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7,742 results for “individuals”
Data from: Fencing amplifies individual differences in movement with implications on survival for two migratory ungulates
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Data From: Effects of disease on foraging behaviour and success in an individual free-ranging northern elephant seal
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Manual annotation of individual ovenbirds in acoustic recordings
This dataset includes acoustic recordings and annotations of those recordings for individually identified Ovenbird songs (Seiurus aurocapilla) created from annotating randomly selected passive acoustic monitoring recordings, largely collected in Alberta, CA. Every Ovenbird song within each recording is tagged in time and frequency. Each Ovenbird tag is labeled with individual identity a number corresponding to each individual’s order of appearance in the recording. If no Ovenbirds were not detected in a given recording, the recording was labeled at approximately 2 seconds into the recording with a three-second long tag containing species label “NONE.” Recordings contain other species’ songs, but no other species are tagged. This dataset was annotated via the WildTrax interface (https://wildtrax.ca/) and can also be found at https://portal.wildtrax.ca/home/aru-tasks.html?sensorId=ARU&projectId=623. These recordings were intended to be used for studies of individual ID, but can be used for a variety of other applications, including count data, song rate and vocal activity, and migratory phenology. Because each individual Ovenbird is numbered, these data can be also be transformed into count data or used to estimate individual Ovenbirds’ song rates. Data were randomly selected with respect to recording time, recording date, and recording location. Because recording time was randomly selected, the dataset can be used to estimate Ovenbird vocal activity over the course of a day. Because recordings were selected from a date range that includes dates before Ovenbirds are likely to be present in Alberta, the dataset can be used to estimate phenology of Ovenbird migration. This dataset is intended as an example open access labeled dataset to encourage development in the field of acoustic individual identification (Knight et al. In Revision for Trends in Ecology and Evolution).
Individual tree height and diameter measurements of Birch spp. in central Sweden (2005 - 2022)
The spacing trial in Skräddarbo was established in 1989 on former agricultural land, testing four square spacing configurations: 1.3 × 1.3 m, 1.5 × 1.5 m, 1.8 × 1.8 m, and 2.6 × 2.6 m. Each spacing treatment was replicated four times for both silver birch and downy birch, totaling 32 plots across approximately 1.2 hectares. Each plot was planted with 100 seedlings, with varying plot sizes based on spacing. Species were randomly assigned to pre-determined plot locations. Data collection began in 2005 and continued annually until 2022 (except 2021). The data includes individual tree height, diameter and living crown measurements. Diameter measurements were recorded cross-sectionally, using a digital caliper, whereas tree height and living crown measurements were done using a hypsometer (Haglöf Vertex Laser Geo). Additional variables include plot area, tree id numbers and other constant variables. The data package is complete with the last revision done by the author in 2022.
Effects of stem canker disease on N fixation inputs by Alnus tenuifolia to early-successional floodplains in interior and south-central Alaska. II. Nodule biomass and incidence of canker for individual genets.
This dataset contains nodule biomass and incidence of canker infection for individual genets of Alnus tenuifolia as part of a project studying disease-mediated declines in N-fixation inputs by Alnus tenuifolia to early-successional floodplains in interior and south-central Alaska
SGS-LTER Ecosystem Stress Area - Aboveground Biomass: Interactions between individual plant species and soil nutrient status in shortgrass steppe on the Central Plains Experimental Range in Nunn, Colorado, USA 1991
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. The effect of plant community structure on nutrient cycling is fundamental to our understanding of ecosystem function. We examined the importance of plant species and plant cover (i.e. plant covered microsites vs bare soil) on nutrient cycling in shortgrass steppe of northeastern Colorado. We tested the effects of both plant species and cover on soils in an area of undisturbed shortgrass steppe and an area that had undergone nitrogen and water additions from 1971 to 1974, resulting in significant shifts in plant species composition.
SGS-LTER Ecosystem Stress Area - Belowground Biomass: Interactions between individual plant species and soil nutrient status in shortgrass steppe on the Central Plains Experimental Range in Nunn, Colorado, USA 1991
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. The effect of plant community structure on nutrient cycling is fundamental to our understanding of ecosystem function. We examined the importance of plant species and plant cover (i.e. plant covered microsites vs bare soil) on nutrient cycling in shortgrass steppe of northeastern Colorado. We tested the effects of both plant species and cover on soils in an area of undisturbed shortgrass steppe and an area that had undergone nitrogen and water additions from 1971 to 1974, resulting in significant shifts in plant species composition. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83317.
Data for: Does migration distance influence intra-individual variation in migratory behaviour in a seabird species with diverse migration strategies?
<p>GPS tracking data from adult lesser black-backed gulls (<em>L. fuscus) </em>with 2 – 7 years of tracking data per individual from several colonies in the Netherlands, Belgium and the UK. This data has gone through initial cleaning to remove faulty GPS locations was combined with meta data from colonies to create a single .RDS file. </p> <p>Result for the manuscript "High repeatability in migratory behaviours in a generalist seabird regardless of migration strategy" can be obtained from this data using the R scripts at https://github.com/jbrow247/LBBG_MigrationPlasticity_Pub. </p>
Individual skyrmion manipulation by local magnetic field gradients - Dataset
<p>Dataset for the article: Casiraghi A, Corte-León H, Vafaee M, Garcia-Sanchez F, Durin G, Pasquale M, Jakob G, Kläui M and Kazakova O 2019 Individual skyrmion manipulation by local magnetic field gradients 25–7. DOI: 10.1038/s42005-019-0242-5.</p> <p>The data is divided in figures and for each figure we report the raw data and the python code to analyse it.</p>
Results "Anti-obesity effects of individual or combination treatment with Spirulina platensis and green coffee bean aqueous extracts in high-fat diet-induced obese rats"
<p><strong>Background</strong>: Obesity, a chronic disease, is associated with serious health risks, including premature mortality. This study aimed to investigate the anti-obesity effects of individual or combination treatment with <em>Spirulina platensis</em> and green coffee bean aqueous extracts in high-fat diet-induced (HFD) obese rats.</p> <p><strong>Methods</strong>: Rats were fed on HFD to induce obesity. Corn oil in the HFD accounted for 50.98 % of the calories. Fifty rats were divided into the following five groups (10 rats/group): control, HFD, HFD-<em>Spirulina</em>, HFD-coffee, HFD-<em>Spirulina</em> and coffee co-treatment groups. The serum levels of lipid, leptin, and insulin, as well as the hepatic mRNA levels of fatty acid synthase (FAS), peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α), and peroxisome proliferator-activated alpha receptor (PPARα) were estimated.</p> <p><strong>Results</strong>: The <em>Spirulina</em> and/or green coffee bean aqueous extracts decreased the final bodyweight and liver weight, and the serum levels of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase. Additionally, the extracts decreased the serum levels of total cholesterol, triacylglycerol, low-density lipoprotein-cholesterol, leptin, and glucose, and enhanced the serum insulin level. Furthermore, the extracts enhanced the PGC-1α and PPARα mRNA levels and decreased the FAS mRNA levels.</p> <p><strong>Conclusion</strong>: The individual or combination treatment with <em>Spirulina</em> and green coffee bean extracts decreased obesity-induced hyperlipidemia. Thus, <em>Spirulina platensis</em> and green coffee can be potentially used to treat obesity.</p>
Data from: Cooperation with closely bonded individuals reduces cortisol levels in long-tailed macaques
<p><span>Many animal species cooperate with conspecifics in various social contexts. While ultimate causes of cooperation are being studied extensively, its proximate causes, particularly endocrine mechanisms, have received comparatively little attention. Here, we present a study investigating the link between the hormone cortisol, cooperation and social bonds in long-tailed macaques (<i>Macaca fascicularis</i>). We tested 14 macaques in a dyadic cooperation task (loose-string paradigm), each with two partners of different social bond strength and measured their salivary cortisol before and after the task. We found no strong link between the macaques' cortisol level before the task and subsequent cooperative success. In contrast, we did find that the act of cooperating in itself led to a subsequent decrease in cortisol levels, but only when cooperating with closely bonded individuals. Two control conditions showed that this effect was not due to the mere presence of such an individual or the pulling task itself. Consequently, our study shows an intricate way in which the hypothalamic-pituitary-adrenal axis is involved in cooperation. Future studies should reveal whether and how our findings are driven by the anxiolytic effect of oxytocin, which has been associated with social bonding.</span></p>
Individual multilocus genotypes of three translocated and two source populations of Arnica montana in southern Belgium
<p>Individual multilocus genotypes based on nine microsatellite loci measured in the framework of a genetic monitoring of translocated populations of the critically endangered Arnica montana. See Van Rossum et al. (2020) in Molecular Ecology for more details.</p>
Data from: Among-individual and within-individual variation in seasonal migration covaries with subsequent reproductive success in a partially-migratory bird
<p>Within-individual and among-individual variation in expression of key environmentally-sensitive traits, and associated variation in fitness components occurring within and between years, determine the extents of phenotypic plasticity and selection and shape population responses to changing environments. Reversible seasonal migration is one key trait that directly mediates spatial escape from seasonally-deteriorating environments, causing spatio-seasonal population dynamics. Yet, within-individual and among-individual variation in seasonal migration versus year-round residence, and dynamic associations with subsequent reproductive success, have not been fully quantified. We used novel capture-mark-recapture mixture models to assign individual European shags (Phalacrocorax aristotelis) to 'resident, 'early migrant' or 'late migrant' strategies in two consecutive years, using year-round local resightings. We demonstrate substantial among-individual variation in strategy within years, and directional within-individual change between years. Further, subsequent reproductive success varied substantially among strategies, and relationships differed between years; residents and late migrants had highest success in the two years respectively, matching the years in which these strategies were most frequently expressed. These results imply that migratory strategies can experience fluctuating reproductive selection, and that flexible expression of migration can be partially aligned with reproductive outcomes. Plastic seasonal migration could then potentially contribute to adaptive population responses to currently changing forms of environmental seasonality.</p>
Data from: Along with intraspecific functional trait variation, individual performance is key to resolving community assembly processes
<ol> <li>Species contributing high proportions to community biomass strongly influence ecosystem processes within the community. Studies have shown that dominant species may serve as nurse plants, helping to ensure biomass stability of the subordinate species under stress conditions. The question is widely debated as to whether either niche differentiation or neutral processes drive the net outcome of plant interactions within a subordinate plant community. To answer this question, requires precise estimates of individual variation in functional traits and performance.</li> <li>In a five-year mesocosm experiment, the functional responses of a subordinate plant community to the removal of the dominant species were evaluated across two drought-stress scenarios. Small scale (i.e., large pots) wetland communities were constructed comprising one dominant species (Carex elata) and three subordinate species. Removal of the dominant species allowed evaluation of the net effects of drought and interspecific interactions. We estimated the functional divergences for three traits (specific leaf area, leaf dry matter content and height growth allocation) and compared these with performance differences quantified individually. This enabled distinctions to be made between deterministic (i.e., niche differentiation) and neutral processes driving the drought response of the subordinate community.</li> <li>We showed that the dominant species decreased relative performance differences within the subordinate plant community under conditions of permanent drought stress. These changes were associated with the convergence of traits related to resource acquisition and growth. The dominant species equalised species performance differences by supressing relatively drought-tolerant species with low competitive ability and by supporting the less drought-tolerant species with relatively high competitive ability. Meanwhile, under conditions of interannual drought, the subordinate species likely coexisted due to differentiation in resource-use strategies and the interaction with the dominant species.</li> <li>Inclusion of individual variation in performance with a functional trait approach provides valuable insights into the processes structuring plant communities. Ours is the first study to provide evidence that subordinate species exposed to drought may coexist via neutral processes arising from their interactions with the dominant species, leading to functional convergence of traits associated with the trade-off between stress tolerance and competitive ability.</li> </ol>
Code for individual-based simulations in "Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios"
<p>Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size, and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change, or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.</p>
Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon vaccination
<p>Data set accompanying the publication "Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon vaccination".</p> <p>In this study, we utilize high-throughput sequencing to profile the memory CD4 TCRβ repertoire and track vaccine-specific and epitope-specific TCRβ clonotypes following the de novo administration of hepatitis B (HepB) vaccine in healthy HepB-naïve individuals.</p> <p>The data set is comprised out of the following parts:</p> <ul> <li>repTCRb: Folder containing CD4+ TCR repertoire data from volunteers. Some of these samples are also available in ImmuneAccess (https://clients.adaptivebiotech.com/pub/deneuter-2018-cmvserostatus).</li> <li>peptideTCRab: Folder containing peptide-specific or peptide-pool-specific TCR data</li> <li>df_all: Meta and FC data for samples and volunteers</li> <li>freqCD154: CD154-based group definitions</li> <li>groups.csv: Group definitions used for classes</li> </ul>
Microfluidic monitoring of the growth of individual hyphae in confined environments
Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass, and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared to measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behavior of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to adress its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
3D photogrammetric reconstructions of individual chickpea plants
<p>3D point clouds and meshed models of individual chickpea plants were reconstructed using photogrammetry. This dataset serves as a companion to the article “Open source 3D phenotyping of chickpea plant architecture across plant development” uploaded as a preprint to <em>BioRxiv</em> (<a href="https://doi.org/10.1101/2020.09.08.288530">https://doi.org/10.1101/2020.09.08.288530</a>).</p> <p><strong>Description of the dataset</strong></p> <p>Individual chickpea plants were imaged using a low-cost, automated turntable and camera set up. Dense point clouds were generated in <a href="http://ccwu.me/vsfm/">VisualSFM</a>, these point clouds were cleaned (denoised and non-plant points removed), scaled and then meshed using a ball-pivoting algorithm. More information on the imaging and reconstruction workflow can be found in our <em>BioRxiv</em> preprint (<a href="https://doi.org/10.1101/2020.09.08.288530">https://doi.org/10.1101/2020.09.08.288530</a>). Scaled, clean point clouds and meshed models are provided in this dataset. All files are in the .PLY format and can be viewed using most 3D imaging software packages, including <a href="https://github.com/cnr-isti-vclab/meshlab">Meshlab</a>.</p> <p>Files are named using the following convention:<br> "GENOTYPE_PLANTIDNUMBER_GROUNDTRUTHINGORWEEKS_POINTCLOUDORMESHED"<br> Where:<br> GENOTYPE is the chickpea genotype.<br> PLANTIDNUMBER is the unique identifier for each plant.<br> GROUNDTRUTHINGORWEEKS refers to whether the plant was used for validation against ground truthing measurements or if growth was tracked after germination.<br> POINTCLOUDORMESHED refers to if the .ply file is a dense point cloud or a meshed 3D model.</p> <p><strong>Plant material</strong></p> <p>Three commercial Australian chickpea cultivars (Genesis Kalkee, PBA Hattrick and PBA Slasher) were grown in pots in a glasshouse and were imaged once per week for five weeks after germination. Three genotypes selected from local and international sources (ICC5878, SonSla and PUSA76) were grown in pots outdoors and were imaged once at five weeks post germination.</p>
Seasonality and interspecific competition shape individual niche variation in co-occurring tetra fish in Neotropical streams
The drivers of intraspecific niche variation and its effects on species interactions are still unclear, especially in species-rich Neotropical environments. Here, we investigated how ecological opportunity and interspecific competition affect the degree of individual trophic specialization and the population niche breadth in tetra fish. We studied the four ecologically similar species (Psalidodon aff. gymnodontus, P. aff. paranae, P. bifasciatus, and Bryconamericus ikaa) in subtropical headwater streams (three sites with two co-occurring species and three sites with only one species). We sampled fish in two contrasting seasons (winter/dry and summer/wet), and quantified their trophic niches using gut content analysis. Psalidodon bifasciatus was the only species distributed over all the sampled streams. We observed seasonal differences in population trophic niche breadth of P. bifasciatus just when this species co-occurred with P. aff. gymnodontus. These findings confirm the complex nature of the effects of interspecific competition, depending, for instance, on the identity of the competitor. The degree of individual specialization of P. bifasciatus was higher in the winter, and it was not influenced by the presence of another species. Conversely, the other two Psalidodon species studied presented greater individual specialization in the summer, when fish consumed a higher proportion of allochthonous items (terrestrial insects and seeds), and there were no effects only for B. ikaa. Herein, our results suggest that seasonality in food-resource availability is a major driver of niche variation and it has the potential to play an important role in how these similar tetra species interact and coexist.
Personality does not predict individual niche variation in a freshwater fish
Animal populations can exhibit considerable inter-individual variation in both behavioral traits and niche use, but the potential connections between these characteristics are rarely compared for the same individuals. We aimed to test whether behavioral syndromes were predictive of individual diet or microhabitat in a native New Zealand freshwater fish, <i>Gobiomorphus cotidianus</i>. We carried out laboratory behavioral assays and repeated habitat and diet measurement in a semi-natural mesocosm system. We found considerable repeatability in individual behavior, largely consistent with a proactive/reactive behavioral syndrome. We also found modest individual repeatability in microhabitat use and relatively strong individual specialization in diet. However, no measure of niche use in the mesocosms was significantly predicted by individual personality. Further studies of this type will be needed to assess whether links between individual behavior and resource use are more important in other species or ecological contexts.
ScienceDex guides
Understand access before you commit
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.