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274 results for “data consistency”
Data from: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
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Raw sequencing data for assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies
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Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography
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Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs
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Data from: A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
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Data from: Feeding impacts thermoregulatory behavior and consistency across day and night in a diurnal lizard
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Data collected by fruit body– and DNA-based survey methods yield consistent species-to-species association networks in wood-inhabiting fungal communities
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Data from: Consistent seasonal flexibility of the gut and its regions across wild populations of a winter-quiescent fish
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Data and scripts from: Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex
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Data from: Freshwater fish functional diversity shows diverse responses to human activities, but consistently declines in the tropics
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Data from: Consistent coordination patterns provide near perfect behavior decoding in a comprehensive motor program for insect flight
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Supplementary data for Cariou et al (2020, Molecular Ecology Resources, "How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?")
<p>This dataset accompanies a paper by Cariou et al, to be published in Molecular Ecology Resources, where we assessed in 92 insect species if the genetic clustering of specimens into species like units, on the basis of mitochondrial DNA, was consistent with genome wide divergence, as estimated by RAD-seq data. The present repository includes: (1) a detailed description of the bioinformatic analysis indicating which programs were used, together with parameter values, (2) the raw RAD-seq data following demultiplexing, (3) the consensus sequences of all RAD loci for all specimens, and (4) large tables indicating genetic distances at all RAD loci for all species.</p>
Data Supplement: U.S. state-level projections of the spatial distribution of population consistent with Shared Socioeconomic Pathways.
<p>These data are to supplement the following in-press publication: </p> <p>Zoraghein, H., and O'Neill B. (2020). U.S. state-level projections of the spatial distribution of population consistent with Shared Socioeconomic Pathways. Sustainability.</p> <p>The data herein were generated using the `population_gravity` model which can be found here: <a href="https://github.com/IMMM-SFA/population_gravity">https://github.com/IMMM-SFA/population_gravity</a></p> <p>CONTENTS:</p> <p><strong>zoraghein-oneill_population_gravity_inputs_outputs.zip</strong></p> <ul> <li>contains a directory for each U.S. state for inputs and outputs</li> <li><strong>inputs</strong> contain the following: <ul> <li><strong><state-name>_<urban or rural>_<yr>_1km.tif: </strong> Urban and Rural population GeoTIF rasters at a 1km resolution <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong><state-name>_mask_short_term.tif: </strong> Mask GeoTIF rasters at a 1km resolution that contain values from 0.0 to 1.0 for each 1 km grid cell to help calculate suitability depending on topographic and land use and land cover characteristics <ul> <li>value per grid cell: values from 0.0 to 1.0 (float) that are generated from topographic and land use and land cover characteristics to inform suitability as outlined in the companion publication</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong><state-name>_<ssp>_popproj.csv: </strong> Population projection CSV files for urban, rural, and total population (number of humans; float) for SSPs 2, 3, and 5 for years 2010-2100</li> <li><strong><state-name>_coordinates.csv: </strong>CSV file containing the coordinates for each 1 km grid cell within the target state. File includes a header with the fields XCoord, YCoord, FID.,Where data types and field descriptions are as follows: (XCoord, float, X coordinate in meters),(YCoord, float, Y coordinate in meters),(FID, int, Unique feature id)</li> <li><strong><state-name>_within_indices.txt: </strong>text file containing a file structured as a Python list (e.g. [0, 1]) that contains the index of each grid cell when flattened from a 2D array to a 1D array for the target state.</li> <li><strong><state-name>_<ssp>_params.csv: </strong>CSV file containing the calibration parameters (alpha_rural, beta_rural, alpha_urban, beta_urban; float) for the `population_gravity` model for each year from 2010-2100 in 10-year time-steps as described in the companion publication</li> </ul> </li> <li><strong>outputs</strong> contain the following: <ul> <li><strong>jones_oneill</strong> directory; these are the comparison datasets used to build Figures 7 and 8 in the companion publication <ul> <li>contains three directories: SSP2, SSP3, and SSP5 that each contain a GeoTIF representing total population (number of humans; float) at 1km resolution for years 2050 and 2100. <ul> <li><strong><state-name>_1km_<ssp>_total_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> </li> <li><strong>model</strong> directory; these are the model outputs from `population_gravity` for SSP2, SSP3, and SSP5 that each contain a GeoTIF representing urban, rural, and total population (number of humans; float) at 1km resolution for years 2020-2100 in 10-year time-steps. <ul> <li><strong><state-name>_1km_<ssp>_<urban, rural, or total>_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> </li> </ul> <p> </p> <p><strong>zoraghein-oneill_population_gravity_national-ssp-maps.zip</strong></p> <ul> <li>Results of the `population_gravity` model mosaicked to the National scale at a 1km resolution and the comparison Jones and O'Neill research. These are used to generate Figure 6 of the companion paper <ul> <li><strong>National_1km_<ssp>_<urban, rural, or total>_<year>_jones_oneill.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> <li><strong>National_1km_<ssp>_<urban, rural, or total>_<year>.tif:</strong> <ul> <li>value per grid cell: number of humans (float)</li> <li>crs: EPSG:102003 - USA_Contiguous_Albers_Equal_Area_Conic - Projected</li> <li>nodata value: -3.40282e+38</li> </ul> </li> </ul> </li> </ul> <p> </p>
Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii)
Cyclura ricordii is an endemic iguana from Hispaniola Island and is threatened on the IUCN Red List. The main threats are predation by introduced mammals, habitat destruction, and hunting pressure. The present study focused on two nesting sites from Pedernales Province in the Dominican Republic. The hypothesis that natal philopatry influences dispersal and nest site selection was tested. Monitoring and sampling took place in 2012 and 2013. Polymorphic markers were used to evaluate whether natal philopatry limits dispersal at multiple spatial scales. Ripley's K revealed that nests were significantly clustered at multiple scales, when both nesting sites were considered and within each nesting site. This suggests a patchy, non-random distribution of nests within nest sites. Hierarchical AMOVA revealed that nest site aggregations did not explain a significant portion of genetic variation within nesting sites. However, a small but positive correlation between geographic and genetic distance was detected using a Mantel's test. Hence, the relationship between geographic distance and genetic distance among hatchlings within nest sites, while detectable, was not strong enough to have a marked effect on fine scale genetic structure. Spatial and genetic data combined determined that the nesting sites included nesting females from multiple locations, and the hypothesis of 'natal philopatry', was not supported because females nesting in the same cluster were no more closely related to each other than to other females from the same nesting site. These findings imply that nesting aggregations are more likely associated with cryptic habitat variables contributing to optimal nesting conditions.
Data from: Microbiomes of a specialist caterpillar are consistent across different habitats but also resemble the local soil microbial communities
<p><b>Background</b>: Insect-associated microorganisms can provide a wide range of benefits to their host, but insect dependency on these microbes varies greatly. The origin and functionality of insect microbiomes is not well understood. Many caterpillars can harbor symbionts in their gut that impact host metabolism, nutrient uptake and pathogen protection. Despite our lack of knowledge on the ecological factors driving microbiome assemblages of wild caterpillars, they seem to be highly variable and influenced by diet and environment. Several recent studies have shown that shoot-feeding caterpillars acquire part of their microbiome from the soil. Here, we examine microbiomes of a monophagous caterpillar (<i>Tyria jacobaeae</i>) collected from its natural host plant (<i>Jacobaeae vulgaris</i>) growing in three different environments: coastal dunes, natural inland grasslands and riverine grasslands, and compare the bacterial communities of the wild caterpillars to those of soil samples collected from underneath each of the host plants from which the caterpillars were collected.</p> <p><b>Results</b>: The microbiomes of the caterpillars were dominated by Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Only 5% of the total bacterial diversity represented 86.2% of the total caterpillar's microbiome. Interestingly, we found a high consistency of dominant bacteria within the family Burkholderiaceae in all caterpillar samples across the three habitats. There was one amplicon sequence variant belonging to the genus <i>Ralstonia</i> that represented on average 53% of total community composition across all caterpillars. On average, one quarter of the caterpillar microbiome was shared with the soil.</p> <p><b>Conclusions</b>: We found that the monophagous caterpillars collected from fields located more than 100 kilometers apart were all dominated by a single <i>Ralstonia</i>. The remainder of the bacterial communities that were present resembled the local microbial communities in the soil in which the host plant was growing. Our findings provide an example of a caterpillar that has just a few key associated bacteria, but that also contains a community of low abundant bacteria characteristic of soil communities.</p>
Data from: Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: a case study across forest plant communities of Italy
Aim. To date, despite their great potential biogeographical regionalization models have been mostly developed on descriptive and empirical bases. This paper aims at applying the beta-diversity framework on a statistically representative data set to analytically test the consistency of the biogeographical regionalization of Italian forests. Location. Italy Taxon. Vascular plants Methods. Forest plant communities were surveyed in 804 plots made in a statistically representative sample of forest communities, made by 201 sites of Italian forests across the three biogeographical regions of the country: Alpine, Continental, and Mediterranean. We conducted an ordination analysis and an analysis of beta diversity, decomposing it into its turnover and nestedness components. Results. Our results provide only partial support to the consistency of the biogeographical regionalization of Italy. While the differences in forest plant communities support the distinction between the Alpine and the other two regions, differences between Continental and Mediterranean regions had lower statistical support. Pairwise beta-diversity and its turnover component are higher between- than within biogeographical regions. This suggests that different regional species pools contribute to assembly of local communities and that spatial distance between-regions has a stronger effect than that within-regions. Main conclusions. Our findings confirm a biogeographical structure of the species pools that is captured by the biogeographical regionalization. However, non-significant differences between the Mediterranean and Continental biogeographical regions suggest that this biogeographical regionalization is not consistent for forest plant communities. Our results demonstrate that an analytical evaluation of species composition differences among regions using beta-diversity analysis is a promising approach for testing the consistency of biogeographical regionalization models. This approach is recommended to provide support to the biogeographic regionalization used in some environmental conservation polices adopted by EU.
Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis
<p>We provide data and code needed to re-do the analyses and figures presented in our preprint <em>Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent </em>Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ):</p> <p>- data table : <em>data_repetition01.xls</em>, with informations about each column in the file <em>data_repetition_info.pdf</em></p> <p>- data table : <em>data_individual01.xls</em>, with informations about each column in the file <em>data_indivdual_info.pdf</em></p> <p><em>- </em>The R code used to do the analyses : <em>Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R</em></p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Data from: No biotic homogenisation across decades but consistent effects of landscape position and pH on macrophyte communities in boreal lakes
<p>It has been predicted that spatial beta diversity shows a decreasing trend in the Anthropocene due to increasing human impact, causing biotic homogenisation. We aimed to discover if vascular aquatic macrophyte communities show different spatial patterns in beta diversity in relation to land use and environmental characteristics in different decades from 1940s to 2010s. We aimed to discover if spatial structures differ between species-, phylogeny- and functional-based beta diversity. We used presence-absence data of aquatic macrophytes from five decades from small boreal lakes. We utilized generalised dissimilarity modelling to analyse spatial patterns in beta diversity in relation to environmental gradients. We found that lake elevation and pH were the most important variables in each decade, while land use was not particularly important in shaping beta diversity patterns. We did not find signs of a decreasing trend in spatial beta diversity in our study area during the past 70 years. We did not find signs of either biotic homogenisation or biotic differentiation (taxonomic, phylogenetic or functional). Vascular aquatic macrophyte communities showed only slightly different beta diversity patterns in relation to human impact across decades. The patterns of different facets of beta diversity diverged only slightly from each other. Lake position in the landscape, reflecting both natural connectivity and lake characteristics, explained the patterns found in beta diversity, probably because our study area has faced only modest changes in land use from 1940s to 2010s when compared globally. Our study highlights the fact that biotic homogenisation is not an unambiguous process acting similarly at all spatial and temporal scales or in different environments and different organism groups.</p>
Data from: Consistent condom use among highly effective contraceptive users in an HIV-endemic area in rural Kenya
<p><strong>Background</strong>: Women of reproductive age are at the highest risk of both HIV infection and unintended pregnancy in sub-Saharan Africa. Highly effective contraceptives (HECs) such as hormonal injectable and implants are widely used in this region. HECs are effective for preventing pregnancies. However, unlike condoms, HECs offer no protection against HIV. Dual-method use, or the use of condoms with HECs, is an ideal option to reduce HIV risk but is infrequently practiced. Rather, women tend not to use condoms when they use HECs and increase their HIV risk from their sexual partners. However, it remains unknown whether HIV status affects such tendency. Given the increasing popularity of HECs in sub-Saharan Africa, this study examined the association between the use of HECs and condom use among HIV-positive and negative women. Methods: A cross-sectional study was conducted among 833 sexually active women aged 18-49 years, recruited from six clinics in Siaya county, Kenya. From March to May 2017, female research assistants interviewed the women using a structured questionnaire. Multiple logistic regression analysis was conducted to examine the association between HEC use and consistent condom use in the past 90 days, adjusting for potential confounders. It was also examined with regular partners (husbands or live-in partners) and non-regular partners, separately. In addition, a sub-sample analysis of HIV-negative or unknown women was conducted. Results: In total, 735 women were available for the analysis. Among the women, 231 (31.4%) were HIV-positive. HIV-positive women were more likely to use HECs than HIV-negative or status unknown women (70.1% vs. 61.7%, p=0.027). HEC use was significantly associated with decreased condom use with a regular partner (adjusted odds ratio (AOR)=0.25; 95% CI 0.15-0.43, p<0.001) and a non-regular partner (AOR=0.25; 95% CI 0.11-0.58, p=0.001). However, compared with HIV-negative or status unknown women, HIV-positive women were more likely to use HECs and condoms consistently with a regular partner (AOR=6.54, 95% CI 2.15-20.00, p=0.001). Other factors significantly associated with consistent condom use included partner's positive attitude toward contraception, partner's HIV-positive status, high HIV risk perception, and desire for children in the future. Conclusion: Dual-method use was limited among HIV-negative women and women who had HIV-negative partners due to inconsistent condom use. The use of HECs was significantly associated with decreased condom use, regardless of partner type and their HIV status. Due to this inverse association, HIV-negative women may increase their HIV risk from their sexual partners. Therefore, interventions should be strengthened to reduce their dual risks of HIV infection and unintended pregnancy by promoting dual-method use. Family planning services should strengthen counseling on the possible risk of HIV infection from their sexual partners and target not only women but also their partners, who may play a key role in condom use.</p>
Data from: Consistent declines in wing lengths of Calidridine sandpipers suggest a rapid morphometric response to environmental change
A recent study demonstrated that semipalmated sandpiper (Calidris pusilla) wing lengths have shortened from the 1980s to the present-day. We examined alternative and untested hypotheses for this change at an important stopover site, James Bay, Ontario, Canada. We evaluated morphometric patterns in wing length and bill length by age and sex, when possible, and assessed if wing shape has also changed during this time-period. We investigated patterns of morphological change in two additional Calidridine sandpipers, white-rumped sandpipers (Calidris fuscicollis) and least sandpipers (Calidris minutilla), to determine if shorter wing lengths are a widespread pattern in small sandpipers. We also examined allometric changes in wing and bill lengths to clarify if wing length declines were consistent with historical scaling relationships and indicative of a change in body size instead of only wing length change. We found that including sex and wing shape in analyses revealed important patterns in morphometric change for semipalmated sandpipers. Wing lengths declined for both sexes, but the magnitude of decline was smaller and not significant for males. Additionally, semipalmated sandpiper wings have become more convex, a shape that increases maneuverability in flight. Wing lengths, but not bill lengths, declined for most species and age classes, a pattern that was inconsistent with historical allometric scaling relationships. For juvenile semipalmated sandpipers, however, both bill and wing lengths declined according to historical scaling relationships, which could be a consequence of nutritional stress during development or a shift in the proportion of birds from smaller-sized, western breeding populations. Except for juvenile semipalmated sandpipers, we did not find evidence for an increase in the proportion of birds from different breeding populations at the stopover site. Given the wide, hemispheric distribution of these sandpipers throughout their annual cycles, our results, paired with those from a previous study, provide evidence for wide-spread reduction in wing lengths of Calidridine sandpipers since the 1980s. The shorter wing lengths and more convex wing shapes found in this study support the hypothesis that selection has favored more maneuverable wing morphology in small sandpipers.
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.