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470 results for “dead”
Dead Again: Predictions of repeat tree die-off under hotter droughts confirm mortality thresholds for a dryland conifer species
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Dead litter of resident species first facilitates and then inhibits sequential life stages of range-expanding species
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Data from: Environmental conditions alter successional trajectories on an ephemeral resource: a field experiment with beetles in dead wood
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Fungal OTUs during dead wood succession of aspen
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Georgia Coastal Ecosystems site, station Melon Bluff, study of plant density of dead Spartina alterniflora (Atlantic cordgrass) in units of stemsPerSquareMeter on a monthly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains plant density of dead Spartina alterniflora (Atlantic cordgrass) measurements in stemsPerSquareMeter units and were aggregated to a monthly timescale.
Figure 7. The new F1000Workspace that provides a in The five deadly sins of science publishing
Figure 7. The new F1000Workspace that provides a set of tools to enable researchers to collect references, write research articles and grant applications, and collaborate with co-authors and colleagues.
Figure 4 in The five deadly sins of science publishing
Figure 4. An example of an F1000Prime recommendation showing the Faculty Members who made the article recommendation, the rating they gave the article, and the associated comment as to why they felt that article was so interesting.
Figure 3 in The five deadly sins of science publishing
Figure 3. Faculty of 1000, which now comprises 3 core services: F1000Prime, F1000Workspace and F1000Research, and is overseen by the F1000 Faculty comprising over 11,000 members.
Supporting data for "Quantifying fluid retention due to natural vegetation in a forest floodplain analogue using the Aggregated Dead Zone (ADZ) dilution approach"
<p>Raw fluorescence data and derived flow metrics from experimental work undertaken in a hydraulic flume facility in support of the publication:</p> <p>"<strong>Quantifying fluid retention due to natural vegetation in a forest floodplain analogue using the Aggregated Dead Zone (ADZ) dilution approach"</strong></p> <p>Water Resources Research <a href="https://doi.org/10.1029/2020WR027070">https://doi.org/10.1029/2020WR027070</a> </p>
Supplementary evaluation files for the paper: Grid-Based Bayesian Filtering Methods for Pedestrian Dead Reckoning Indoor Positioning Using Smartphones
<p>This package contains evaluation supplementary files for the paper: <em>Grid-Based Bayesian Filtering Methods for Pedestrian Dead Reckoning Indoor Positioning Using Smartphones</em> by Miroslav Opiela and František Galčík.</p> <p><strong>Contents: </strong></p> <ul> <li>ground_truth - real positions of checkpoints for given input files</li> <li>input - sensor measurements recordings with initial positions (also after floor transitions) and checkpoint labels </li> <li>maps - processed map models containing positions of points and connections (e.g., walls) in custom coordinate system. Reference to GNSS and map rotation is inducted in maps-meta.xml</li> <li>output - data processed by the localization system. JSON containing the applied method, its configuration, and all estimated positions. Errors for every folder are summarized in the csv file</li> <li>visualization - trajectories visualized for selected output files</li> <li>readme.txt - describes data formats used for particular files in this dataset and summarizes output files</li> </ul> <p><strong>Venues</strong></p> <p>Data are recorded in three buildings:</p> <ul> <li>codename: SA1, SA1_rotated - recorded by the author in the faculty building (Park Angelinum 9, 04001, Košice, Slovakia) using Lenovo tablet</li> <li>codename: AtlantisR0, AtlantisR-1, AtlantisR+1, AtlantisR+2 - the shopping mall Atlantis Le Centre (Boulevard Salvador Allende, 44800 Saint-Herblain, France). Dataset is from IPIN 2018 competition and loc_20180922_160206 is recorded by the author using Xiaomi Mi 5.</li> <li>codename: CNR_0, CNR_1, CNR_2 - the research institute building CNR (Via Giuseppe Moruzzi, 56127 Pisa, Italy). Dataset is from IPIN 2019 competition. </li> </ul> <p><strong>Used datasets</strong></p> <p>A subset of input data is derivated from available logfiles provided by organizers of IPIN 2018 and IPIN 2019 competitions:</p> <ul> <li>Jimenez, A.R.; Mendoza-Silva, G.M.; Ortiz, M.; Perez-Navarro, A.; Perul, J.; Seco, F.; Torres-Sospedra, J. Datasets and Supporting Materials for the IPIN 2018 Competition Track 3 (Smartphone-based, off-site). <a href="http://dx.doi.org/10.5281/zenodo.2823964">http://dx.doi.org/10.5281/zenodo.2823964</a></li> <li>Jiménez, A. R.; Perez-Navarro, A.; Crivello, A.; Mendoza-Silva, G.; Ortiz, M.; Perul, J.; Seco, F. and Torres-Sospedra, J. Datasets and Supporting Materials for the IPIN 2019 Competition Track 3 (Smartphone-based, off-site), Zenodo 2019. <a href="http://dx.doi.org/10.5281/zenodo.3606765">http://dx.doi.org/10.5281/zenodo.3606765</a> </li> </ul> <p><strong>Funding</strong></p> <p>The work was partially supported by the Slovak Grant Agency of the Ministry of Education and Academy of Science of the Slovak Republic under grant no. 1/0056/18 and by the Slovak Research and Development Agency under the contract no. APVV-15-0091.</p> <p><strong>Contact</strong></p> <p>For any further questions, please contact:</p> <p>Miroslav Opiela, miroslav.opiela@upjs.sk Institute of Computer Science, Faculty of Science, P. J. Šafárik University (UPJS), Košice, Slovakia</p>
Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina
<p>Some but not all of the species of 'little brown mushrooms' in the genus <i>Galerina</i> contain deadly amatoxins at concentrations equaling those in the death cap, <i>Amanita</i> <i>phalloides.</i> However, <i>Galerina</i>'s ~300 species are notoriously difficult to identify by morphology and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which <i>Galerina</i> species contain toxins and which do not. We selected specimens for toxin analysis using a preliminary phylogeny of the fungal DNA barcode region, the ribosomal internal transcribed spacer (ITS) region. Using liquid chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of <i>Galerina</i> and close relatives, collected in western British Columbia, Canada. To put the presence of toxins into a phylogenetic context, we included the 70 samples in maximum likelihood analyses of 438 taxa, using ITS, RNA polymerase II second largest subunit gene (<i>RPB2</i>), and nuclear large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA from types where possible to aid with applications of names. We detected amatoxins only in the 24 samples of the <i>G. marginata</i> s.l. complex in the <i>Naucoriopsis</i> clade. We delimited 56 putative <i>Galerina</i> species using Automatic Barcode Gap Detection software. Phylogenetic analysis showed moderate to strong support for <i>Galerina</i> infrageneric clades <i>Naucoriopsis</i>, <i>Galerina</i>, <i>Tubariopsis</i>, and<i> Sideroides</i>. <i>Mycenopsis </i>appeared paraphyletic and included <i>Gymnopilus</i>. Amatoxins were not detected in 46 samples from <i>Galerina</i> clades outside of <i>Naucoriopsis</i> or from outgroups. Our data show significant quantities of toxin in all mushrooms tested from the <i>G. marginata</i> s.l. complex. DNA barcoding revealed consistent accuracy in morphology-based identification of specimens to <i>G.</i> <i>marginata </i>s.l. complex. Prompt and careful morphological identification of ingested <i>G.</i> <i>marginata </i>s.l. has the potential to improve patient outcomes by leading to fast and appropriate treatment.</p>
Peaceful coexistence between people and deadly wildlife: why are recreational users of the ocean so rarely bitten by sea snakes?
<p>1) Research on interactions between humans and deadly snakes has focused on situations that result in high rates of snakebite; but we can also learn from cases where snakes and people coexist peacefully. For example, coastal bays near Noumea, in the Pacific archipelago of New Caledonia, are used by thousands of tourists and snakes, but bites are rare.</p> <p>2) Our long-term studies clarify reasons for this coexistence. Although 97% of snakes encountered in standardized snorkel surveys were a harmless species (<em>Emydocephalus annulatus</em>), we recorded dangerously venomous taxa often enough (one snake per eight hours snorkelling) that we would expect many risky human- snake interactions in these crowded bays. However, the risk is reduced by low overlap between humans and snakes in the timing of activity, both seasonally and on the diel cycle. Mate-searching male snakes, the group most likely to approach divers, enter the bays only in cooler months of the year when few beach users are present. Also, snakes tend to be active by night whereas people are not.</p> <p>3) Risk is further reduced by spatial divergence: bare-footed beach users stay in sandy areas rather than the adjacent coral-reef areas that are preferred by snakes. The response of snakes to disturbance is important also: most sea snakes are reluctant to bite even when harassed. Water currents frequently push sea snakes against hard objects, perhaps explaining why the snakes do not interpret brief contact with a human as an attack. The ability of snakes to flee is increased by uniformly high body temperature, and a complex three-dimensional aquatic environment.</p> <p>4) Thus, the danger of snakebite for recreational users of these popular beaches is reduced by aspects of human and snake behaviour that (i) decrease encounter rates, and (ii) render snakes unlikely to bite even if contacted. The risk to snakes is also reduced, because snakes are more difficult to detect and kill underwater than on land. As a result, thousands of snakes and people coexist harmoniously within these small bays.</p>
Data from: Dead before detection: addressing the effects of left truncation on survival estimation and ecological inference for neonates
1. Neonate survival is a key life history trait, yet remains challenging to measure in wild populations because neonates can be difficult to capture at birth. Estimates of survival from neonates that are opportunistically captured might be inaccurate because some individuals die before sampling, resulting in data that are left truncated. The resulting overestimation of survival rates can further affect ecological inference through biased estimates of covariate effects in survival models, yet is not addressed in most studies of animal survival. Here, we quantify the effects of left truncation on survival estimates and subsequent ecological inference. 2. Vaginal implant transmitters (VITs) enable capture of ungulates at birth, yielding data without left truncation. The effects of left truncation on survival estimation were quantified using age-dependent survival models for VIT and opportunistically captured neonatal deer. Differences in daily survival rates (DSRs) and cumulative survival probability were calculated for the first 70 days of life. In addition, left truncation was simulated by removing fawns that died during the first 1 or 2 days of life from the VIT-caught sample, isolating the effect of left truncation. 3. Cumulative probability of survival during the first 70 days of life was overestimated by 7–23% for fawns caught opportunistically compared with those caught by VIT, depending on model design. Differences in DSRs were large at age 1 day, but had converged by age 30 days. Simulated left truncation resulted in overestimates of survival of up to 31%. Model selection and covariate coefficients were strongly affected by left truncation, producing spurious ecological inference, including changes to sign and/or magnitude of inferred effects of all covariates. 4. We recommend (i) every effort be made to capture neonates; (ii) consistent capture methods, using at least in part non-truncating techniques, be implemented across years and study areas; and (iii) exclusion of left-truncated data from survival estimates until DSRs converge with those calculated from non-truncated data. This work emphasizes the importance of accounting for left truncation in survival estimation for any species with strong age-dependent survival in order to prevent biased conclusions produced by sampling method rather than true ecological effects.
Data from: The downed and dead wood inventory of forests in the United States
The quantity and condition of downed dead wood (DDW) is emerging as a major factor governing forest ecosystem processes such as carbon cycling, fire behavior, and tree regeneration. Despite this, systematic inventories of DDW are sparse if not absent across major forest biomes. The Forest Inventory and Analysis program of the United States (US) Forest Service has conducted an annual DDW inventory on all coterminous US forest land since 2002 (~1 plot per 38,850 ha), with a sample intensification occurring since 2012 (~1 plot per 19,425 ha). The data are organized according to DDW components and by sampling information which can all be linked to a multitude of auxiliary information in the national database. As the sampling of DDW is conducted using field efficient line-intersect approaches, several assumptions are adopted during population estimation that serve to identify critical knowledge gaps. The plot- and population-level DDW datasets and estimates provide the first insights into an understudied but critical ecosystem component of temperate forests of North America with global application.
Data from: Conservation value of low-productive forests measured as the amount and diversity of dead wood and saproxylic beetles
In many managed landscapes, low-productive land comprises most of the remaining relatively untouched areas, and is often over-represented within protected areas. The relationship between the productivity and conservational value of a site is poorly known; however, it has been hypothesized that biodiversity increases with productivity due to higher resource abundance or heterogeneity, and that the species communities of low-productive land are a nested sub-set of communities from more productive land. We tested these hypotheses for dead wood-dependent beetles by comparing their species richness and composition, as well as the amount and diversity of dead wood, between low-productive (potential forest growth < 1 m3 ha-1 year-1) and productive Scots pine-dominated stands in Sweden. We included four stand types: stands situated on (i) thin soils and (ii) mires (both low-productive), (iii) managed stands, and (iv) unmanaged stands set aside for conservation purposes (both productive). Beetle species richness and number of red-listed species were highest in the productive set-asides. Species richness was positively correlated with the volume and diversity of dead wood, but volume appeared to be a better predictor than diversity for the higher species richness in set-asides. Beetle species composition was similar among stand types, and the assemblages in low-productive stands were largely subsets of those in productive set-asides. However, 11% of all species and 40% of red-listed species only occurred in productive stands, while no species were unique to low-productive stands. We conclude that low-productive forests are less valuable for conservation than productive forest land. Given the generally similar species composition among stand types, a comparable conservational effect could be obtained by setting aside a larger area of low-productive forest in comparison to the productive. In terms of dead wood volumes, 1.8–3.6 ha of low-productive forest has the same value as 1 ha of unmanaged productive forest. This figure can be used to estimate the conservation value of low productive forests; however, as productive forests harbored some unique species, they are not completely exchangeable.
Data from: The walking dead: blender as a tool for palaeontologists with a case study on extinct arachnids
This paper serves two roles. First, it acts as an introduction to Blender, an open-source computer graphics program, which can be of utility to paleontologists. To lessen the software's otherwise steep learning curve, a step-by-step guide to create an idealized reconstruction of a fossil in the form of a three-dimensional model in Blender, or to use the software to render results from 'virtual paleontology' techniques, is provided as an online supplemental data file. Second, here we demonstrate the use of Blender with a case study on the extinct trigonotarbid arachnids. We report the limb articulations of members of the Devonian genus Palaeocharinus on the basis of exceptionally preserved fossils from the Rhynie Cherts of Scotland. We use these newly reported articulations to create a Blender model, and draw comparisons with the gait of extant arachnids to produce as accurate a representation of the trigonotarbid flexing its limbs and walking as possible, presented in additional online supplemental data files. Knowledge of the limb articulations of trigonotarbid arachnids also allows us to discuss their functional morphology: trigonotarbids' limbs and gait were likely comparable to extant cursorial spiders, but lacked some innovations seen in more derived arachnids.
Data from: Large-effect mutations generate trade-off between predatory and locomotor ability during arms race coevolution with deadly prey
Adaptive evolution in response to one selective challenge may disrupt other important aspects of performance. Such evolutionary trade-offs are predicted to arise in the process of local adaptation, but it is unclear if these phenotypic compromises result from the antagonistic effects of simple amino acid substitutions. We tested for trade-offs associated with beneficial mutations that confer tetrodotoxin (TTX) resistance in the voltage-gated sodium channel (NaV1.4) in skeletal muscle of the common garter snake (Thamnophis sirtalis). Separate lineages in California and the Pacific Northwest independently evolved TTX-resistant changes to the pore of NaV1.4 as a result of arms race coevolution with toxic prey, newts of the genus Taricha. Snakes from the California lineage that were homozygous for an allele known to confer large increases in toxin resistance (NaV1.4LVNV) had significantly reduced crawl speed compared to individuals with the ancestral TTX-sensitive channel. Heterologous expression of native snake NaV1.4 proteins demonstrated that the same NaV1.4LVNV allele confers a dramatic increase in TTX resistance and a correlated decrease in overall channel excitability. Our results suggest the same mutations that accumulate during arms race coevolution and beneficially interfere with toxin-binding also cause changes in electrophysiological function of the channel that may affect organismal performance. This trade-off was only evident in the predator lineage where coevolution has led to the most extreme resistance phenotype, determined by four critical amino acid substitutions. If these biophysical changes also translate to a fitness cost—for example, through the inability of T. sirtalis to quickly escape predators—then pleiotropy at this single locus could contribute to observed variation in levels of TTX resistance across the mosaic landscape of coevolution.
Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end
Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are 'evolutionary dead-ends.' This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave-adaptation is not a 'dead-end' for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.
Data from: Priority effects of early successional insects influence late successional fungi in dead wood
Community assembly is an integral process in all ecosystems, producing patterns of species distributions, biodiversity, and ecosystem functioning. Environmental filters and colonization history govern the assembly process, but their relative importance varies depending on the study system. Dead wood decomposition is a slow process, allowing decomposer communities to develop within a slowly changing substrate for decades. Despite this, there are few long-term studies of priority effects from colonization history in this ecosystem. In this study, we investigate the importance of insects in early succession of dead wood on the fungal community present one decade later. Sixty aspen trees were killed in two study landscapes, each tree producing one aspen high stump and log. Insects were sampled with flight interception traps during the first 4 years after tree death, and fungal fruiting bodies were registered in year twelve. We found positive priority effects of two fungivorous beetles, the sap beetle Glischrochilus quadripunctatus and the round fungus beetle Agathidium nigripenne, on the Artist's bracket (Ganoderma applanatum) and a positive priority effect of wood-boring beetles on the ascomycete Yellow fairy cup (Bisporella citrina). The Aspen bracket (Phellinus tremulae) did not respond to insects in early succession of the dead wood. Our results suggest that early successional insects can have significant, long-lasting effects on the late successional fungal community in dead wood. Also, the effect can be specific, with one fungus species depending on one or a few fungivorous beetle species. This has implications for decomposition and biodiversity in dead wood, as loss of early colonizing beetles may also affect the successional pathways they seem to initiate.
Data from: Contests with deadly weapons: telson sparring in mantis shrimp (Stomatopoda)
Mantis shrimp strike with extreme impact forces that are deadly to prey. They also strike conspecifics during territorial contests, yet theoretical and empirical findings in aggressive behaviour research suggest competitors should resolve conflicts using signals before escalating to dangerous combat. We tested how Neogonodactylus bredini uses two ritualized behaviours to resolve size-matched contests: meral spread visual displays and telson (tailplate) strikes. We predicted that (i) most contests would be resolved by meral spreads, (ii) meral spreads would reliably signal strike force and (iii) strike force would predict contest success. The results were unexpected for each prediction. Contests were not resolved by meral spreads, instead escalating to striking in 33 of 34 experiments. The size of meral spread components did not strongly correlate with strike force. Strike force did not predict contest success; instead, winners delivered more strikes. Size-matched N. bredini avoid deadly combat not by visual displays, but by ritualistically and repeatedly striking each other's telsons until the loser retreats. We term this behaviour 'telson sparring', analogous to sparring in other weapon systems. We present an alternative framework for mantis shrimp contests in which the fight itself is the signal, serving as a non-lethal indicator of aggressive persistence or endurance.
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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.