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799 results for “abundance data”
Data from: N-mixture models estimate abundance reliably: a field test on Marsh Tit using time-for-space substitution
<p>Imperfect detection in field studies on animal abundance, including birds, is common and can be corrected for in various ways. The binomial N-mixture (hereafter binmix) model developed for this task is widely used in ecological studies owing to its simplicity: it requires replicated count results as the input. However, it may overestimate abundance and be sensitive to even small violations of its assumptions. We used a 33-year dataset on the Marsh Tit, Poecile palustris, a sedentary forest passerine, from Białowieża Forest, Poland to validate inference from binmix models by comparing model-estimated abundances to the true number of breeding pairs within the plots, determined by exhaustive population study. The abundance estimates, derived from six springtime (April-May) counts of males on each plot in each year, were highly reliable: 116 out of 132 year-plot estimates (88%) included the true number of pairs within the 95% confidence intervals. Over- and underestimations were thus rare and similarly frequent (9 and 12 cases, respectively), with a tendency to overestimate at low densities and underestimate at high densities. Marsh Tits sing rarely but the frequency of countersinging increases with abundance, leading to non-independence in detections. When accounted for in a submodel for detection, the per-survey number of countersinging events positively affected detection probability but only weakly affected abundance estimates. Simulations further demonstrate that this property, overestimation at low densities and underestimation at high densities, may be a systematic bias of binmix model even if density-dependent detection is absent. While the behaviour of binmix models in specific situations requires more study, we conclude that these models are a valid tool to estimate abundance reliably when intensive population monitoring is not feasible.</p>
A Nuclear Equation of State Inferred from Stellar r-Process Abundances: Data
<p>This repository contains the raw MCMC posteriors as H5 files for the three cases presented in "A Nuclear Equation of State Inferred from Stellar <em>r</em>-Process Abundances" (<a href="https://ui.adsabs.harvard.edu/abs/2021arXiv211006432H/abstract">Holmbeck et al., arXiv:2110.06432</a>).</p> <p>Also included are Python scripts with a variety of functions to read the H5 files and interpret the data with <a href="https://git.ligo.org/lscsoft/lalsuite">LALSuite</a>. These include:</p> <ul> <li>reading the data contained in the H5 file (likelihood, acceptance, and values for each MCMC step)</li> <li>generating a corner plot of the data</li> <li>finding the maximum likelihood in the posterior distribution</li> <li>calculating a neutron star mass-radius curve for a posterior EOS</li> <li>calculating pressure and density for a posterior EOS</li> <li>calculating observables (M_TOV, R_1.4, and L) associated with an EOS</li> </ul> <p>The scripts are written for Python3 compatibility and depend on:</p> <ul> <li><a href="https://pypi.org/project/lalsuite/">lalsuite</a></li> <li><a href="https://docs.h5py.org/en/stable/">h5py</a></li> <li><a href="https://numpy.org/">numpy</a></li> <li><a href="https://scipy.org/">scipy</a></li> <li><a href="https://matplotlib.org/">matplotlib</a></li> <li><a href="https://corner.readthedocs.io/en/latest/">corner</a></li> </ul> <p>For more information and how to use these scripts, see the comments in `example.py` or contact Erika Holmbeck.</p> <p>If any of our posterior samples are used in your work, we ask that you appropriately cite this repository and the original paper (<a href="https://ui.adsabs.harvard.edu/abs/2021arXiv211006432H/abstract">Holmbeck et al., arXiv:2110.06432</a>).</p>
CW EPR data supporting : Twenty-three–millisecond electron spin coherence of erbium ions in a natural-abundance crystal
<p>Continuous Wave electron spin resonance. Data corresponding to supporting information. Sample: CaWO4 recorded at 8K</p> <p>Dataset for the reference :</p> <p>Twenty-three–millisecond electron spin coherence of erbium ions in a natural-abundance crystal</p> <p>https://doi.org/10.1126/sciadv.abj9786</p> <p> </p> <p><strong>Marianne Le Dantec</strong><strong>, Miloš Rančić</strong><strong>, Sen Lin</strong><strong>, Eric Billaud</strong><strong>, Vishal Ranjan</strong><strong>,<br> Daniel Flanigan, Sylvain Bertaina</strong><strong>, Thierry Chanelière</strong><strong>, Philippe Goldner</strong><strong>, Andreas Erb</strong><strong>, </strong><br> <strong>Ren Bao Liu , Daniel Estève , Denis Vion , Emmanuel Flurin , Patrice Bertet * </strong></p>
Data archive for "Rock abundance on the lunar mare on surfaces of different age: Implications for regolith evolution and thickness"
<p>This is associated data for the study "<strong>Rock abundance on the lunar mare on surfaces of different age: Implications for regolith evolution and thickness </strong>" in GRL.</p> <p>The zipfile FT2014-Dense50kmN-n800mto5km.tif.zip is a raster of neighborhood crater frequencies from Fassett and Thomson 2014 (JGR) that are used for the age information in this paper. </p> <p>The csv file is the extracted rock abundance for every frequency pixel in this dataset. </p> <p>A github software release associated with the paper is also available on <a href="https://zenodo.org/badge/latestdoi/417542233">as a Zenodo software repository</a>, as well as on <a href="https://github.com/cfassett/MareRockAbundances">Github</a>.</p>
Data set for "Local and landscape correlates of coccinellid species richness, abundance, and assemblage change along a rural–urban gradient in Quintana Roo, Mexico."
<p>Data set for original article "Local and landscape correlates of coccinellid species richness, abundance, and assemblage change along a rural–urban gradient in Quintana Roo, Mexico"<strong> </strong>accepted at Biotropica.</p> <p>We studied changes in coccinellid assemblage composition, diversity, species richness and abundance in domestic gardens along a rural to urban gradient in southeastern Mexico, and identified local and lanscape variables that determine their species richness and abundance. </p>
Data from: Woody plant secondary chemicals increase in response to abundant deer and arrival of invasive plants in suburban forests
<p>Plants in suburban forests of eastern North America face the dual stressors of high white-tailed deer density and invasion by nonindigenous plants. The combination of chronic deer herbivory and strong competition from invasive plants could alter a plant's stress- and defense-related secondary chemistry, especially for long-lived juvenile trees in the understory, but this has not been studied. We measured foliar total antioxidants, phenolics, and flavonoids in juveniles of two native trees, <em>Fraxinus pennsylvanica</em> (green ash) and <em>Fagus grandifolia </em>(American beech), growing in six forests in the suburban landscape of central New Jersey, USA. The trees grew in experimental plots that had been subject for 2.5 years to factorial treatments of deer access/exclosure X addition/no addition of the nonindigenous invasive grass <em>Microstegium vimineum </em>(Japanese stiltgrass). As other hypothesized drivers of plant secondary chemistry, we also measured non-stiltgrass herb layer cover, light levels, and water availability. Univariate mixed model analysis of the deer and stiltgrass effects and multivariate structural equation modeling (SEM) of all variables showed that both greater stiltgrass cover and greater deer pressure induced antioxidants, phenolics, and flavonoids, with some variation between species. Deer were generally the stronger factor, and stiltgrass effects were most apparent at high stiltgrass density. SEM also revealed that soil dryness directly increased the chemicals; deer had additional positive, but indirect, effects via influence on the soil; in beech PAR positively affected flavonoids; and herb layer cover had no effect. Juvenile trees' chemical defense/stress responses to deer and invasive plants can be protective, but also could have a physiological cost, with negative consequences for recruitment to the canopy. Ecological implications for species and their communities will depend on costs and benefits of stress/defense chemistry in the specific environmental context, particularly with respect to invasive plant competitiveness, extent of invasion, local deer density, and deer browse preferences.</p>
Soil property, microbial abundance, and plant and invertebrate biomass data across a natural soil temperature gradient in Iceland from August 2018
<p><span>This is a dataset of soil physiochemical properties, bacterial and fungal abundance, and above and belowground plant and invertebrate biomass, sampled at 40 plots in the Hengill geothermal valley, Iceland, from 15<sup>th</sup> to 22<sup>nd</sup> August 2018. The plots span a temperature gradient of 10</span><span>-35 °C over the sampling period, and this temperature gradient is consistent over time. The dataset also includes data on the decomposition rate of soil organic matter, which was sampled at 60 plots in the Hengill valley from May to July 2015.</span></p>
Subarctic soil carbon losses after deforestation for agriculture depend on permafrost abundance - study data
<p>Contains the dataset and R code used for the study "Subarctic soil carbon losses after deforestation for agriculture depend on permafrost abundance".</p>
Data from: Modeling spatiotemporal abundance and movement dynamics using an integrated spatial capture-recapture movement model
<p>Animal movement is a fundamental ecological process affecting the survival and reproduction of individuals, the structure of populations, and the dynamics of communities. Methods to quantify animal movement and spatiotemporal abundances, however, are generally separate and thus omit linkages between individual-level and population-level processes. We describe an integrated spatial capture-recapture (SCR) movement model to jointly estimate (1) the number and distribution of individuals in a defined spatial region and (2) movement of those individuals through time. We applied our model to a study of polar bears (Ursus maritimus) in a 28,125 km<sup>2</sup> survey area of the eastern Chukchi Sea, USA in 2015 that incorporated capture-recapture and telemetry data. In simulation studies, the model provided unbiased estimates of movement, abundance, and detection parameters using a bivariate normal random walk and correlated random walk movement process. Our case study provided detailed evidence of directional movement persistence for both male and female bears, where individuals regularly traversed areas larger than the survey area during the 36-day study period. Scaling from individual- to population-level inferences, we found that densities varied from < 0.75 bears/625 km<sup>2</sup> grid cell/day in nearshore cells to 1.6–2.5 bears/grid cell/day for cells surrounded by sea ice. Daily abundance estimates ranged from 53–69 bears, with no trend across days. The cumulative number of unique bears that used the survey area increased through time due to movements into and out of the area, resulting in an estimated 171 individuals using the survey area during the study (95% credible interval 124–250). Abundance estimates were similar to a previous multi-year integrated population model using capture-recapture and telemetry data (2008–2016; Regehr et al. 2018). Overall, the SCR-movement model successfully quantified both individual- and population-level space use, including the effects of landscape characteristics on movement, abundance, and detection, while linking the movement and abundance processes to directly estimate density within a prescribed spatial region and temporal period. Integrated SCR-movement models provide a generalizable approach to incorporate greater movement realism into population dynamics and link movement to emergent properties including spatiotemporal densities and abundances.</p>
Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference
<p>1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.</p> <p>2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species-specific estimates by leveraging detection information among species. Here we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.</p> <p>3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N-mixture models. Our approach substantially increases precision in estimates of abundance compared to models that do not share detection information among species. We then expand this model, and apply it to repeated detection/non-detection data collected on six species of tits (Paridae) breeding at 119 1 km<sup>2</sup> sampling sites across a <em>P. montanus</em> hybrid zone in northern Switzerland (2004-2020). We find strong impacts of forest cover and elevation on population persistence and colonisation in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonisation probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.</p> <p>4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper, and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.</p>
Fruit-feeding butterfly populations respond to variation in adult food availability: evidence from longitudinal body mass and abundance data
<p>The degree to which variation in adult food availability affects the population dynamics of a species depends on its position on the capital-income breeding continuum. The long-lived butterflies that feed on fruits as adults constitute an example of Lepidoptera with a high degree of income breeding. For three species of fruit-feeding butterflies in Uganda, we assessed the contribution of the income to breeding in the wild, and the consequences of variation in fruit availability for body mass and population dynamics. We interpreted body mass loss within individuals as well as younger individuals having higher body mass than older ones as evidence for the depletion of capital reserves. Despite large sample sizes, we were able to show only modest body mass loss in one species, indicating that large-bodied fruit-feeding butterflies are functionally income breeders in the wild. Butterfly body mass was sensitive to environmental factors, although the responses to fruit availability and weather parameters were dominated by interactive effects. In all three species, periods of higher availability of fruit were followed by periods of higher adult abundance three to five months later, fitting the egg-to-adult time. Our results suggest that adult food is rapidly used for reproduction so that body mass remains stable and population size responds to adult food availability. For these income breeding species, the frequent periods of low adult food availability may select for extended adult longevity for the purpose of postponing reproduction to the onset of more favorable conditions. </p>
Microarthropoda abundance and background data for the mesocosm experiment
<p><span>Soil microarthropods have a pivotal role in soil nitrogen</span> <span>cycling in that they affect microbial decomposers.</span><span> A high</span><span> abundance of microarthropods may increase </span><span>the </span><span>mobility of inorganic nitrogen ions in the soil, mainly in nitrogen-limited habitats. However, it is difficult to study</span><span> ecological processes with </span><span>small-sized, soil-dwelling arthropods</span><span>.</span> <span>The effects </span><span>of soil microarthropods on nitrogen</span> <span>cycling have mainly been studied in laboratory microcosm experiments. Therefore, we face many practical issues in investigating these effects under field conditions that remain to be resolved.</span></p> <p><span>We developed an open-field mesocosm setup with growing plants. In a two-part experiment, spring wheat and grass species were </span><span>grown</span><span> in chernozem and sandy soils. Leached ammonium and nitrate ions were measured with percolation lysimeters. Half of the mesocosms included natural</span><span> assemblages, and</span><span> the other half included less abundant Acari and Collembola assemblages. </span><span>The application</span><span> of nitrogen fertilisation assured </span><span>differences</span><span> in nitrogen sources.</span></p> <p><span>We found a large difference in ammonium and nitrate leaching between the two soil types. In chernozem soil, the leached ion concentrations were higher in mesocosms with more abundant mite and springtail assemblages. The expected patterns were less pronounced in sandy soil. </span><span>Adding</span><span> nitrogen-fertiliser did not modify the effects of soil microarthropods.</span></p> <p><span>Open-field mesocosms are promising </span><span>for studying</span><span> the role of soil-dwelling mesofauna in ecological processes. We solved the problem </span><span>of keeping</span><span> mesofauna abundance lower in treated plots than that in control plots. Plants successfully grew in our </span><span>semi-closed</span><span> systems with functioning percolation lysimeters. The use of the equipment in the experiments in this study helped reveal that the role of soil-dwelling microarthropods in nitrogen</span> <span>cycling depends on </span><span>the </span><span>soil type and not on the application of nitrogen fertiliser.</span></p>
Data from: Wild bee abundance declines with urban warming, regardless of floral density
<p>As cities expand, conservation of beneficial insects is essential to maintaining robust urban ecosystem services such as pollination. Urban warming alters insect physiology, fitness, and abundance, but the effect of urban warming on pollinator communities has not been investigated. We sampled bees at 18 sites encompassing an urban warming mosaic within Raleigh, NC, USA. We quantified habitat variables at all sites by measuring air temperature, percent impervious surface (on local and landscape scales), floral density, and floral diversity. We tested the hypothesis that urban bee community structure depends on temperature. We also conducted model selection to determine whether temperature was among the most important predictors of urban bee community structure. Finally, we asked whether bee responses to temperature or impervious surface depended on bee functional traits. Bee abundance declined by about 41% per °C urban warming, and temperature was among the best predictors of bee abundance and community composition. Local impervious surface and floral density were also important predictors of bee abundance, although only large bees appeared to benefit from high floral density. Bee species richness increased with floral density regardless of bee size, and bee responses to urban habitat variables were independent of other life-history traits. Although we document benefits of high floral density, simply adding flowers to otherwise hot, impervious sites is unlikely to restore the entire urban pollinator community since floral resources benefit large bees more than small bees.</p>
Model data to investigate wood frog abundance in 17-year post harvest variable retention mixed wood forests
<p>Variable retention forest harvesting aims to reduce negative effect of harvesting on forest biodiversity, but its effectiveness is not well understood for many taxa. To better understand the effects of variable retention forest management and environmental features on amphibians, we used pitfall traps to capture wood frogs (<em>Lithobates sylvaticus</em>) across 4 levels of retention harvest (clearcut [0%], 20%, 50%, and unharvested control [100%]), and 2 forest types (deciduous and coniferous), in 17-year post-harvest forests in northwest Alberta. We mapped breeding sites and used a terrain moisture index (Depth-to-Water) derived from airborne LiDAR to examine relationships between relative abundance, breeding site proximity and soil moisture. Retention level alone had no effect on relative abundance, but in late summer (July and August) there was a significant interaction between retention level and forest type: capture rates decreased with amount of retention for deciduous forests, but increased with amount of retention in conifer forests. During late summer, capture rates were higher in conifer forests than in deciduous forests, with soil moisture (lower Depth-to-Water) positively related to capture rates. Though timber retention may be beneficial to wood frogs in the short-term, any impacts of forest harvesting on wood frog abundance was undetectable in stands 17 years post-harvest. </p>
Yellow creek abundance data for stream fish response to drought
<p>Climate change projections in the western United States suggest that snowpack levels and winter precipitation will decline, but mean annual precipitation levels will remain unchanged. Mountain streams that once saw a constant source of water from snowpack will begin to see large seasonal variation in flow. Increased stream intermittency will create significant conservation risks for fish species; however, few studies have examined the abundance responses of fish in high elevation streams to the shift from perennial to intermittent flow. To determine the effects of stream intermittency on fish abundance in a montane stream, we quantified changes in abundance for five species over a five-year period that exhibited extreme variation in streamflow. Responses varied by species and life stage, suggesting that the shift from perennial to intermittent flow will cause significant declines in abundance for some species. Northern leatherside chub, may experience large decreases in their range as the availability of perennial streams decreases. The study of drought effects on fish abundance will be crucial to the conservation of biodiversity in montane regions of the world.</p>
OTU table, lefse result and ARGs abundance data.
<ul> <li> <p><strong>Table_otu.raw.txt.xls</strong>: OTU table processed by Uparse(97% similarity) on the <a href="http://cloud.magigene.com/" rel="nofollow">Magigene Cloud Platform</a>. Chloroplasts, mitochondria, Unclassified, archaea otus were removed.</p> </li> <li> <p><strong>rpkm.type.txt</strong>: Abundance of Antibiotic-resistant genes (ARGs) grouped by types processed by <a href="https://github.com/xinehc/args_oap">ARGs-OAP v3.0</a></p> </li> <li> <p><strong>rpkm.subtype.txt</strong>: ARGs grouped by subtypes processed by <a href="https://github.com/xinehc/args_oap">ARGs-OAP v3.0</a></p> </li> <li> <p><strong>rpkm.genes.txt</strong>: ARGs grouped by genes processed by <a href="https://github.com/xinehc/args_oap">ARGs-OAP v3.0</a></p> </li> <li> <p><strong>lefse_results.txt.xls</strong>: lefse analysis result produced by <a href="http://cloud.magigene.com/" rel="nofollow">Magigene Cloud Platform</a>.</p> </li> <li> <p><strong>otus.fa</strong>: Representative otu sequences processed by Uparse(97% similarity) on the <a href="http://cloud.magigene.com/" rel="nofollow">Magigene Cloud Platform</a>. Chloroplasts, mitochondria, Unclassified, archaea otus were removed.</p> </li> <li> <p><strong>otus_aligned.fasta</strong>: Aligned otu sequences by mafft.</p> <p><code>Bash: mafft otus.fa > otus_aligned.fa </code></p> </li> <li> <p><strong>otus_fasttree.tre</strong>: Construct phylogenic tree from <code>otus_aligned.fa</code> by fasttree.</p> </li> </ul>
Data from: Among-species variation in six decades of changing migration timings explained through ecology, life-history and abundance
<p>Species utilising seasonal environments must now alter timings of key life-history events in response to large-scale climatic changes, thereby maintaining trophic synchronies. Yet substantial among-species variation in cross-decadal phenological changes is observed. Transitioning from basic description of such variation towards prediction of future phenological responses now requires standardised studies that rigorously quantify and explain variation in the direction, magnitude and form of changing timings across diverse species in relation to key ecological and life-history variables. Accordingly, we fitted multi-quantile regressions to 59 years of high-quality multi-species data on spring and autumn bird migration timings through northern Scotland. We demonstrate substantial variation in cross-decadal changes in timings among 72 species, and quantify the degree to which variation can be explained through differences in species ecology, life-history and population trajectories. Consistent with predictions, species with seasonal diets, narrower breeding habitat breadths, shorter generation lengths and capability to produce multiple offspring broods per year advanced their migration timing in one or both seasons. In contrast, species with less seasonal diets, and that produce single annual offspring broods, showed no change. Meanwhile, contrary to prediction, long-distance migrants advanced their migration timings as much as short-distance migrants. Changes in migration timing also varied with changes in local migratory abundance, such that species with increasing seasonal abundance apparently altered their migration timing, whilst species with decreasing abundance did not. These patterns concur with expectation if changing migration timing is adaptive. However, we demonstrate that similar patterns can be generated through numerical sampling processes given changing abundances, implying that apparent phenology-abundance relationships should be carefully validated and interpreted. Overall, our results show that migrant bird species with differing ecologies and life-histories have shown systematically differing phenological changes over six decades contextualised by large-scale environmental changes, potentially facilitating future predictions and altering temporal dynamics of seasonal species co-occurrences.</p>
Data for Estimate of water and hydroxyl abundance on asteroid (16) Psyche from JWST data
<p>The data as ASCII files used to produce the figures in the manuscript, " Estimate of water and hydroxyl abundance on asteroid (16) Psyche from JWST data". Almost all the files are ECSV files created from astropy Table. These files have complete metadata headers. Otherwise, the data, where appropriate, include s3d fits IFU data cubes used to produce 1D spectra, the solar spectra output by the Planetary Spectrum Generator, a thermophysical model output, asteroid reflectance measurements, and chondrite reflectance measurements all of which are described in further detail below. </p> <p>The Figures folder contains data behind the figures where data were used.</p> <p>For Figure 2 this corresponds to the NIRSpec and MIRI flux observations with a column for wavelength (in microns), flux (in Jansky), and error (in Jansky). </p> <p>For Figure 3 this corresponds to the normalized reflectance for the NIRSpec observations. The first column in each dataset corresponds to the wavelength in microns, the second column to the normalized reflectance (unitless), the third column to the error (unitless), and in the case of the .txt files the fourth column corresponds to the gaussian fit to the normalized reflectance. </p> <p>For Figure 4 these are the normalized reflectance divided by the continuum of the groups of data along wavelength ranges described in the manuscript for Figure 4. The first column corresponds to the wavelength in microns, the second column to the reflectance, the third column to the continuum fit to the data, the fourth column is the normalized reflectance divided by the continuum, and the error. </p> <p>For Figure 5 these are the data used to produce the 3-micron feature plot with the gaussian fit for each NIRSpec observation. The first column corresponds to the wavelength in microns, second column to the normalized reflectance divided by the continuum (unitless) and subtracted from the mean of the continuum between 3.6 and 3.7 microns such that the average of the continuum would be 0, the fourth column the error (unitless), and the fifth column the gaussian fit to the data. </p> <p>For Figure 6 the only additional data needed to produce this plot beyond what is provided for Figure 5 is the IRTF data which is provided as a text file. The first column corresponds to the wavelength in microns, the second column to the normalized reflectance divided by the continuum (unitless), and the third column to the error (unitless). </p> <p>For Figure 7 the additional data used to produce this plot beyond what is provided for Figure 5 includes laboratory reflectance measurements of various chondrites. The .scl files are the original laboratory measurements where the first column corresponds to the wavelength in microns, the second column to the normalized reflectance (unitless) and the third column to the error to 1 significant digit (unitless). The scaled_lab_reflectance.txt file has all the laboratory reflectance data used to produce the Figure 7 plot that includes the wavelength in microns, the normalized scaled reflectance for the CM chondrite, the normalized scaled reflectance for the CH/CBb chondrite, and the normalized scaled reflectance for the CY chondrite. </p> <p>For Figure 8 the additional data include original normalized reflectance data for asteroids interamnia, themis, bamberga, and europa as .trim files. The columns for these files correspond to wavelength in microns, normalized reflectance (unitless), and the error (unitless). The 'continuumremoved' .txt files correspond to the wavelength in microns and the normalized reflectance divided by the continuum (unitless). </p> <p>For Figure 9 these are the MIRI emissivity data for the two sets of observations. The first column corresponds to the wavelength in microns, the second column to the normalized emission by taking the flux subtracting the solar flux and dividing by a thermophysical model (unitless), the error (unitless), and the gaussian fit to the normalized emission. </p> <p>For the supplemental figures these are the additional fit absorption features that are located in the appendix of the manuscript. For the 1.25 - 4.8 micron text files the columns correspond to the wavelength in microns, the continuum divided normalized reflectance (unitless), the error (unitless), and the gaussian fit. For the 5.74 - 5.98 micron text files the columns correspond to wavelength in microns, normalized emission divided by a linear fit to a region outside any potential features (unitless), the error (unitless), and the gaussian fit to the feature. </p> <p>The MIRI 1D spectra folder contains the ASCII files corresponding to the 1 arcsec aperture summed spectra from the MIRI observations. The columns correspond to wavelength in microns, flux in Jansky, and error in Jansky. </p> <p>The NIRSpec 1D spectra folder contains the ASCII files corresponding to the 1 arcsec aperture summed spectra from the NIRSpec observations. The columns correspond to wavelength in microns, flux in Jansky, and error in Jansky. </p> <p>The Solar Spectra folder contains the solar spectra flux used to reduce the data to produce the reflectance and emission spectra. The lbl text files are equivalent to the files with the same name without the lbl but also include the column information. The first column corresponds to the wavelength in microns, the second column to the total spectral irradiance in Jansky, the third column to the flux from the object in Jansky, the fourth column to the reflected sunlight in Jansky, and the fifth column to the thermal contribution in Jansky. The only column used for the solar reflectance used in the analysis corresponds to the fourth column. </p> <p>The ThermalModel folder contains the ASCII files with the data corresponding to the thermophysical model used to produce the reflectance (by subtracting the thermal contribution) and the emission (by dividing by the thermal contribution). The first column corresponds to the wavelength in microns, the second to the thermal flux in Jansky, the third to the smoothed thermal flux in Jansky, and the fourth column to the normalized thermal flux. Only column two corresponding to the thermal flux in Jansky was used in the analysis associated with the manuscript. </p>
Data from: The abundance and distributional (in)equalities of forageable street tree resources in Lagos Metropolis, Nigeria
<p>Foraging for wild resources links urban citizens to nature and biodiversity while providing resources important for local livelihoods and culture. However, the abundance and distributional (in)equity of forageable urban tree resources have rarely been examined. Consequently, this study assessed the abundance of forageable street trees and their distribution in Lagos metropolis, Nigeria. During a survey of 32 randomly selected wards across 16 local government areas (LGAs) in the metropolis, 4,017 street trees from 46 species were enumerated. The LGA with the highest number of street trees was Ikeja, with 818 trees, while Lagos Island had the lowest count, with two trees. This disparity in tree numbers could be attributed to variations in human population density within each LGA. Ninety-four percent of the street trees surveyed had at least one documented use and 76 % had two, and thus were potentially forageable. However, the most common species had relatively low forageability scores. Only 5.6 % of the total street tree population was rated as highly forageable, with a usability score of at least 11 out of 15. The most forageable street trees were fruit trees and non-native species. The forageable street trees in the LGAs showed a significant disparity in their distribution, as evidenced by a Gini coefficient of 0.81. Overall, richer neighbourhoods had a higher street tree abundance, richness, and forageability potential. To meet greening and foraging goals and address the current inequitable distribution, we suggest allocating more funds for greening, particularly in low-income neighbourhoods. Further research should evaluate forageable species from other sites to acquire a detailed understanding of the distribution and abundance of forageable resources in Lagos metropolis.</p>
Species abundance information improves sequence taxonomy classification accuracy - Qiita data
<p><a href="https://qiime2.org">QIIME 2</a> Artifacts containing microbiome samples, organised by EMPO 3 classification.</p> <p>Used to test <a href="https://library.qiime2.org/plugins/q2-clawback/">q2-clawback</a>.</p> <p>Downloaded from <a href="https://qiita.ucsd.edu">Qiita</a>. Draws from the following Qiita study ids:</p> <p>11113[1], 11444, 1716, 10369[2], 990[3], 2080, 1713, 894, 1289, 1883, 1673, 1288, 10353, 2192[4], 10323, 678, 1773, 662, 1799, 864, 1481, 1024[5], 1064, 2182, 10934, 1674, 1795[6], 10273, 10283[7], 10422[8], 804, 10308, 1056[9], 2382[5], 1240, 889, 1041, 1717, 1222, 11149, 11669, 807[10], 10245, 1711, 1721, 910, 1001, 895, 550[11], 1747[12], 713[13], 755, 861, 958[14], 11161[15], 11154[16], 945, 723, 1715, 1714, 10798.</p> <p>References<br> 1. Schulfer, A. F. et al. Nat Microbiol 3, 234–242 (2017).<br> 2. Ruhe, J. et al. Front Plant Sci 7 (2016).<br> 3. O'Brien, S. L. et al. Environ Microbiol 18, 2039–2051 (2016).<br> 4. Lax, S. et al. Science 345, 1048–1052 (2014).<br> 5. Zarraonaindia, I. et al. mBio 6 (2015).<br> 6. Navas-Molina, J. A. et al. in Methods Enzymol 371–444 (2013).<br> 7. Fang, X. et al. Front Microbiol 9 (2018).<br> 8. Tripathi, A. et al. mSystems 3 (2018).<br> 9. Delsuc, F. et al. Mol Ecol 23, 1301–1317 (2013).<br> 10. Gibbons, S. M. et al. PLoS ONE 9, e97435 (2014).<br> 11. Caporaso, J. G. et al. Genome Biol 12, R50 (2011).<br> 12. Hyde, E. R. et al. mSystems 1 (2016).<br> 13. Brazelton, W. J., Nelson, B. & Schrenk, M. O. Front Microbiol 2 (2012).<br> 14. Vitaglione, P. et al. Am J Clin Nutr 101, 251–261 (2014).<br> 15. Spirito, C. M., Marzilli, A. M. & Angenent, L. T. Environ Sci Technol 52, 13438–13447 (2018).<br> 16. Pham, V. T. H. et al. Sci Rep 7 (2017).</p>
ScienceDex guides
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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.