3 times the global average, rates of sea-level rise have accelerated, and precipitation has increased. Coupled with these changes in climate and sea level are substantial changes within the rapidly urbanizing watersheds that influence water, sediment, and nutrient delivery to the marsh and estuary. In PIE IV our focus is on: Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts. NSF OCE LTER-Plum Island Ecosystems: Dynamics of coastal ecosystems in a region of rapid climate change, sea-level rise, and human impacts.
SGS-LTER Ecosystem Stress Area - long-term point-frame (percent basal cover) dataset following nutrient enrichment stress on the Central Plains Experimental Range in Nunn, Colorado, USA 1982-2011, ARS Study Number 3 (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-sgs/521/7. The abstract below was extracted from the Level 0 data package and is included for context: This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Water, nitrogen, and water-plus-nitrogen at levels beyond the range normally experience by shortgrass steppe communities were applied from 1971 through 1975, plant densities were sampled through 1977, and then sampling resumed in 1982, with sampling frequencies changing from annually to every other year. The initial sampling from 1970 to 1974 showed that the water and water plus nitrogen treatments had the strongest effect on plant community structure, both treatments increased biomass, and exotic weed species were noted on the water plus nitrogen treatment. Later sampling from 1982 to 1991 showed a ten-fold increase in exotic weed species on the water plus nitrogen plots as compared to the controls (Milchunas and Lauenroth 1995), a community change that has persisted on this site due to a chronic elevation of soil nitrogen caused by a plant tissue/soil organic matter feedback mec
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings. in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.
Text-fig. 8. Carpolithes (a–t). a–e: Carpolithes sp. 1. USNM PAL 772366. Scale bar = 1 cm. a: Lateral view of endocarp, note two longitudinal ridges. b: Lateral view of endocarp rotated 90° from (a), note single lateral ridge in center, a, b reflected light, palladium coated. c: Lateral view, Micro-CT scan surface rendering. d: View of rounded end of the endocarp, reflected light, palladium coated. e: View of the opposite (pointed) end of the endocarp, note split; reflected light, palladium coated. f–j: Carpolithes sp. 2. USNM PAL 772367. Scale bar = 5 mm. f: Lateral view, base down; note raphe-like structure (arrow), reflected light, palladium coated. g: Lateral view, the raphe-like structure extending vertically from the base. h: Lateral view, rotated 90° from (g). i: Lateral view, the opposite face to that in (h). j: Basal view, raphe-like structure running from the center to the right of the image. g–j: CT scan surface renderings. k–o: Carpolithes sp. 3 USNM PAL 772368. Scale bar = 5 mm. k: Ventral view of the specimen, note flared apical extension, reflected light, uncoated. l: Dorsal view illustrating the flared apical extension, rotated 180o from (k). m: Lateral view rotated 90° from that in (l). n: Apical view, the apical extension with central pore (arrow) and a clear lineation running down the side to the top of the image. o: Basal view. l–o: Micro-CT scan surface renderings. p–t: Carpolithes sp. 4. USNM PAL 772369. Scale bar = 3 mm. p: Basal view illustrating the concentric rings of radiating possible cells surrounding a central depression. q: Lateral view, base down, note possible cellular pattern. r: Lateral view, rotated 180° from (q), base down; p–r: reflected light, palladium coated. s, t: Basal and lateral views, micro-CT scan surface renderings.
Text-fig. 5. Reyispermum parvum gen. et sp. nov. seeds from the Early Cretaceous Vale de Água locality, Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype (S174178; Vale de Agua sample 141) in lateral view showing shape and cell pattern; remains of mounting media (¤). b) Cut volume rendering of seed (cut at yz0553) showing the slightly raised tissue immediately adjacent to the lower edge of the hilum (arrow head) and palisade-shaped cells of exotesta. c) Apical view of seed showing hilar depression (hi), position of micropylar slit (mi) and the slightly raised raphal ridge (ra). d) Seed in lateral view showing raised tissue immediately adjacent to the lower edge of the hilum (arrow head) (S174495, Vale de Água sample 300). e) Cut volume rendering (cut at yz0500) of the seed in (5d) showing the raised tissue (arrow head) immediately adjacent to the lower edge of the hilum and sclerenchyma cells of exotesta. f) Detail of seed in (5d) showing micropylar slit (mi), hilum (hi) and raised tissue (arrow head) immediately adjacent to the lower edge of the hilum. g, h) Seed in lateral view (g) and view towards raphe (h) showing seed shape, the raised tissue below hilum (arrow head) and the raphal ridge (ra); note pointed micropylar area (S174179, Vale de Água sample 141). i) Seed surface of seed in (5d) showing the raised outlines of the undulate anticlinal walls of the exotestal cells. Scale bars = 250 µm (a–e, g, h); 125 µm (f, i). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 5. Reyispermum parvum gen. et sp. nov. seeds from the Early Cretaceous Vale de Água locality, Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a) Holotype (S174178; Vale de Agua sample 141) in lateral view showing shape and cell pattern; remains of mounting media (¤). b) Cut volume rendering of seed (cut at yz0553) showing the slightly raised tissue immediately adjacent to the lower edge of the hilum (arrow head) and palisade-shaped cells of exotesta. c) Apical view of seed showing hilar depression (hi), position of micropylar slit (mi) and the slightly raised raphal ridge (ra). d) Seed in lateral view showing raised tissue immediately adjacent to the lower edge of the hilum (arrow head) (S174495, Vale de Água sample 300). e) Cut volume rendering (cut at yz0500) of the seed in (5d) showing the raised tissue (arrow head) immediately adjacent to the lower edge of the hilum and sclerenchyma cells of exotesta. f) Detail of seed in (5d) showing micropylar slit (mi), hilum (hi) and raised tissue (arrow head) immediately adjacent to the lower edge of the hilum. g, h) Seed in lateral view (g) and view towards raphe (h) showing seed shape, the raised tissue below hilum (arrow head) and the raphal ridge (ra); note pointed micropylar area (S174179, Vale de Água sample 141). i) Seed surface of seed in (5d) showing the raised outlines of the undulate anticlinal walls of the exotestal cells. Scale bars = 250 µm (a–e, g, h); 125 µm (f, i).
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>
Utilising quadrat.count and quadrat.test to understand metal axes as spatial point patterns
<p>As part of a Master's thesis, the spatial distribution and density of metal axes found by private metal detectorists were assessed in relation to different covariates: soil type, soil texture, land cover and estimated preservation capacity (Kibblewhite et al. 2016). The data derives from England and Wales (Portable Antiquities Scheme), Denmark (Digitale Metaldetektorfund) and the Netherlands (Portable Antiquities Scheme). Calculations were performed with the functions 'quadrat.count', 'intensity.quadratcount' and 'quadrat.test' in R. There are three separate .Rmd files per country, each refering to a particular covariable.</p>
Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
<p>A major objective of plant ecology research is to determine the underlying processes responsible for the observed spatial distribution patterns of plant species. Plants can be approximated as points in space for this purpose, and thus, spatial point pattern analysis has become increasingly popular in ecological research. The basic piece of data for point pattern analysis is a point location of an ecological object in some study region. Therefore, point pattern analysis can only be performed if data can be collected. However, due to the lack of a convenient sampling method, a few previous studies have used point pattern analysis to examine the spatial patterns of grassland species. This is unfortunate because being able to explore point patterns in grassland systems has widespread implications for population dynamics, community-level patterns and ecological processes. In this study, we develop a new method to measure individual coordinates of species in grassland communities. This method records plant growing positions via digital picture samples that have been sub-blocked within a geographical information system (GIS). Here, we tested out the new method by measuring the individual coordinates of <i>Stipa</i><i> grandis</i> in grazed and ungrazed <i>S. grandis</i> communities in a temperate steppe ecosystem in China. Furthermore, we analyzed the pattern of <i>S. grandis</i> by using the pair correlation function <i>g</i>(<i>r</i>) with both a homogeneous Poisson process and a heterogeneous Poisson process. Our results showed that individuals of <i>S. grandis</i> were overdispersed according to the homogeneous Poisson process at 0-0.16 m in the ungrazed community, while they were clustered at 0.19 m according to the homogeneous and heterogeneous Poisson processes in the grazed community. These results suggest that competitive interactions dominated the ungrazed community, while facilitative interactions dominated the grazed community. In sum, we successfully executed a new sampling method, using digital photography and a Geographical Information System, to collect experimental data on the spatial point patterns for the populations in this grassland community.</p>
Active season body mass patterns of Little Brown Bats and Northern Myotis: Raw and fitted mass values, environmental conditions and inflection point estimates
<p><span>Animals are expected to adjust their behavioural patterns to improve fitness outcomes, such as fecundity or offspring survival. For long-lived hibernators, decisions made in each annual cycle may reflect considerations not just for concurrent survival and reproduction, but also the pressure to maximize overwinter survival and future reproductive success. We examined how these elements manifest themselves in the body mass variation patterns of North American northern latitude temperate bats, whose size and roosting habits present considerable monitoring challenges. We characterized and compared the summer and fall mass variation patterns of little brown myotis (<em>Myotis lucifugus</em>) and northern myotis (<em>M. septentrionalis</em></span><span>) from a historic dataset. In summer, the estimated date of parturition was strongly associated with spring foraging conditions (low wind, low precipitation, warm temperatures), and mass gain associated with female reproduction conferred considerable differentiation between the mass variation patterns of females and males. In fall, differences were most apparent among species, although adults exhibited a greater capacity for rapid mass gain than juveniles. These results demonstrate how reproductive constraints and interannual survival have important influences on the behaviour of temperate bats. Future work should seek to quantify the fitness benefits of patterns identified in this study, such as the rate of prehibernation mass gain.</span></p>
Feldman_dataset_PoD: Dataset containing results from the research project Points of Discontinuity concerning Morton Feldman, Why Patterns? for flute, glockenspiel and piano (1978)
<p>The complete datasets resulting from the research project <em>Points of Discontinuity</em> contain 23 datasets for the musical works or excerpts that were part of the online listening experiment, with each dataset containing seven or eight files (all audio files are stored in a dataset with restricted access), as well as a dataset (PoD_general_dataset) with five additional files.</p> <p>This dataset<strong> Feldman_dataset_PoD </strong>contains eight files:</p> <ul> <li>Feldman_01_ReadMe.pdf</li> <li>Feldman_02_data.xlsx (processed data for this work)</li> <li>Feldman_03_individual_data.xlsx (raw data for each participant obtained from the experiment)</li> <li>Feldman_04_audio.mp3 <strong>[non-public] </strong>(audio recording used in the experiment) [stored in the restricted dataset <a href="https://doi.org/10.5281/zenodo.13981214" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13981214</a>]</li> <li>Feldman_05_model_results.sv (graphical representation of results and the model in Sonic Visualiser) [requires audio file Feldman_04_audio.mp3 to display correctly]</li> <li>Feldman_06_SV-data_model+results.zip (text files with the marker locations for all layers in Sonic Visualiser)</li> <li>Feldman_07_model+results_SV-screenshot.pdf (a screenshot of the full-screen display of the SV-file)</li> <li>Feldman_08_annotated_score.pdf (model analysis annotated in the score)</li> </ul>
Data from: Levels and spatial patterns of effective population sizes in the southern damselfly (Coenagrion mercuriale): On the need to carefully interpret single-point and temporal estimations to set conservation guidelines
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Data from: A new digital method of data collection for spatial point pattern analysis in grassland communities
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Active season body mass patterns of Little Brown Bats and Northern Myotis: Raw and fitted mass values, environmental conditions and inflection point estimates
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Data from: Disparate patterns of movements and visits to points of interest located in urban hotspots across U.S. metropolitan cities during COVID-19
<p>We examined the effect of social distancing on changes in visits to urban hotspot points of interest. In a pandemic situation, urban hotspots could be potential superspreader areas as visits to urban hotspots can increase the risk of contact and transmission of a disease among a population. We mapped origin-destination networks from census block groups to points of interest (POIs), such as restaurants, museums, and schools, in sixteen cities in the United States. We adopted a coarse-grain approach to examine patterns of visits to POIs among hotspots and non-hotspots from January to May 2020. Also, we conducted chi-square tests to identify POIs with significant flux-in changes during the analysis period. The results showed disparate patterns across cities in terms of reduction in hotspot POI visits. Sixteen cities are divided into two categories. In one category, which includes the cities of, San Francisco, Seattle, and Chicago, we observe a considerable decrease in hotspot POI visits, while in another category, including the cites of, Austin, Houston, and San Diego, the visits to hotspots did not greatly decrease. While all the cities exhibited overall decreasing visits to POIs, one category maintained the proportion of visits to hotspot POIs. The proportion of visits to some POIs (e.g., Restaurants) remained stable during the social distancing period, while some POIs had an increased proportion of visits (e.g., Grocery Stores). We also identified POIs with significant flux-in changes, showing that related businesses were greatly affected by social distancing.</p>
Spatial point pattern analysis of traces (SPPAT): an approach for visualizing and quantifying site-selectivity patterns of drilling predators
<p>Site-selectivity analysis in drilling predation may provide useful behavioral information of a predator interacting with its prey. However, traditional approaches exclude some spatial information (i.e., oversimplified trace position) and are dependent on the scale of analysis (e.g., arbitrary grid system used to divide the prey skeleton into sectors). Here we introduce the spatial point pattern analysis of traces (<i>SPPAT</i>), an approach for visualizing and quantifying the distribution of traces on shelled invertebrate prey, which includes improved collection of spatial information inherent to drillhole location (morphometric-based estimation), improved visualization of spatial trends (Kernel density and hotspot mapping), and distance-based statistics for hypothesis testing (<i>K</i>-, <i>L</i>-, and pair correlation functions). We illustrate the <i>SPPAT</i> approach through case studies of fossil samples, modern beach-collected samples, and laboratory feeding trials of naticid gastropod predation on bivalve prey. Overall results show that Kernel density and hotspot maps enable visualization of subtle variations in regions of the shell with higher density of predation traces, which can be combined with the maximum clustering distance metric to generate hypotheses on predatory behavior and anti-predatory responses of prey across time and geographic space. Distance-based statistics also capture the major features in the distribution of traces across the prey skeleton, including aggregated and segregated clusters, likely associated with different combinations of two modes of drilling predation, edge- and wall-drilling. The <i>SPPAT </i>approach is transferrable to other paleoecologic and taphonomic data such as encrustation and bioerosion, allowing for standardized investigation of a wide range of biotic interactions.</p>
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites
Data from: A new non-parametric method for analyzing replicated point patterns in ecology
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Data from: Disparate patterns of movements and visits to points of interest located in urban hotspots across U.S. metropolitan cities during COVID-19
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Spatial point pattern analysis of traces (SPPAT): an approach for visualizing and quantifying site-selectivity patterns of drilling predators
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.