Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
470
datasets available to search
ShareScore release 0.9.0
Dataset results
470 results for “dead”
CO2 and CH4 fluxes from living and standing dead trees in Howland Research Forest, Maine USA, 2024
Methane (CH4) is the second-largest contributor to human-induced climate change, with significant uncertainties in its terrestrial sources and sinks. Tree stems, both living and dead, play crucial roles in forest ecosystem CH4 and carbon dioxide (CO2) flux dynamics, yet much remains unknown regarding the environmental drivers of fluxes. We measured CH4 and CO2 fluxes from 51 living trees (Picea rubens, Tsuga canadensis, Acer rubrum) along an upland-to-wetland gradient at Howland Research Forest, a net annual sink of CH4, in Maine USA. We also measured CH4 and CO2 fluxes from six standing dead red spruce stems (snags). We measured fluxes every two weeks throughout the growing season (April to November 2024) and at three heights (for a subset of red spruce stems) to capture a range of environmental conditions.
MCR LTER: Coral Reef: Dead coral skeletons impair key recovery processes following coral bleaching; data for Kopecky et al., 2024 Global Change Biology
The data included in this data package were collected on the North shore of Moorea, French Polynesia, from 2015-2023 to explore how dead coral skeletons (e.g,, left after coral bleaching events) influence critical processes tied to coral reef resilience. Together, these various datasets were used for analyses in the manuscript entitled "Changing disturbance regimes, material legacies, and stabilizing feedbacks: dead coral skeletons impair key recovery processes following coral bleaching", published in Global Change Biology. These data are in support of a publication Kopecky et al. (2024) Global Change Biology, and were a part of the thesis of K. Kopecky. The manuscript title and author list are as follows: Changing disturbance regimes, material legacies, and stabilizing feedbacks: dead coral skeletons impair key recovery processes following coral bleaching. Kai Kopecky, Russell J. Schmitt, Sally J. Holbrook. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 22-24354 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2024). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Consumption rates of tethered live and dead pinfish and dried squid in mudflat and seagrass habitats in the Upper Laguna Madre in 2018.
These data were recorded during surveys of a tethering experiment conducted on June 7, 2018, during which 180 tethered prey were deployed in two habitat types (seagrass and mudflat) in the Upper Laguna Madre, Texas, USA (27.544006, -97.285912). In each habitat, the following prey types were deployed: squidpops (1 cm2 discs of dried squid (Duffy et al. 2015) attached to 5 cm tethers, n=50), live (n=20) and dead (n=20) pinfish (Lagodon rhomboides, 4 cm fork length, attached to 20 cm tethers) at midday in each habitat. The presence/absence of tethered prey on each stake was observed and recorded after 1 hour and 24 hours. The rate of decay (i.e., disappearance or consumption rate of tethered prey over time) was calculated as the slope of an exponential model fit to discrete observations of the presence/absence of tethered prey over time. Additional environmental variables (temperature, salinity) were also recorded at the site.
Alaska 2004 Burns: Counts of live and dead seedlings of lodgepole pine in a post-fire seeding experiment at 39 sites
This dataset contains counts of emerged seedlings of lodgepole pine from seeds sown in an experimental seeding study. The experiment started in 2005 at sites that burned in 2004 in interior Alaska. Records are from a set of 39 intensive study sites that were formerly dominated by black spruce along the Steese, Taylor, and Dalton highways. Seeds were sown in five 50 x 50 cm quadrats at each site in August 2005 and most emerged in early summer 2005. Seedling counts were measured for 6 years, in 2006, 2007 2008, and 2011. All pine seedlings were removed in 2011.
Effects of marsh periwinkle (Littoraria irrorata) size and density on cordgrass (Spartina aterniflora) biomass and dead standing material
Marsh periwinkles (Littoraria irrorata) are common in southeastern US salt marshes, including those on Sapelo Island, GA. They are known to affect the productivity of cordgrss (Spartina alterniflora) and also contribute to its decomposition following senescence. The population struture of Littoraria, in terms of the size and densities of individuals, varies widely in space and time. No previous experiments have, however, attempted to manipulate the density and body size of populations of Littoraria and assessd the response of Spartina. We perforned such an experiment in Airport Marsh on Sapelo Island, using small experimental enclosures and measured Spartina biomass and dead standing material after 3 months (mid July - mid Oct, 2012). We assessed response variables by removing all Spartina material from plots before seperating and drying them in the lab.
OPD01 Konza Prairie standing dead and litter decomposition (1981-1983)
Standing dead and litter decomposition of big bluestem foliage and flowering stems were measured for two years using litterbag methods. Mass, nitrogen and phosphorus content were measured.
MCR LTER: Coral Reef Resilience: Live and Dead Pocillopora and Acropora Coral Colony Time Series from 2006 to 2011
These data describe the abundance, size structure, and morphologies of living and dead corals belonging to the genera Pocillopora and Acropora on the forereef (depth = 10 meters) in 2006, 2009, 2010, and 2011. Data were derived from a randomly chosen subset of photo quadrats associated with knb-lter-mcr.4. For each quadrat, individual coral colonies were identified to genus, scored as living or dead, and the total area of their footprint calculated. In addition, branch morphology was scored on a scale from 1 to 3, with 1 representing very tight spacing, and 3 representing open spacing among adjacent branches. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Data from: Choosy beetles: how host trees and southern boreal forest naturalness may determine dead wood beetle communities
<p>See methods section of paper for detailed information on dataset and sources; briefly, these .csv files includes numbers of each beetle species captured at all sites used in the project, as well as information about each site and about each species.</p> <p> </p> <p>Data from:</p> <p><strong>Choosy beetles: how host trees and southern boreal forest naturalness may determine dead wood beetle communitie</strong><strong>s</strong></p> <p>Ryan C. Burner, Tone Birkemoe, Jörg G. Stephan, Lukas Drag, Jörg Muller, Otso Ovakainen, Mária Potterf, Olav Skarpaas, Tord Snall, Anne Sverdrup-Thygeson</p> <p>Forest Ecology and Management, 2021</p> <p> </p> <p>From abstract of paper:</p> <p>Wood-living beetles make up a large proportion of forest biodiversity, and contribute to important ecosystem services, including decomposition. Beetle communities in managed southern boreal forests are less species rich than in natural and near-natural forest stands. In addition, many beetle species rely primarily on specific tree species. Yet, the associations between individual beetle species, forest management category, and tree species are seldom quantified, even for red-listed beetles. We compiled a beetle capture dataset from flight intercept traps placed in Norway spruce (<em>Picea abies</em>), oak (<em>Quercus sp.</em>), and Eurasian aspen (<em>Populus tremulae</em>) trees in 413 sites in mature managed forest, near-natural forest, and clear-cuts in southeastern Norway. We used joint species distribution models to estimate the strength of associations for 368 saproxylic beetle species (including 20 vulnerable, endangered, or critical red-listed species) for each forest management category and tree species. Tree species on which traps were mounted had the largest effect on beetle communities; oaks had the most highly associated beetle species, including most of the red-listed species, followed by Norway spruce and Eurasian aspen. Most beetle species were more likely to be captured in near-natural than in mature managed forest. Our estimated associations were compatible – for many species – with categorical classifications found in several existing databases of saproxylic beetle preferences. These quantitative beetle-habitat associations will improve future analyses that have typically relied on categorical classifications. Our results highlight the need to prioritize conservation of near-natural forests and oak trees in Scandinavia to protect the habitat of many red-listed species in particular. Furthermore, we underline the importance of carefully considering the species of trees on which traps are mounted in order to representatively sample beetle communities in forest stands.</p>
SETDB1 knock-out and reexpression of a WT, a catalytic-dead variant (CA) or a NLS-tagged SETDB1 protein
<p>In order to generate the Setdb1 cKO allele, exons 15 and 16, which encode the core amino acids of the catalytic domain, have been flanked with two lox-P sites recognized by Cre recombinase enzyme. Cre-oestrogen receptor fusion gene Mer-Cre-Mer has been introduced to induce acute Setdb1 KO after Tamoxifen treatment. Setdb1 cKO mESCs where Setdb1 expression is stably rescued by wild type 3xFlag-Setdb1 (WT) or by the catalytic dead mutant 3xFlag-Setdb1 (CA) were generously given by Pr Yoichi Shinkai. The catalytic dead mutant was obtained with a single lysine mutation. In the lab, Setdb1 cKO mESCs, where Setdb1 expression is stably rescued by NLS-3xFlag-Setdb1 which localizes only in the nucleus, have been established (3 NLS sequences have been added in order to retain Setdb1 in the nucleus).</p> <p>The quality of the RNA was determined on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), the RNA integrity number was above 8 for all the samples. To construct libraries, 1 mg of high-quality total RNA sample was processed using Truseq® stranded total RNA kit (Illumina®). After the removal of ribosomal RNAs (using Ribo-zero® rRNA), confirmed by QC control on pico chipTM on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), total RNA molecules are fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis will permit to achieve the strand specificity. Addition of a single A base to the cDNA is followed by ligation of adapters. Libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina Libraries (KapaBiosystems) and library profiles were assessed using the DNA High SensitivityTMHS kit on an Agilent Bioanalyzer 2100. Libraries were sequenced on an Illumina® Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode.</p>
Dataset for "Deflected Mantle Flow and Shearing-aligned Lithospheric Melt under the Strike-slip Dead Sea Rift"
<p>Dataset 1: All of the individual shear-wave splitting measurements in the Dead Sea rift, including 1855 A and B measurements and 1088 Null measurements</p> <p>Dataset 2: Three component seismic waveforms used for shear-wave splitting measurement, for PKS, SKKS, and SKS, respectively</p> <p>Dataset 3: Earthquake catalogue with magnitude Mb 2.6 or above in the Dead Sea rift. Downloaded from the International Seismological Centre (https://www.isc.ac.uk/)</p> <p> Reference: International Seismological Centre (2024), On-line Bulletin, [Dataset] doi:10.31905/D808B830</p> <p>Dataset 4: Holocene Volcano List. Downloaded from Global Volcanism Program (https://volcano.si.edu/volcanolist_holocene.cfm)</p> <p> Reference: Global Volcanism Program, 2024. Volcanoes of the World (v. 5.2.2; 22 Aug 2024). Distributed by Smithsonian Institution, compiled by Venzke, E. [Database] doi:10.5479/si.GVP.VOTW5-2024.5.2</p>
Tree species identity, diameter and qualitative canopy health measurements (full, partial or dead) from 2005 to 2023 on 12 experimental oak loss plots in Black Rock Forest, NY.
Black Rock Forest established a series of 12, 0.56 ha plots in 2005 to assess impacts of the loss of tree in the genus Quercus on the forest ecosystem (entitled the Future of Oak Forests experiment). Three trunk girdling treatments, with control plots were instituted in 2008. Each plot also contained an ~10m by ~15m deer exclosure to assess the impact of herbivory post-disturbance. Trees were measured twice per year from 2008 to 2013 (except 2009 when trees were measured once) and once per year from 2014 to 2023. Data include tree species identity, diameter at breast height (DBH), canopy health (a qualitative assessment of approximate cover as full, partial or dead), presence/absence of sprouts, and location within the plot. All live trees equal to or larger than 2.5 cm DBH are included in the dataset.
Relyea, R. A., and N. Mills. 2001. Predator-induced stress makes the pesticide carbaryl more deadly to grey treefrog tadpoles (Hyla versicolor). PNAS 98:2491-2496.
Global declines in amphibians likely have multiple causes, including widespread pesticide use. Our knowledge of pesticide effects on amphibians is largely limited to short-term (4-d) toxicity tests conducted under highly artificial conditions to determine lethal concentrations (LC50). We found that if we used slightly longer exposure times (10–16 d), low concentrations of the pesticide carbaryl (3–4% of LC504-d) killed 10–60% of gray treefrog (Hyla versicolor) tadpoles. If predatory cues also were present, the pesticide became 2–4 times more lethal, killing 60–98% of tadpoles. Thus, under more realistic conditions of increased exposure times and predatory stress, current application rates for carbaryl can potentially devastate gray treefrog populations. Further, because predator-induced stress is ubiquitous in animals and carbaryl’s mode of action is common to many pesticides, these negative impacts may be widespread in nature.
Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla)
<p>The stipple-throated antwrens of the genus <i>Epinecrophylla</i> (Aves: Thamnophilidae) are represented by eight species primarily found in the lowlands of the Amazon Basin and the Guiana Shield. The genus has a long and convoluted taxonomic history, with many attempts made to address the taxonomy and systematics of the group. Here we employ massively parallel sequencing of thousands of ultraconserved elements (UCEs) to provide both the most comprehensive subspecies-level phylogeny of <i>Epinecrophylla</i> antwrens and the first population-level genetic analyses for most species in the genus. Most of our results are robust to a diversity of phylogenetic and population genetic methods, but we show that even with thousands of loci we are unable to fully resolve the relationships between some western Amazonian species in the <i>haematonota </i>group. We uncovered phylogenetic relationships between taxa and patterns of population structure that are discordant with both morphology and current taxonomy. For example, we found deep genetic breaks between taxa in the <i>ornata </i>group that are currently regarded as species, and in the <i>haematonota </i>and <i>leucophthalma</i> groups we found paraphyly at the species and subspecies levels, respectively. As has been found in many Amazonian taxa, our phylogenetic results show that the major river systems of the Amazon Basin appear to have an effect on the genetic structure and range limits within <i>Epinecrophylla</i>. Our population genetics analyses showed extensive admixture between some taxa despite their deep genetic divergence. We present a revised taxonomy for the group and suggest areas for further study.</p>
Detection of ultra-weak laser pulses by free-running single-photon detectors: modeling dead time and dark counts effects
<p>In quantum communication systems, the precise estimation of the detector´s response to the incoming light is necessary to avoid security breaches. The typical working regime uses a free-running single-photon avalanche diode in combination with attenuated laser pulses at telecom wavelength for encoding information. We demonstrate the validity of an analytical model for this regime which considers the effects of dark counts and dead time on the measured count rate. For the purpose of gaining a better understanding of these effects, the photon detections were separated from the dark counts via a software-induced gating mechanism. The model was verified by experimental data for mean photon numbers covering three orders of magnitude as well as for laser repetition frequencies below and above the inverse dead time. Consequently, our model would be of interest for predicting the detector response not only in the field of quantum communications, but also in any other quantum physics experiment where high detection rates are needed.</p>
'Twitter Is Dead, Long Live X!' A Decade of Microblog Research and Implications for Knowledge and Research
<p>Talk at the <a href="https://www.digital-philosophy.org/" target="_blank" rel="noopener">Philosophy [in:of:for:and] Digital Knowledge Infrastructures</a> online workshop 2023 (28/09/2023).</p>
Data from: The evolution of the traplining pollinator role in hummingbirds, specialization is not an evolutionary dead end
<p>Trapliners are pollinators that visit widely dispersed flowers along circuitous foraging routes. Through coevolution with the flowers they pollinate, trapliners are hypothesised to become more morphologically and ecologically specialised than their non-traplining counterparts. We hypothesised that independent transitions to traplining in hummingbirds should entail convergent morphological specialisation, and we tested whether such transitions are irreversible and lead to lower rates of diversification as predicted by the hypothesis that specialisation is an 'evolutionary dead end'. We find that there have been multiple independent transitions to traplining across the hummingbird phylogeny, but reversals have been rare or incomplete at best. Multiple independent lineages of trapliners have become morphologically specialised, convergently evolving relatively large bills for their body size. Traplining is not an evolutionary dead end however, since trapliners continue to give rise to new traplining species at a rate comparable to non-trapliners.</p>
Fig. 2 in Dead wood modifies mobility of ground beetles
Fig. 2. The average amount of time spent by carabids inside the fenced plots with dead wood (DW) and inside the fenced control plots (C)
Fig. 4 in Dead wood modifies mobility of ground beetles
Fig. 4. The catch rate of unmarked individuals of P. oblongopunctatus inside fenced the DW and C plots
Fig. 1 in Dead wood modifies mobility of ground beetles
Fig. 1. The four zones on the ground beetle elytra where respective numbers were incised (drawing by J. Skłodowski)
Dead Sea Scrolls data collection (images, labels, prediction plots) for dating ancient manuscripts using radiocarbon and AI-based writing style analysis
<p>The dataset is associated with the following article:<br>Title: <strong>Dating ancient manuscripts using radiocarbon and AI-based writing style analysis</strong><br>Authors: Mladen Popović, Maruf A. Dhali, Lambert Schomaker, Johannes van der Plicht, Kaare Lund Rasmussen, Jacopo La Nasa, Ilaria Degano, Maria Perla Colombini, and Eibert Tigchelaar<br><em>(Under review)</em></p> <p>This data set is collected for the ERC project:<br>The Hands that Wrote the Bible: Digital Palaeography and Scribal Culture of the Dead Sea Scrolls<br>PI: Mladen Popović<br>Grant agreement ID: 640497<br>Project website: <a href="https://cordis.europa.eu/project/id/640497">https://cordis.europa.eu/project/id/640497</a></p> <p> </p> <p><strong>Copyright (c) </strong> University of Groningen, 2024. All rights reserved.<br><strong>Disclaimer and copyright notice for all data contained on the *.tar.gz files:</strong></p> <p><strong>1)</strong> permission is hereby granted to use the data for research purposes. It is not allowed to distribute this data for commercial purposes.</p> <p><strong>2) </strong>provider gives no express or implied warranty of any kind, and any implied warranties of merchantability and fitness for purpose are disclaimed.</p> <p><strong>3) </strong>provider shall not be liable for any direct, indirect, special, incidental, or consequential damages arising out of any use of this data.</p> <p><strong>4) </strong>the user should refer to the first public article mentioned above on this data set.</p> <p><strong>5) </strong>the recipient should refrain from proliferating the data set to third parties external to his/her local research group. Please refer interested researchers to this site to obtain their own copy.</p> <p> </p> <p><strong>Organization of the data:<br></strong><em>(Update on 19 April 2024: OxCal data for accepted 2-sigma ranges are updated with the incusion and exclusion of minor peaks. New prediction plots are added after the model is trained with accepted 2-sigma ranges, including minor peaks. The old plots are also kept. <br><br><OLD Updates below; disregard><br>updated on 07-Feb-2024: OxCal data for selected ranges added in a new directory in addition to previously available original OxCal data. Enoch's prediction plots and test images are reorganized for easy access to the users.<br><OLD Updates above; disregard><br><br>Please use the files from this version and disregard the previous two versions: 10.5281/zenodo.10629480 and 10.5281/zenodo.8168210)</em></p> <p>There are four *.tar.gz files:</p> <p><em><strong>C14-Oxcal-data-updated.tar.gz</strong></em> contains one directory with radiocarbon data (OxCal [1] raw data) for all 30 manuscripts. Three additional directories contain name-corrected files for original OxCal data, files with accepted ranges, and files with accepted ranges including minor peaks. Please refer to the original article for details about OxCal data and the manuscripts. 25 out of 30 raw OxCal data are used (accepted ranges only) as the training labels during the training of Enoch, the date prediction model.</p> <p><em><strong>train-images-c14.tar.gz</strong></em> contains the clean and preprocessed (binarized, aligned, and arrangement corrected) training images for the 25 radiocarbon-dated training manuscripts (including 4Q52; 64 images in total). </p> <p><em><strong>test-images-all.tar.gz</strong></em> contains the clean and preprocessed test images for 135 previously undated manuscripts. The images are organized in three different directories: the first one with all 359 images for the 135 manuscripts, the second one with the selected 135 images, and the final one with 25 images to illustrate the poor quality of images. </p> <p><em><strong>Enoch-prediction-new-with-minor-peaks.tar.gz</strong></em> contains the new date prediction plots for each of the 135 test images, where Enoch was trained with the inclusion of minor peaks for the 2-sigma accepted ranges and with a data balancing threshold of 0.05. These plots are used by expert palaeographers' evaluation of Enoch's style-based date predictions of 135 previously undated manuscripts.</p> <p><em><strong>Enoch-predictions.tar.gz</strong></em> contains the date prediction plots for each of the 135 test images. There are two directories inside the *.tar.gz file:<br><br>- <em>prediction-plots-for-selected-135:</em> Prediction plots with data balancing threshold of 0.05. <br>- <em>extra-plots:</em> contains four additional directories:<br> - <em>Enoch-predictions-c14wo4Q52-balanced05:</em> Prediction plots with data balancing threshold of 0.05. <br> - <em>Enoch-predictions-c14wo4Q52-balanced10:</em> Prediction plots with data balancing threshold of 0.1.<br> - <em>Enoch-predictions-c14wo4Q52-unbalanced:</em> Unbalanced raw predictions.<br> - <em>Enoch-predictions-c14wo4Q52-combined:</em> Combined plots with all three prediction plots (unbalanced, 0.05, 0.1).<br>Please refer to the original article for more details.</p> <p>The updated code to run the plot is available here: <a href="https://doi.org/10.5281/zenodo.10998860">https://doi.org/10.5281/zenodo.10998860</a></p> <p><strong>If you have any questions, please get in touch with us:</strong><br>Mladen Popović <m.popovic(at)rug.nl><br>Maruf A. Dhali <m.a.dhali(at)rug.nl><br>Lambert Schomaker <l.r.b.schomaker(at)rug.nl></p> <p> </p> <p><strong>References:</strong><br>1. Bronk Ramsey, C. (2001). Development of the radiocarbon calibration program. <em>Radiocarbon</em>, <em>43</em>(2A), 355-363.</p>
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.