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954 results for “survival data”
Survival Data of Strengthened and Non-Strengthened Oysters on Two Restored Reefs in Georgia, USA
The eastern oyster, Crassostrea virginica, is known to respond to chemical cues from their predators by strengthening their shell in defense. The chemical cues homarine and trigonelline, found in the urine of blue crabs, Callinectes sapidus, are two metabolic waste products known to cause this inducible defense in juvenile oysters. We tested whether this shell strengthening defense is beneficial for juvenile oysters in a restored reef setting by inducing oyster spat with chemical cues, placing them onto a restored reef and measuring their survival for 50-100 days. The first reef location is a previously restored reef (approximately 10 years old) with limited physical exposure to wind waves and boat wake. Juvenile oysters were placed at this site in September of 2021 and survival was measured for 49 days. The second reef location is a newly restored oyster reef (less than 1 year old) that acts as a living shoreline, with significant exposure to boat wake and wind waves. Juvenile oysters were protected from predation using mesh wrapping with an opening of 1 square cm and placed at the reef site in April 2023, where survival was monitored for 103 days. Site locations: Reef 1 (dock site) - 31.988948°, -81.024001° Reef 2 (living shoreline reef) - 32.067957°,-80.985005°
Data from: "Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups"
<p>This data repository contains:</p> <ul> <li><span>"msats_growth_individuals.xlsx" - Microsatellite data (39 loci) of Antarctic fur seals<br></span></li> <li><span>"pup_growth_2017-2020.xlsx" - Birth weight and tagging weight data for pups collected in 2017-2020.<br></span></li> <li><span>"Rebeccas_Samples_Mendel_OriginalPedigree" - SNP array data (75k SNPs) in PLINK format for a subset of individuals<br></span></li> <li><span>"GrowthRM_BI1820_Day60.new.csv" - Repeated weight measures for a subset of individuals</span></li> </ul> <p><strong><br>Manuscript abstract</strong></p> <p><span>Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability.<span> </span>We therefore investigated inbreeding effects in a declining population of Antarctic fur seals (<em>Arctocephalus gazella</em>) at Bird Island, South Georgia.<span> </span>Here, localised warming has reduced the availability of the seal’s staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population.<span> </span>However, it remains unclear whether selection operates before or after nutritional independence at weaning.<span> </span>We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother-offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth.<span> </span>We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits.<span> </span>This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment.<span> </span>Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.</span></p> <p><strong><span>Funding</span></strong></p> <p><span>This research was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) priority programme “Antarctic Research with Comparative Investigations in Arctic Ice Areas” SPP 1158 (project number 424119118) and the SFB TRR 212 (NC³) (Project Numbers 316099922 & 396774617). This work contributes to the Ecosystems project of the British Antarctic Survey, Natural Environmental Research Council, and is part of the Polar Science for Planet Earth Programme.</span></p>
Supporting data for: Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
<p><strong>SUMMARY OF THE STUDY</strong></p> <p>We combined functional genomics and human genetics to investigate processes that affect type 1 diabetes (T1D) risk by mediating beta-cell survival in response to proinflammatory cytokines. We mapped 38,931 cytokine-responsive candidate <em>cis-</em>regulatory elements (cCREs) in beta-cells using ATAC-seq and snATAC-seq and linked them to target genes using co-accessibility and HiChIP. Using a genome-wide CRISPR screen in EndoC-βH1 cells we identified 867 genes affecting cytokine-induced survival, and genes promoting survival and up-regulated in cytokines were enriched at T1D risk loci. Using SNP-SELEX, we identified 2,229 variants in cytokine-responsive cCREs altering transcription factor (TF) binding, and variants altering binding of TFs regulating stress, inflammation and apoptosis were enriched for T1D risk. At the 16p13 locus, a fine-mapped T1D variant altering TF binding in a cytokine-induced cCRE interacted with <em>SOCS1</em>, which promoted survival in cytokine exposure. Our findings reveal processes and genes acting in beta-cells during inflammation that modulate T1D risk.</p> <p><strong>DESCRIPTION OF FILES:</strong></p> <ul> <li>Supplementary Data 1. List of islet cCREs annotated with cell type and cytokine response - also in GSE205853</li> <li>Supplementary Data 2. Coaccessible sites in untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 3. Coaccessible sites in cytokine-treated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 4. Coaccessible sites in cytokine treated and untreated beta cells and promoter annotations - also in GSE205853</li> <li>Supplementary Data 5. Chromatin interactions in EndoC-BH1 cells - also in GSE205853</li> <li>Supplementary Data 6. Variants selected for SNP-SELEX assay </li> <li>Supplementary Data 7. Variants with TF binding and allelic binding results from SNP-SELEX</li> <li>Supplementary Data 8. snATAC-seq barcodes and metadata - also in GSE205853</li> <li>Supplementary Data 9. CRISPR-KO screen results - also in GSE205853</li> <li>Supplementary Data 10. Bulk ATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 11. Bulk RNA-seq count matrix - also in GSE205853</li> <li>Supplementary Data 12. Alpha cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 13. Acinar cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 14. Beta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 15. Stellate cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 16. Endothelial cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 17. Delta cells snATAC-seq count matrix - also in GSE205853</li> <li>Supplementary Data 18. Luciferase assay rs10483809</li> <li>Supplementary Data 19. SOCS1 knockdown qPCR results</li> <li>Supplementary Data 20. SOCS1 knockdown Apotracker (flow-cytometry)results</li> </ul> <p><strong>Raw data deposited at GEO, accessions GSE205853 and GSE118725.</strong></p> <p><em>Please refer to publication and GEO for details on methods.</em></p>
Data for predicting piglet survival until weaning using birth weight and within-litter birth weight variation as easily measured proxy predictors
<p>The data was used in the analysis presented in the manuscript: Predicting piglet survival until weaning using birth weight and within-litter birth weight variation as easily measured proxy predictors. The manuscript is published in <em>Animal</em> journal. The data is for piglet survival survival at different time-points from birth to weaning from two research farms.</p>
Data to support "Stochastic density effects on adult fish survival and implications for population fluctuations"
Data on stage-specific abundance of black surfperch (Embiotoca jacksoni), the amount of foraging habitat and the availability of surfperch prey (crustaceans) were collected at fixed sites on the north shore of Santa Cruz Island, California annually (autumn) from 1993-2009. Data are grouped into four regions. Counts of fish distinguished among young-of-year, juveniles (1 year old) and adults (>= 2 years old). These data have been presented in Okamoto, D. K., R. J. Schmitt and S. J. Holbrook. 2016. Sochastic density effects on adult fish survival and implications for population fluctuations. Ecology Letters, 19:153-162. doi: 10.1111/ele.12547.
Survival, fecundity and reproductive tissue data from false killer whales (Pseudorca crassidens)
<p>These data come from specimens from false killer whales from combined strandings (South Africa, 1981) and harvest (Japan 1979-80). The South African material was collected from 65 false killer whales that stranded en masse on the west coast of the Western Cape Province. Scientists reached the site two days after the stranding event was reported, so the material was not fresh and fixation of tissue samples was suboptimal. Data are available from 41 (including 32 mature) females. The Japanese material (96 females, 57 mature) originated from 6 schools harvested during shore-drive fisheries operations at Iki Island. In each case, as many false killer whales as possible were randomly examined. Data presented here come from 91 females if which 89 were mature. The Japanese and South African data were combined to estimate survival, but fecundity information is available for each separately. These data are associated with the following publication: Theoni Photopoulou, Ines M. Ferreira, Peter B. Best, Toshio Kasuya and Helene Marsh. 2017. Evidence for a postreproductive phase in female false killer whales <em>Pseudorca crassidens. </em>Frontiers in Zoology. 14:30. DOI 10.1186/s12983-017-0208-y</p>
Ash (Fraxinus excelsior L.) in vitro survival data for the UKs Living Ash Project
<p><em>In-vitro</em> propagation and survival data sets (including nursery survival) of the ash plants generated i.e. <em>Fraxinus excelsior</em> L., plus the PCR primers used and conditions applied.</p> <p>Surveyed from a range of ash seed material taken from across the UK, and held at the UK ash collection hosted by the Earth Trust in Oxfordshire, UK.</p> <p>A more detailed analysis of this data is currently expected to be be published in the <em>Annals of Forest Science</em>, and which has already provisionally accepted this work for publication, subject to the underlying data being made available i.e. here</p> <p>The data deposited here represents the underlying data that will be presented in graphical form in the forthcoming paper by Fenning et al., plus the associated metadata and statistical analyses, along with the original .jpg of the photos used.</p>
Data from: Estimation in the multinomial reencounter model - Where do migrating animals go and how do they survive in their destination area?
<p><strong>Abstract</strong></p> <p>Spatial variation in survival has individual fitness consequences and influences population dynamics. Which space animals use during the annual cycle determines how they are affected by this spatial variability. Therefore, knowing spatial patterns of survival and space use is crucial to understand demography of migrating animals. Extracting information on survival and space use from observation data, in particular dead recovery data, requires explicitly identifying the observation process. We build a fully stochastic model for animals marked in populations of origin, which were found dead in spatially discrete destination areas. It acts on the population level and includes parameters for use of space, survival and recovery probability. The model is based on the division coefficient and the multinomial reencounter model. We use a likelihood-based approach, derive Restricted Maximum Likelihood-like estimates for all parameters and prove their existence and uniqueness. In a simulation study we demonstrate the performance of the model by using Bayesian estimators derived by the Markov chain Monte Carlo method. We obtain unbiased estimates for survival and recovery probability if the sample size is large enough. Moreover, we apply the model to real-world data of European robins <em>Erithacus rubecula</em> ringed at a stopover site. We obtain annual survival estimates for different spatially discrete non-breeding areas. Additionally, we can reproduce already known patterns of use of space for this species. We would like to thank the Greifswalder Oie Bird Observatory of the Verein Jordsand, Ahrensburg, and the Hiddensee Bird Ringing Centre, Güstrow, for providing the robin data.</p>
Data and code for: Growth, development and survival in the brown widow spider, Latrodectus geometricus under different feeding regimes.
<p><span>Here, we compared mortality, growth and development of the brown widow spider, <em>Latrodectus geometricus</em>, from neonate to adult under two different prey availability regimes. </span></p>
Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer - pre-processed data
<p>A multicentre, prospective observational study was conducted of colorectal cancer (CRC) patients undergoing primary surgical resection in the United Kingdom and Czech Republic. Analysis was performed using metataxonomics (microbiome) and ultra-performance liquid chromatography mass spectrometry (UPLC-MS, metabolomics). Both datasets were pre-processed as described in the methods section of the main article. The data here were used as the input to the data analysis workflows available from <a href="https://github.com/jmp111/CRC">Github</a>.</p>
Nest survival data of Anthus hellmayri
<p><strong>File 1: a_hellmayri_survival.csv</strong></p> <p>Nest survival data of <em>Anthus hellmayri </em>collected during 2017-2018, 2018-2019, and 2019-2020 breeding seasons in Punta Indio, Buenos Aires, Argentina. Used to estimate daily nest survival rates and include covariates in the models.</p> <p><strong>File 2: Readme_a_hellmayri_survival.docx</strong></p> <p>File conainting information about the columns and data</p> <p><strong>File 3: script_ah.R</strong></p> <p>Example code to be used in R software. This code leads to the main result of the paper.</p>
ArrayCGH microarray images for 'Autoencoder and NCA based neural network model to estimate survival prognosis in multiple myeloma using arrayCGH data'
<p>ArrayCGH microarray images for 'Autoencoder and NCA based neural network model to estimate survival prognosis in multiple myeloma using arrayCGH data'</p>
Digitized patient level time to event data of overall survival
<p>This dataset contains digitized patient level time to event data for overall survival of patients with locally advanced and metastatic (stage IIIB/IV) Non-small cell lung cancer (NSCLC). The data can be used to recreate the original Kaplan-Meier survival curves that were published in randomized controlled trials, in order to perform secondary analysis on the survival data. In order to recreate a survival curve, you need two csv.files per trial arm that are in this <br> database: (1) starting with 'surv_', containing the individual patient level time to event data, and (2) starting with 'natrisk_', containing the corresponding numbers at risk table. For the methodology and r-code that can be used for this purpose we refer to article that is linked to this dataset. </p>
Data from: Ability of seedlings to survive heat and drought portends future demographic challenges for five southwestern US conifers
<p>Climate change and disturbance are altering forests and the rates and locations of tree regeneration. We examined seedling survival of five southwestern United States (US) conifer species found in warmer and drier woodlands (<em>Pinus edulis</em>, <em>P. ponderosa</em>) and cooler and wetter subalpine forests (<em>Pseudotsuga menziesii</em>, <em>Abies concolor</em>, and <em>Picea engelmanii</em>) under hot and dry conditions in incubators. We constructed models that explained 53% to 76% of the species-specific survival variability, then applied these to recent climate (1980-2019) and projected climate (1980-2099) for the southwestern US. We found that lower elevations within species' range would have low survival under projected climate and that range contraction would be greatest for species that currently occupy warm-dry conditions. These results demonstrate that empirically derived physiological limitations can be used to identify where species composition or vegetation type change are likely to occur in the southwest US.</p>
Data for: Thermoregulation enhances survival but not reproduction in a plant-feeding insect
<p>Temperature influences nearly all aspects of fitness. However, reproduction is often more thermally sensitive than survival. Thermoregulation must maintain performance in both components of fitness to buffer populations from environmental change. We assessed the fitness benefits of thermoregulation in <em>Enchenopa binotata</em> treehoppers. Under realistic mesocosm conditions, we quantified fine-scale microclimates using 3D-printed operative temperature models. We then compared operative temperatures to treehopper body temperatures and translated patterns of thermoregulation into variation in survival and reproduction. We also assessed two thermoregulatory mechanisms: precise microclimate choice and heat escape behaviors. Finally, we applied our results to evaluate if arthropod thermoregulation is accurately characterized by two theoretical models commonly used to simulate responses to environmental change. We found substantial thermal variation at fine spatial scales relevant to insects: at a single point in time, temperatures within 30cm-tall plants spanned ranges up to 19ºC (23-42ºC). Lethal operative temperatures were common when air temperatures were high. However, heat escapes allowed treehoppers to almost entirely avoid lethal temperatures. By contrast, individuals thermo-conformed in the absence of lethal operative temperatures. This finding suggests that precise microclimate choice imposes high costs due to thermal uncertainty at fine spatial scales. Furthermore, given the narrow range of temperatures in which reproduction occurs, thermoregulation is unlikely to maintain reproduction. Thermoregulation was most effective in the lowest-quality and most spatially variable thermal habitats. Treehopper thermoregulation therefore more closely follows cost-benefit models of thermoregulation compared to models that account for inhibited movement at extreme temperatures. Overall, even if thermoregulation can prevent lethal heat stress, thermoregulation may have limited capacity to buffer arthropods and other small ectotherms from environmental change if it cannot maintain reproductive performance.<strong> </strong></p>
Data from: Early-life variation in migration is subject to strong fluctuating survival selection in a partially migratory bird
<p>Population dynamic and eco-evolutionary responses to environmental variation and change fundamentally depend on combinations of within- and among-cohort variation in phenotypic expression of key life-history traits, and on corresponding variation in selection on those traits. Specifically, in partially migratory populations, spatio-seasonal dynamics depend on the degree of adaptive phenotypic expression of seasonal migration versus residence, where more individuals migrate when selection favours migration.</p> <p>Opportunity for adaptive (or, conversely, maladaptive) expression could be particularly substantial in early life, through initial development of migration versus residence. However, within- and among-cohort dynamics of early-life migration, and of associated survival selection, have not been quantified in any system, preventing any inference on adaptive early-life expression. Such analyses have been precluded because data on seasonal movements and survival of sufficient young individuals, across multiple cohorts, have not been collected.</p> <p>We undertook extensive year-round field resightings of 9,359 colour-ringed juvenile European Shags (<em>Gulosus aristotelis</em>) from 11 successive cohorts in a partially-migratory population. We fitted advanced Bayesian multi-state capture-mark-recapture models to quantify early-life variation in migration versus residence and associated survival across short temporal occasions through each cohort's first year from fledging, thereby quantifying the degree of adaptive phenotypic expression of migration within and across years.</p> <p>All cohorts were highly partially migratory, but the degree and timing of migration varied considerably within and among cohorts. Episodes of strong survival selection on migration versus residence occurred both on short timeframes within years, and cumulatively across whole years, generating instances of instantaneous and cumulative net selection that would be obscured at coarser temporal resolutions. Further, the magnitude and direction of selection varied among years, generating strong fluctuating survival selection on early-life migration across cohorts, as rarely evidenced in nature. Yet, the degree of migration did not strongly covary with the direction of selection, indicating limited early-life adaptive phenotypic expression.</p> <p>These results reveal how dynamic early-life expression and selection on a key life-history trait, seasonal migration, can emerge across seasonal, annual, and multi-year timeframes, yet be substantially decoupled. This restricts the potential for adaptive phenotypic, micro-evolutionary, and population dynamic responses to changing seasonal environments.</p>
Data from: Corals that survive repeated thermal stress show signs of selection and acclimatization
<p>Climate change is transforming coral reefs by increasing the frequency and intensity of marine heatwaves, often leading to coral bleaching and mortality. Coral communities have demonstrated modest increases in thermal tolerance following repeated exposure to moderate heat stress, but it is unclear whether these shifts represent acclimatization of individual colonies or mortality of thermally susceptible individuals. For corals that survive repeated bleaching events, it is important to understand how past bleaching responses impact future growth potential. Here, we track the bleaching responses of 1,832 corals in leeward Maui through multiple marine heatwaves and document patterns of coral growth and survivorship over a seven-year period. While we find limited evidence of acclimatization at population scales, we document reduced bleaching over time in specific individuals, primarily in the stress-tolerant taxa <em>Porites lobata</em>, indicative of acclimatization. For corals that survived both bleaching events, we find no relationship between bleaching response and coral growth in three of four taxa studied. This decoupling between bleaching and growth suggests that coral survivorship is a better indicator of future growth than is a coral's bleaching history. Based on these results, we recommend restoration practitioners in Hawaiʻi obtain outplants from <em>Porites</em> and <em>Montipora</em> colonies with a proven track-record of growth and survivorship, rather than devote resources toward identifying and cultivating bleaching-resistant phenotypes. Survivorship followed a latitudinal thermal stress gradient, but because this gradient was small, it is likely that local environmental factors also drove differences in coral performance between sites. Efforts to reduce human impacts at low performing sites would likely improve coral survivorship in the future.</p>
Reproduction code and data for the plot of "Synthesizing survival robot behavior through reinforcement learning for homeostasis"
<pre># Reproduction code and data for the plot of "Synthesizing survival robot behavior through reinforcement learning for homeostasis"<br>Author: Naoto Yoshida<br><br>How to use:<br>1. Clone https://github.com/ugo-nama-kun/journalpaper_robot_2024 from github.<br>2. Extract data_20241119.zip in the cloned repository.<br>3. Run each plot_Fig*.py</pre>
Data For Survival of the Fittest: Testing Superradiance Termination with Simulated Binary Black Hole Statistics
<p>This repository is associated with the GitHub repository: https://github.com/jacquelynzhy/Statistical_Superradiance, which includes the code to reproduce the findings of Zhu et al. (2025). Specifically, the file "Output1.dat" here represents the output of running ZEVN with the initial conditions outlined in Section 3.1 of Zhu et al. (2025), which only included BH-BH binaries. For the values generated by a ZEVN run and instructions on how to select the type of remnants you are interested in, please refer to <a href="https://ui.adsabs.harvard.edu/abs/2019MNRAS.485..889S/abstract">Spera et al. (2019)</a> and the ZEVN GitHub page at: https://gitlab.com/sevncodes/sevn.</p>
Data from: Integrating tracking and resight data enables unbiased inferences about migratory connectivity and winter range survival from archival tags
<p>Archival geolocators have transformed the study of small, migratory organisms but analysis of data from these devices requires bias correction because tags are only recovered from individuals that survive and are re-captured at their tagging location. Data and code provided in this repository can be used to replicate the simulation and Painted Bunting case study results presented by Rushing et al. (2021) showing that integrating geolocator recovery data and mark–resight data enables unbiased estimates of both migratory connectivity between breeding and nonbreeding populations and region-specific survival probabilities for wintering locations.</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.