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1,551 results for “Availability”
Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability
<p>Prophages, viral sequences integrated into bacterial genomes, can confer fitness benefits and costs. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding about the selective forces that maintain prophages in bacterial populations is scarce. Combining experimental evolution with stochastic modelling we found that prophage maintenance and loss are primarily determined by environmental conditions that amplify the net fitness effect of the prophage. Whole genome sequencing revealed that prophage loss occurs through environment-specific sequences of selective sweeps, leading to rapid prophage loss when prophages are costly. However, conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can prolong prophage maintenance. The extent of prolonged maintenance depends on the sociality of this accessory gene. Selection for non-cooperative genes is more effective for prophage maintenance as cooperative genes allow for protection of phage-free 'cheaters' that may emerge if prophage costs outweigh their benefits. Our mathematical model suggests that environmental variation plays a larger role than mutation rates in determining prophage maintenance. This challenges our understanding of the role of random chance events relative to environmental factors in shaping the evolutionary trajectory of bacterial populations.</p>
Data supporting "Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence"
<p>Data supporting </p> <p><strong>Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence </strong></p> <p>E. M. Windels, L. Cool, E. Persy, J. Swinnen, P. Matthay, B. Van den Bergh, T. Wenseleers, J. Michiels</p> <p>Version April 16th, 2024</p>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
Data for: Brown juice assisted ensiling of straw and press cake for enhanced biogas production and nutrient availability in digestates
<p>Data for: <span>Brown juice assisted ensiling of straw and press cake for enhanced biogas production and nutrient availability in digestates (https://doi.org/10.1016/j.eti.2023.103248)</span></p>
Data from: Effects of resource availability and interspecific interactions on Arctic and red foxes' winter use of ungulate carrion in the Fennoscandian low-Arctic tundra
<p>In the Arctic tundra, predators face recurrent periods of food scarcity and often turn to ungulate carcasses as an alternative food source. As important and localized resource patches, carrion promotes co-occurrence of different individuals, and its use by predators is likely to be affected by interspecific competition. We studied how interspecific competition and resource availability impact winter use of carrion by Arctic and red foxes in low Arctic Fennoscandia. We predicted that presence of red foxes limits Arctic foxes' use of carrion, and that competition depends on the availability of other resources. We monitored Arctic and red fox presence at supplied carrion using camera traps. From 2006 to 2021, between 16 and 20 cameras were active for two months in late winter (288 camera-winters). Using a multi-species dynamic occupancy model at a week-to-week scale, we evaluated use of carrion by foxes while accounting for the presence of competitors, rodent availability and supplemental feeding provided to Arctic foxes. Competition affected carrion use by increasing both species' probability to leave occupied carcasses sites between consecutive weeks. This increase was similar for the two species, suggesting symmetrical avoidance. Increased rodent abundance was associated with a higher probability of colonizing carrion sites for both species. For Arctic foxes, however, this increase was only observed at carcasses unoccupied by red foxes, showing greater avoidance when alternative preys are available. Supplementary feeding increased Arctic foxes' carrion use, regardless of red fox presence. Contrary to expectations, we did not find strong signs of asymmetric competition for carrion in winter, which suggests that interactions for resources at a short time scale are not necessarily aligned with interactions at the scale of the population. In addition, we found that competition for carcasses depends on the availability of other resources, suggesting that interactions between predators depend on the ecological context.</p>
Dataset for "Assessing the availability and feasibility of renewable energy on the Great Barrier Reef-Australia"
<p>This repository contains all the dataset used in "Assessing the availability and feasbility of renewable energy on the Great Barrier Reef-Australia"</p>
Abiotic conditions along altitude shape plant-fungal associations by influencing both fungal availability and association strength
<p>These files contains the description of the data and scripts to reproduce the analyses of:<br>"Abiotic conditions along altitude shape plant-fungal associations by influencing both fungal availability and association strength" which can be found here: <a href="https://doi.org/10.1111/1365-2745.70075">https://doi.org/10.1111/1365-2745.70075</a></p> <p>As detailed in the study, the data consist of fungal DNA data from ten high and low <em>Bistorta vivipara </em>populations across Fennoscandia. Species-level fungal OTUs have been identified applying ITS2-based metabarcoding to the different parts of the focal plant <em>B. vivipara </em>(bulbils, leaves and roots) and its surrounding soil and leaves of surrounding plants. In total, the data contains data on 253 fungal OTUs across 641 sampling units.</p> <p>The README file describes the contents of the metadata and explains how the scripts are to be run in order to reproduce the results of the study.</p> <p> </p>
Light availability and light demand of plants shape the arbuscular fungal communities in their roots
<p>Plants involved in the arbuscular mycorrhizal (AM) symbiosis trade photosynthetically derived carbon for fungal-provided soil nutrients. However, little is known about how plant light demand and ambient light conditions influence root-associating AM fungal communities.</p> <p>We conducted a manipulative field experiment to test whether plants' shade tolerance influences their root AM fungal communities in open and shaded grassland sites. We found similar light-dependent shifts shifts in AM fungal community structure for experimental bait plant roots and the surrounding soil. Yet, deviation from the sorrounding soil towards lower AM fungal beta-diversity in the roots of shade-intolerant plants in shade suggested preferential carbon allocation to specific AM fungi in conditions where plant-assimilated carbon available to fungi was limited. We conclude that favourable environmental conditions widen the plant biotic niche, as demonstrated here with optimal light availability reducing plants' selectivity for specific AM fungi, and promote compatibility with a larger number of AM fungal taxa.</p> <p>The deposited dataset contains the raw fungal sequence table for each sample and information on the characteristics of the sample (light treatment, sample type, sampling point in time etc).</p>
Dataset: Improving the prediction of fertilizer phosphorus availability to plants with simple, but non-standardized extraction techniques
<p>Dataset: Improving the prediction of fertilizer phosphorus availability to plants with simple, but non-standardized extraction techniques</p>
Availability and use of technology for e-learning in Bangladesh
<p>There are 1162 responses in the dataset. Respondents’ gender, division, and residence were obtained. Here, 6 items stand (“availability_item_1” to “availability_item_6”) for availability and 11 items (“usability_item_1” to “usability_item_11”) for use of technology measure, where the initial responses were in 5 points Likert scale (1 for “strongly disagree” and 5 for “strongly agree”). On the other hand, 14 items’ (“pss_item_1” to “pss_item_14”) PSS scale was used for measuring stress, where responses were also in five-point Likert scale (0 for “Never” and 4 for “Very often”). However, reverse scoring for items 4, 5, 7, & 8 are given in this data set, according to the instruction of scale scoring. In the dataset, “availability_item_1_binary” to “availability_item_6_binary” and “usability_item_1_binary” to “usability_item_11_binary” represent the categories (1 for “sub-optimum” and 2 for “optimum”) of the availability and usability of technology measure.</p>
An Empirical Study on the Usage and Availability of Machine Learning Libraries in Open-Source Python Projects - Dataset
<p>This repository contains the dataset of the manuscript:</p> <p>"An Empirical Study on the Usage and Availability of Machine Learning Libraries in Open-Source Python Projects"</p>
Earthworm abundance and availability does not influence the reproductive decisions of black-tailed godwits in an agricultural grassland
<ol> <li>Maintaining the biodiversity of agricultural ecosystems has become a global imperative. Across Europe, species that occupy agricultural grasslands, such as Black-tailed Godwits (<i>Limosa limosa limosa</i>), have undergone steep population declines. In this context, there is a significant need to both determine the root causes of these declines and identify actions that will promote biodiversity while supporting the livelihoods of farmers.</li> <li>Food availability, and specifically earthworm abundance (Lumbricidae), during the pre-breeding period has often been suggested as a potential driver of godwit population declines. Previous studies have recommended increasing the application of nitrogen to agricultural grasslands to enhance earthworm populations and aid agricultural production. Here we test whether food availability during the pre-breeding period affects when and where godwits breed.</li> <li>Using large-scale surveys of food availability, a long-term mark-recapture study, focal observations of foraging female godwits, and tracking devices that monitored godwit movements, we found little evidence of a relationship between earthworm abundance and the timing of godwit reproductive efforts or the density of breeding godwits. Furthermore, we found that the soils of intensively managed agricultural grasslands may frequently be too dry for godwits to forage for those earthworms that are present.</li> <li>The increased application of nitrogen to agricultural grasslands will therefore likely have no positive effects on godwit populations. Instead, management efforts should focus on increasing the botanical diversity of agricultural grasslands, facilitating conditions that prevent hardening soils, and reducing the populations of generalist predators.</li> </ol>
List of publicly available cellular reprogramming HTS datasets
<p>These datasets were obtained by manual curation via the following procedure: First, I queried GEO using keywords in the list below. </p> <ol> <li>Yamanaka</li> <li>Yamanaka AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>Reprogramming AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>OSKM AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>Sox2 AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>Sox2 reprogramming AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>somatic reprogramming AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>somatic cell reprogramming AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>Reprogramming pluripotency AND ("Genome binding/occupancy profiling by high throughput sequen"[Filter]) </li> <li>Reprogramming pluripotency </li> <li>Reprogramming pluripotency AND ("Methylation profiling by high throughput sequencing"[Filter]) </li> <li>OSKM AND ("Methylation profiling by high throughput sequencing"[Filter]) </li> <li>Sox2 Reprogramming AND ("Methylation profiling by high throughput sequencing"[Filter]) </li> </ol> <p>Results were selected for manual input if they contained either transcriptomic (e.g., RNA-Sequencing) or epigenomics (e.g., RRBS) data and had at least one intermediate cellular reprogramming timepoint. </p> <p> </p>
anabreuinsp/Code-availability-: Code availability for the paper Seroprevalence in Mexico published in nature communication.
<p>Here you can find two do-file (.do) in stata to run the main analysis and the sensitivity analysis to take into account a possible response bias. In both cases, after running the script, you need to adjust for sensitivity and specificity of the test, using the excel file that generates confidence intervals. The provided excel file (.xlsx) contains the in-house' sensitivity and specificity. If you want to run the manufacturer test performance (another sensitivity analysis) you need to change the values in D6, D7, E6, E7, F6, and F7. The database in .dta is provided to run the sensitivity analysis.</p>
Decay by ectomycorrhizal fungi couples soil organic matter to nitrogen availability
<p>Interactions between soil nitrogen (N) availability, fungal community composition, and soil organic matter (SOM) regulate soil carbon (C) dynamics in many forest ecosystems, but context dependency in these relationships has precluded general predictive theory. We found that ectomycorrhizal (ECM) fungi with peroxidases decreased with increasing inorganic N availability across a natural inorganic N gradient in northern temperate forests, whereas ligninolytic fungal saprotrophs exhibited no response. Lignin-derived SOM and soil C were negatively correlated with ECM fungi with peroxidases and were positively correlated with inorganic N availability, suggesting decay of lignin-derived SOM by these ECM fungi reduced soil C storage. The correlations we observed link SOM decay in temperate forests to tradeoffs in tree N nutrition and ECM composition, and we propose SOM varies along a single continuum across temperate and boreal ecosystems depending upon how tree allocation to functionally distinct ECM taxa and environmental stress covary with soil N availability.</p>
No impact of biocontrol agent's predation cues on development time or size of surviving Aedes albopictus under optimal nutritional availability
<p>Cyclopoid copepods have been applied successfully to limit populations of highly invasive <em>Aedes albopictus</em> mosquitoes that can transmit diseases of public health importance. However, there is concern that changes in certain mosquito traits, induced by exposure to copepod predation, might increase the risk of disease transmission. In this study, third instar <em>Ae. albopictus</em> larvae, hereafter referred to as "focal individuals", were exposed to <em>Megacyclops viridis</em> predator cues associated with both consumption of newly-hatched mosquito larvae and attacks on focal individuals. The number of newly-hatched larvae surrounding each focal larva was held constant to control for density effects on size, and the focal individual's day of pupation and wing length were recorded for each replicate. Exposing late instar <em>Ae. albopictus</em> to predation decreased their chances of surviving to adulthood, and three focal larvae that died in the predator treatment showed signs of melanization, indicative of wounding. Among surviving focal <em>Ae. albopictus</em>, no significant difference in either pupation day or wing length was observed due to copepod predation. The absence of a significant sublethal impact from <em>M. viridis</em> copepod predation on surviving later-stage larvae in this analysis supports the use of <em>M. viridis</em> as a biocontrol agent against <em>Ae. albopictus</em>.</p>
Data for: Habitat diversity, resource availability, and island age in the species-area relationship
<p><strong>Aim: </strong>The island species-area relationship (ISAR) and its theoretical justifications assume the area of islands to be homogeneous across an archipelago, which is generally not the case. We compare the performance of models that adjust or substitute for island area with measures of habitat diversity, island age, and resource availability to account for the violation of this assumption. We further compare the performance of models for two taxonomic groups.</p> <p><strong>Location: </strong>Five hotspot archipelagos (Azores, Galapagos, Hawaii, Cape Verde, Canary Islands).</p> <p><strong>Taxa:</strong> Vascular plants and birds.</p> <p><strong>Methods: </strong>We used the mathematical framework of the power law to compare relevant models, treating the one containing only area as a null model against which others were compared. Data was collated from the GIFT database and from the literature. Models were compared using linear regression within archipelagos and via mixed effect models with archipelago as a random effect.</p> <p><strong>Results:</strong> Weighting of island area by habitat diversity and resource availability systematically improved statistical significance and model fits versus the area only power law. Models including island age did not show the same systematic improvement in model fits. For vascular plants, weighting islands by resource availability (energy and water) performed better than weighting by habitat diversity, although for birds these weightings performed equally well.</p> <p><strong>Main Conclusions:</strong> Given that islands within archipelagos are fairly uniform in climate, topography, and geology, it is worth accounting for this in ISARs. Our results suggest that, for islands in volcanic hotspot archipelagos this is best done by using direct measures of habitat diversity and resource availability rather than using island age as a proxy. Because weighting area by habitat diversity and resource availability produced better predictors of species diversity, the proposed approach may be particularly valuable in conservation science.</p>
Data from: Influences of summer warming and nutrient availability on Salix glauca L. growth in Greenland along an ice to sea gradient
<p>The combined effects of climate change and nutrient availability on Arctic vegetation growth are poorly understood. Archaeological sites in the Arctic could represent unique nutrient hotspots for studying the long-term effect of nutrient enrichment. In this study, we analysed a time-series of ring widths of <em>Salix glauca</em> L. collected at nine archaeological sites and in their natural surroundings along a climate gradient in the Nuuk fjord region, Southwest Greenland, stretching from the edge of the Greenlandic Ice Sheet in the east to the open sea in the west. We assessed the temperature-growth relationship for the last four decades distinguishing between soils with past anthropogenic nutrient enrichment (PANE) and without (controls). Along the East–West gradient, the inner fjord sites showed a stronger temperature signal compared to the outermost ones. Individuals growing in PANE soils had wider ring widths than individuals growing in the control soils and a stronger climate-growth relation, especially in the inner fjord sites. Thereby, the individuals growing on the archaeological sites seem to have benefited more from the climate warming in recent decades. Our results suggest that higher nutrient availability due to past human activities plays a role in Arctic vegetation growth and should be considered when assessing both the future impact of plants on archaeological sites and the general greening in landscapes with contrasting nutrient availability.</p>
Ignoring species availability biases occupancy estimates in single-scale occupancy models
<p>1. Most applications of single-scale occupancy models do not differentiate between availability and detectability, even though species availability is rarely equal to one. Species availability can be estimated using multi-scale occupancy models, and the availability process includes elements of species movement, behavior, and phenology. However, for the practical application of multi-scale occupancy models, it can be unclear what a robust sampling design looks like and what the statistical properties of the multi-scale and single-scale occupancy models are when availability is less than one.</p> <p>2. Using simulations, we explore the following common questions asked by ecologists during the design phase of a field study: (Q1) what is a robust sampling design for the multi-scale occupancy model when there are <i>a priori</i> expectations of parameter estimates?, (Q2) what is a robust sampling design when we have no expectations of parameter estimates?, and (Q3) can a single-scale occupancy model with a random effects term adequately absorb the extra heterogeneity produced when availability is less than one and provide reliable estimates of occupancy probability?.</p> <p>3. Our results show that there is a tradeoff between the number of sites and surveys needed to achieve a specified level of acceptable error for occupancy estimates using the multi-scale occupancy model. We also document that when species availability is low (< 0.40 on the probability scale), then single-scale occupancy models underestimate occupancy by as much as 0.40 on the probability scale, produce overly precise estimates, and provide poor parameter coverage. This pattern was observed when a random effects term was and was not included in the single-scale occupancy model, suggesting that adding a random-effects term does not adequately absorb the extra heterogeneity produced by the availability process. In contrast, when species availability was high (> 0.60), single-scale occupancy models performed similarly to the multi-scale occupancy model.</p> <p>4. As a companion, we provide an RShiny app that allows users to further explore our results and sampling designs across a number of different scenarios <a href="https://gdirenzo.shinyapps.io/multi-scale-occ/"><span>https://gdirenzo.shinyapps.io/multi-scale-occ/</span></a>. Our results suggest that unaccounted for availability can lead to underestimating species distributions when using single-scale occupancy models, which can have large implications on ecological inference and predictions for practitioners, such as those working at the front lines of invasion ecology, disease emergence, and species conservation. </p>
Water security in an uncertain future: contrasting realities from an availability-demand perspective
<p>Here we provide the climate change data from the Coupled Model Intercomparison Project phase 6 (CMIP6) used in an assessment of future water security of two Brazilian basins: Guariroba River basin and Jaguari River basin responsible for supplying water to Campo Grande city and the São Paulo Metropolitan Region, respectively. The basins' hydrological response was simulated using the SWAT+ model considering three climate change scenarios from a CMIP6 multimodel ensemble: SSP2-4.5 (medium forcing), SSP3-7.0 (high forcing), and SSP5-8.5 (high forcing). The ensemble was constructed using seven General Circulation/Earth System models (variant ID r1i1p1f1 and further processed for bias correction using quantile delta mapping.</p> <p>The manuscript of "<em>Water security in an uncertain future: contrasting realities from an availability-demand perspective</em>" has been published in <strong>Water Resources Management</strong>, please find it <a href="https://doi.org/10.1007/s11269-022-03160-x">here</a>.</p>
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.