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951 results for “Data release”
Assessing impacts of social-ecological diversity on resilience in a wetland coupled human and natural system: Data release
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hannahcgunderman/INSC590_DataPreservation: Release for INSC590: Data Preservation Project
<p>This is the version 2 release of the repository for the Data Preservation Project for INSC590: Data Management at the School of Information Sciences at UT-Knoxville.</p>
Data for: Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation
<p>Data for:</p> <p>Houde P, Braun EL, Zhou L. 2020. Deep-time demographic inference suggests ecological release as driver of Neoavian adaptive radiation. Diversity, in review</p> <p>**************************************************<br> The .tar.gz file will expand to yield a directory named "Houde_Braun_Zhou_data_files". That directory has three subdirectories:</p> <p>1. alignments<br> 2. indel_matrices<br> 3. trees</p> <p>The Houde_Braun_Zhou_data_files directory also includes a README.txt file with complete details regarding the contents of each subdirectory.</p>
Galactic Plane Infrared Polarization Survey: Data Release 4
<p>The Galactic Plane Infrared Polarization Survey (GPIPS) used the Mimir near-infrared instrument to survey stellar linear polarization in the H-band (1.6 microns) from Galactic longitude 18 to 56 degrees and latitudes -1 to +1 degrees as 3,237 individual pointings of the 10x10 arcmin field of view of the instrument. This file presents values and uncertainties for Mimir H-band photometry and linear polarimetry for over 13 million stars across this portion of the northern Milky Way. Each of the 13,861,329 stars represented in the file has new H-band photometry reported. Of these, 8,486,028 have linear polarimetry reported. In addition, matching Gaia, 2MASS, GLIMPSE, and WISE matching photometry, parallax, and proper motion values are listed for the tabulated stars. Details regarding the data, data processing, and contents of the file contents may be found in the Astrophysical Journal Supplements article Clemens et al. (2020; DOI 10.3847/1538-4365/ab9f30).</p>
Data from: Allelopathic effects of volatile organic compounds released from Pinus halepensis needles and roots
The Mediterranean region is recognized as a global biodiversity hotspot. However, over the last decades, the cessation of traditional farming in the north part of Mediterranean basin has given way to strong afforestation leading to occurrence of abandoned agricultural lands colonized by pioneer expansionist species like Pinus halepensis. This pine species is known to synthesize a wide range of secondary metabolites and previous studies have demonstrated strong allelopathic potentialities of its needle and root leachates. Pinus halepensis is also recognized to release significant amounts of volatile organic compounds (VOC) with potential allelopathic effects that has never been investigated. In this context, the objectives of the present study were to improve our knowledge about the VOC released from P. halepensis needles and roots, determine if these VOC affect the seed germination and root growth of two herbaceous target species (Lactuca sativa and Linum strictum), and evaluate if soil microorganisms modulate the potential allelopathic effects of these VOC. Thirty terpenes were detected from both needle and root emissions with β-caryophyllene as the major volatile. Numerous terpenes, such as β-caryophyllene, -terpinene or -pinene showed higher headspace concentrations according to the gradient green needles < senescent needles < needle litter. Seed germination and root growth of the two target species were mainly reduced in presence of P. halepensis VOC. In strong contrast with the trend reported with needle leachates in literature, we observed an increasing inhibitory effect of P. halepensis VOC with the progress of needle physiological stages (i.e. green needle < senescent needle < needle litter). Surprisingly, several inhibitory effects observed on filter paper were also found or even amplified when natural soil was used as a substrate, highlighting that soil microorganisms do not necessarily limit the negative effects of VOC released by P. halepensis on herbaceous target species.
Data release for 'Ensemble Forecasting of Major Solar Flares: Methods for Combining Models'
<p>This is a release of the data that were used for validation in the paper 'Ensemble Forecasting of Major Solar Flares: Methods for Combining Models' by J. A. Guerra, S. A. Murray, D. S. Bloomfield, and P. T. Gallagher, that has been submitted to the Journal of Space Weather and Space Climate.</p> <p> </p> <ul> </ul> <p>The naming scheme for the files is in the format:</p> <pre><code>class_type_metric.dat</code></pre> <ul> <li>'class' denotes whether the forecast is for M- or X- class flares.</li> <li>'type' is what kind of forecast, i.e., the original ensemble members, an ensemble created from probabilistic validation metrics, or an ensemble created from categorical validation metrics.</li> <li>'metric' specifies the metric used to create the ensemble in the case of 'probabilistic' or 'categorical' types as above (see paper for further details), or in the case of the original ensemble members the name of the operational forecasting method.</li> </ul> <p> </p> <p>The data files are in the format:</p> <pre><code>obs,prob</code></pre> <ul> <li>'obs' denotes whether or not a flare was observed within 24 hours of the forecast issue time (1 for yes and 0 for no).</li> <li>'prob' gives the probabilistic forecast value (between 0.0 and 1.0).</li> </ul> <p> </p> <p>These data files can easily be read into the <a href="https://cran.r-project.org/web/packages/verification/verification.pdf">R verification package</a> to replicate the results presented in the paper.</p>
Data from quantitative real-time PCR of corticotropin-releasing hormone and glucocorticoid receptor in the hippocampus and hypothalamus of rats subjected to midline fluid percussion injury or control sham surgery.
<p>These files contain all data from quantitative real-time PCR of corticotropin-releasing hormone (CRH) and glucocorticoid receptor (GR) measured in the hippocampus and hypothalamus of male and female rats. Rats were randomly assigned to a treatment group before the initiation of the study. Rats received a control sham surgery or were subjected to midline fluid percussion injury to induce a diffuse traumatic brain injury. Tissue biopsies were collected at 7 days post-injury and analyzed via quantitative real-time PCR. </p> <p> </p>
NMR data in 'Ca2+-dependent release of Synaptotagmin-1 from the SNARE complex on phosphatidylinositol 4,5-bisphosphate-containing membranes' by Voleti, Jaczynska and Rizo, eLife 2020
<p>The Ca<sup>2+</sup> sensor synaptotagmin-1 and the SNARE complex cooperate to trigger neurotransmitter release. Structural studies elucidated three distinct synaptotagmin-1-SNARE complex binding modes involving 'polybasic', 'primary' and 'tripartite' interfaces of synaptotagmin-1. We investigated these interactions using NMR and fluorescence spectroscopy. Synaptotagmin-1 binds to the SNARE complex through the polybasic and primary interfaces in solution. Ca<sup>2+</sup>-free synaptotagmin-1 binds to SNARE complexes anchored on PIP<sub>2</sub>-containing nanodiscs. R398Q/R399Q and E295A/Y338W mutations at the primary interface, which strongly impair neurotransmitter release, disrupt and enhance synaptotagmin-1-SNARE complex binding, respectively. Ca<sup>2+</sup> induces tight binding of synaptotagmin-1 to PIP<sub>2</sub>-containing nanodiscs, releasing synaptotagmin-1-SNARE interactions. Specific effects of mutations in the polybasic region on Ca<sup>2+</sup>-dependent synaptotagmin-1-PIP<sub>2</sub>-membrane interactions correlate with their effects on release. Our data suggest that synaptotagmin-1 binds to the SNARE complex through the primary interface and that Ca<sup>2+</sup> releases this interaction, inducing PIP<sub>2</sub>/membrane binding and allowing cooperation between synaptotagmin-1 and the SNAREs in membrane fusion to trigger release.</p>
phylogeography/travelHistory: first release fo travel history data associated with a manuscript
<p>This is the first release</p>
herminiogg/shexml-paper-2019-data: First release of ShExML paper data
<p>Data and examples about the ShExML paper testing the usability of first time users</p>
The dynamics and stoichiometry of dissolved organic carbon release by kelp: Carbon fixation, DOC release and nutrient uptake data
<p>Canopy-forming kelps are foundational species in coastal ecosystems, fixing tremendous amounts of carbon, yet we know little about the ecological and physiological determinants of dissolved organic carbon (DOC) release by kelps. We examined DOC release by the bull kelp, <i>Nereocystis luetkeana</i>, in relation to carbon fixation, nutrient uptake, tissue nitrogen content, and light availability. DOC release was approximately 3.5 times greater during the day than at night. During the day, <i>N. luetkeana</i> blades released an average of 16.2% of fixed carbon as DOC. Carbon fixation increased with light availability but DOC release did not, leading to a lower proportion of fixed carbon released as DOC at high light levels. We found no relationship between carbon fixation and DOC release rates measured concurrently. Rather, DOC release by <i>N. luetkeana</i> blades declined with marginal significance as blade tissue nitrogen content increased and with experimental nitrate addition, supporting the role of stoichiometric relationships in DOC release. Using a stable isotope (<sup>13</sup>C) tracer method, we demonstrated that inorganic carbon is rapidly fixed and released by <i>N. luetkeana</i> blades as <sup>13</sup>DOC, within hours. However, recently fixed carbon (<sup>13</sup>DOC) comprised less than 20% of the total DOC released, indicating that isotope studies that rely on tracer production alone may underestimate total DOC release, as it is decoupled from recent kelp productivity. Comparing carbon and nitrogen assimilation dynamics of the annual kelp <i>N. luetkeana</i> with the perennial kelp <i>Macrocystis pyrifera</i> revealed that <i>N. luetkeana </i>had significantly higher carbon fixation, DOC production and nitrogen uptake rates per unit dry mass. Both kelp species were able to perform light-independent carbon fixation at night. Carbon fixation by the annual kelp <i>N. luetkeana </i>is as high as 2.35 kg C m<sup>-2</sup> yr<sup>-1</sup>, but an average of 16% of this carbon (376 g C m<sup>-2</sup> yr<sup>-1</sup>) is released as DOC. As kelp forests are increasingly viewed as vehicles for carbon sequestration, it is important to consider the fate of this substantial quantity of DOC released by canopy-forming kelps.</p>
Data from: Phosphorus release from unamended and gypsum-or biochar-amended soils under simulated spring snowmelt and summer flooding conditions
<p>Prolonged flooding changes the oxidation–reduction status of soils, often enhancing phosphorus (P) release to overlying floodwater. We studied P release from unamended, gypsum-amended and biochar- amended soils under simulated snowmelt flooding (previously frozen, cold flooding at +4°C) and summer flooding (unfrozen, warm flooding at +22°C), using two soils, Fyala clay (FYL-Cl) and Neuenberg sandy loam (NBG-SL) from Manitoba, Canada. Amended and unamended soils were packed into vessels and flooded under cold and warm temperatures in the laboratory. Pore water and floodwater samples were taken weekly for 6 weeks after flooding (WAF) and thereafter biweekly for 10 WAF, and analyzed for dissolved reactive P (DRP), pH and cation concentrations. NBG-SL showed a significantly higher DRP concentration in pore water and floodwater despite its low Olsen P content. Redox potential (Eh) decreased slowly under cold compared to warm flooding; hence redox-induced P release was substantially lower under cold flooding. Gypsum amendment significantly decreased the floodwater DRP concentrations in NBG-SL by 38% and 35% under cold and warm flooding, respectively, but had no significant effect in FYL-Cl, which had low DRP concentrations (<1.2 mg L-1) throughout flooding period. Biochar amendment significantly increased floodwater DRP concentrations by 27 to 68% in FYL-Cl under cold and warm flooding, respectively, but had no significant effect in NBG-SL. The results indicate substantially less P release under cold, than under warm flooding. Gypsum was effective in reducing floodwater DRP concentrations only at high DRP concentrations; thus the effectiveness was greater under warm, than under cold flooding conditions.</p>
Source data for: Presynaptic NMDARs cooperate with local spikes toward GABA release from the reciprocal olfactory bulb granule cell spine
<p><span>In the rodent olfactory bulb the smooth dendrites of the principal glutamatergic mitral cells (MCs) form reciprocal dendrodendritic synapses with large spines on GABAergic granule cells (GC), where unitary release of glutamate can trigger postsynaptic local activation of voltage-gated Na<sup>+</sup>-channels (Na<sub>v</sub>s), i.e. a spine spike. Can such single MC input evoke reciprocal release? We find that unitary-like activation via two-photon uncaging of glutamate causes GC spines to release GABA both synchronously and asynchronously onto MC dendrites. This release indeed requires activation of Na<sub>v</sub>s and high-voltage-activated Ca<sup>2+</sup>-channels (HVACCs), but also of NMDA receptors (NMDAR). Simulations show temporally overlapping HVACC- and NMDAR-mediated Ca<sup>2+</sup>-currents during the spine spike, and ultrastructural data prove NMDAR presence within the GABAergic presynapse. The cooperative action of presynaptic NMDARs allows to implement synapse-specific, activity-dependent lateral inhibition and thus could provide an efficient solution to combinatorial percept synthesis in a sensory system with many receptor channels. </span></p>
xltu/GSL_Joint_Min_Entropy: First release of the GSL paper related data and model
<p>First release</p>
metabaRfactory/metabaR_external_data: metabaR_external_data first release
<p>This is the first release</p>
Gene family data from the PhyloGenes (release version 2.2, phylogenes.org)
<p>About the two zip files: </p> <p>1. phyloXML.zip</p> <p>PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. <family_ID>.xml).</p> <p>The following information is provided for each node of a tree:<br> 1) leaf node:<br> branch length<br> name <gene_id><br> taxonomy scientific_name<br> sequence accession <UniProt ID></p> <p>2) non-leaf node:<br> branch length<br> events <duplication or speciation></p> <p><br> 2. CSV.zip</p> <p>Functional information of family members in CSV format, one file per family (e.g. <family_ID>.csv). </p> <p>A CSV file includes the following columns:<br> Uniprot ID<br> Gene <Gene name. If none then Gene ID><br> Gene ID<br> Gene name<br> Organism<br> Subfamily name</p> <p>The columns displayed after 'Subfamily name', if any, are GO annotations. Each column is a GO molecular function or biological process term that is annotated to at least one member of the gene family AND the annotation is supported by an experimental evidence (indicated by 'EXP') or phylogenetic inference (indicated by 'IBA'). A '0' indicates absence of either annotations.</p>
Data from: Competitive release leads to range expansion and rampant speciation in Malagasy dung beetles
Competition is often thought to promote ecological diversification and thereby to facilitate the coexistence of competitors during evolutionary radiations. At large spatial scales, species may also coexist by having allopatric distributions, which raises the question about the role of range expansion in the proliferation of species during radiations. Here, we integrate a well-sampled (50 out of 74 species) and timed phylogeny of Nanos and Apotolamprus dung beetles (Canthonini) in Madagascar with data on species' geographical ranges, abundances, and body sizes. There is an overall decline in lineage accumulation through time since the colonization of northern Madagascar in the mid Miocene (24 to 13 Ma). A clade of 24 extant Nanos species (clade L) originating 6.0 Ma exhibits a secondary increase in speciation rate, which is associated with a significant increase in body size and strikingly allopatric distributions of the species. Large body size typically confers a competitive advantage in dung beetles, which is here reflected by strong numerical dominance of clade L species in local communities. We suggest that the 'key innovation' of large body size has allowed range expansion due to competitive release, which has created extensive opportunities for allopatric speciation and differentiation along environmental gradients. Most theories to explain diversification patterns in Madagascar rely on allopatric modes of speciation, but they fail to explain how ancestral species became widespread in the first place. The mechanism proposed here, involving range expansion following competitive release via a "key innovation", may have operated in other Malagasy taxa with large numbers of species with small geographic ranges.
Data from: Parting ways: Parasite release in nature leads to sex-specific evolution of defense
We evaluate the extent to which males and females evolve along similar or different trajectories in response to the same environmental shift. Specifically, we use replicate experimental introductions in nature to consider how release from a key parasite (Gyrodactylus) generates similar or different defense evolution in male versus female guppies (Poecilia reticulata). After 8-12 generations of evolution, guppies were collected from the ancestral (parasite still present) and derived (parasite now absent) populations and bred for two generations in the laboratory to control for non-genetic effects. These F2 guppies were then individually infected with Gyrodactylus and infection dynamics were monitored on each fish. We found that parasite release in nature led to sex-specific evolutionary responses: males did not show much evolution of resistance, whereas females showed the evolution of increased resistance. Given that male guppies in the ancestral population had greater resistance to Gyrodactylus than did females, evolution in the derived populations led to reduction of sexual dimorphism in resistance. We argue that previous selection for high resistance in males constrained (relative to females) further evolution of the trait. We advocate more experiments considering sex-specific evolutionary responses to environmental change.
Data from: Learning and robustness to catch-and-release fishing in a shark social network
Individuals can play different roles in maintaining connectivity and social cohesion in animal populations and thereby influence population robustness to perturbations. We performed a social network analysis in a reef shark population to assess the vulnerability of the global network to node removal under different scenarios. We found that the network was generally robust to the removal of nodes with high centrality. The network appeared also highly robust to experimental fishing. Individual shark catchability decreased as a function of experience, as revealed by comparing capture frequency and site presence. Altogether, these features suggest that individuals learnt to avoid capture, which ultimately increased network robustness to experimental catch-and-release. Our results also suggest that some caution must be taken when using capture–recapture models often used to assess population size as assumptions (such as equal probabilities of capture and recapture) may be violated by individual learning to escape recapture.
Data from: Humpback whales feed on hatchery-released juvenile salmon
Humpback whales are remarkable for the behavioural plasticity of their feeding tactics and the diversity of their diets. Within the last decade at hatchery release sites in Southeast Alaska, humpback whales have begun exploiting juvenile salmon, a previously undocumented prey. The anthropogenic source of these salmon and their important contribution to local fisheries makes the emergence of humpback whale predation a concern for the Southeast Alaska economy. Here, we describe the frequency of observing humpback whales, examine the role of temporal and spatial variables affecting the probability of sighting humpback whales and describe prey capture behaviours at five hatchery release sites. We coordinated twice-daily 15 min observations during the spring release seasons 2010–2015. Using logistic regression, we determined that the probability of occurrence of humpback whales increased after releases began and decreased after releases concluded. The probability of whale occurrence varied among release sites but did not increase significantly over the 6 year study period. Whales were reported to be feeding on juvenile chum, Chinook and coho salmon, with photographic and video records of whales feeding on coho salmon. The ability to adapt to new prey sources may be key to sustaining their population in a changing ocean.
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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.