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1,947 results for “fate”
Efficacy and fate of fluridone applications for control of invasive submersed aquatic vegetation in the estuarine environment of the Sacramento-San Joaquin Delta
We conducted a study in the Sacramento-San Joaquin Delta to determine efficacy of the widely used herbicide fluridone in an estuarine ecosystem. The primary goal of SAV removal was restoration of open water habitat for endangered Hypomesus transpacificus (Delta Smelt). Over 18 months and multiple sets of multi-week fluridone applications, we monitored concentrations of fluridone and responses by SAV across pairs of treated and reference sites. Fluridone concentrations in the water were generally below the 2-5 parts per billion required for SAV control. Monitoring demonstrated these low water concentrations were likely due to dissipation by tides, despite use of pelleted fluridone formulations marketed for flowing water environments. Fluridone did, however, accumulate in sediment at concentrations hundreds of times higher than those measured in the water. Nonetheless, we did not observe lasting reductions in SAV abundance or changes in SAV community composition. By demonstrating lack of efficacy of one of the few herbicides permitted for use in this estuary, this study highlights the need for development of SAV management tools tailored to the challenges of hydrologically complex environments like estuaries.
The fate of a plant defense mutualism in a warming world at the University of Michigan Biological Station, Pellston, MI (2024-2026)
Mutualisms are vital to plant survival and reproduction, but climate warming has the potential to alter these interactions. One such mutualism involves foliar mites, which provide plants with defense by consuming harmful fungi. In exchange, plants offer protective structures on their leaves called domatia. Both mite and fungal communities are potentially temperature-sensitive, and warming may shift community composition, potentially altering trophic interactions between botch groups. However, the specific changes in mite and fungal community composition and their implications for plant-mite mutualism and plant performance remain unclear. To investigate the responses of both of these communities to warming, and the effects these changes will have on plants, I conducted a nested factorial field experiment with 96 P. serotina seedlings at the University of Michigan Biological Station. Plants were warmed using open top chambers, nested within which were fully factorial manipulations of the mite and fungal communities. Each group was manipulated using either pruning tar to exclude mites or Quilt fungicide to exclude fungi.
Supporting data for review article: The Global Distribution, Formation, and Fate of Mineral-Associated Soil Organic Matter Under a Changing Climate – A Trait-Based Perspective
<p>Supporting data and code for review article: Sokol N.W., Whalen E.D., Kallenbach C., Pett-Ridge J., Georgiou K. The Global Distribution, Formation, and Fate of Mineral-Associated Soil Organic Matter Under a Changing Climate – A Trait-Based Perspective. <em>Functional Ecology, </em>2022.</p> <p>We leveraged data from a global synthesis of soil fractionation measurements (DOI: 10.5281/zenodo.5987415). For this review article, we specifically focused on measurements of bulk and mineral-associated soil organic carbon concentrations (reported in units of gC/kg soil) and the proportion of bulk soil organic carbon that is mineral-associated (reported as a %). This subset also includes auxiliary data regarding climate and biome characteristics extracted from the synthesized papers; for more variables, see the original full dataset. Köppen-Geiger climate zones were extracted from a georeferenced global database (using R package 'kgc' v1.0.0.2) with site coordinates, where available. Three files are provided in this repository: (1) data file, (2) metadata file, and (3) code for manuscript figures and summary statistics.</p>
Simulation output for seven simulations with CLM-FATES in the Land Sites Platform
<p>Supporting data for a manuscript involving simulation of vegetation with the<a href="https://www.cesm.ucar.edu/models/clm"> Community Land Model </a>and<a href="https://github.com/NGEET/fates"> FATES</a>. Simulations were run using the <a href="https://noresmhub.github.io/noresm-land-sites-platform/">Land Sites Platform </a>on two virtual linux machines provided by <a href="https://nrec.no/">NREC</a>. The manuscript is part of my (EL) PhD thesis. <br> <br> See the associated GitHub repository for notebooks and workflow documentation, and the thesis chapter or manuscript for further information.</p> <p>In this dataset:</p> <ul> <li>Concatenated model history files for the entire simulation period (e.g. "alp4-1500-cosmo-IA.0-1500.nc")</li> <li>Readme files per simulation specifying the variables passed to the Land Sites Platform to start the simulation (e.g. "readme.md")</li> <li>Zipped case folders, containing the standard CLM case folder structure. Individual monthly history files are found under /archive/lnd/hist. E.g. "2985cbd23a2e3d7b1ac057abd862abb7_alp4-1500-cosmo-ia.zip"</li> </ul>
Known-fate survival information for radio-tagged snowshoe hares captured in Bonanza Creek Experimental Forest from June 2008 to November 2012
This dataset contains known-fate survival information for radio-tagged snowshoe hares captured in two 200 x 450 m live-trapping grids in Bonanza Creek Experimental Forest from June 2008 to November 2012. The data can be sorted and viewed by year, site, number at risk, and number of mortalities.
Fates and morphometrics of snowshoe hares collared in Bonanza Creek Experimental Forest from 2008 to present
This dataset contains the fates and morphometric measurements of snowshoe hares collared in Bonanza Creek Experimental Forest, including dates of collaring and recovery, cause or mortality, weight, hind foot length, and sex.
Inferring and perturbing cell fate regulomes in human cerebral organoids
<p>Supplementary data for the manuscript: Inferring and perturbing cell fate regulomes in human cerebral organoids.</p> <p>Note: Due to the size limit of the repository, this update doesn't include all the relevant data. The following data are available via the same repository but different versions:</p> <ul> <li>Processed data in Seurat objects: <a href="https://doi.org/10.5281/zenodo.7687749" target="_blank" rel="noopener">Version 3</a> - seurat_objects.tar.gz</li> <li>scATAC-seq fragment files by Cell Ranger: <a href="https://zenodo.org/records/13254037" target="_blank" rel="noopener">Version 4</a></li> </ul>
Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids
<p><strong>Abstract: </strong>Disruptions in the tightly regulated process of human brain development have been linked to increased risk for brain and mental illnesses. While the genetic contribution to these diseases is well established, important environmental factors have been less studied at molecular and cellular levels. In this study, we used single-cell and cell-type-specific techniques to investigate the effect of glucocorticoid (GC) exposure, a mediator of antenatal environmental risk, on gene regulation and lineage specification in unguided human neural organoids. We characterized the transcriptional response to chronic GC exposure during neural differentiation and studied the underlying gene regulatory networks by integrating single-cell transcriptomics- with chromatin accessibility data. We found lasting cell type-specific changes that included autism risk genes and several transcription factors associated with neurodevelopment. Chronic GCs influenced lineage specification primarily by priming the inhibitory neuron lineage through key transcription factors like PBX3. We provide evidence for convergence of genetic and environmental risk factors through a common mechanism of altering lineage specification.</p>
Toward greater realism in inclusive fitness models: the case of caste fate conflict in insect societies
<p>In the field of social evolution, inclusive fitness theory has been successful in making a wide range of qualitative predictions on expected patterns of cooperation and conflict. Nevertheless, outside of sex ratio theory, inclusive fitness models that make accurate quantitative predictions remain relatively rare. Past models dealing with caste fate conflict in insect societies, for example, successfully predicted that if female larvae can control their own caste fate, an excess should opt to selfishly develop as queens. Available models, however, were unable to accurately predict levels of queen production observed in <em>Melipona</em> bees – a genus of stingless bees where caste is self-determined – as empirically observed levels of queen production are ca. two times lower than the theoretically predicted ones. Here, we show that this discrepancy can be resolved by explicitly deriving the colony-level cost of queen overproduction from a dynamic model of colony growth, requiring incorporation of parameters of colony growth and demography, such as the per-capita rate at which new brood cells are built and provisioned, the percentage of the queen's eggs that are female, costs linked with worker reproduction and worker mortality. Our revised model predicts queen overproduction to more severely impact colony productivity, resulting in an evolutionarily stable strategy (ESS) that is ca. half that of the original model, and is shown to accurately predict actual levels of queen overproduction observed in different <em>Melipona</em> species. Altogether, this shows how inclusive fitness models can provide accurate quantitative predictions, provided that costs and benefits are modelled in sufficient detail and are measured precisely.</p>
Fate and detectability of rare gas hydride ions in nova ejecta: A case study with nova templates
<p>The electron-impact HeH+ rovibrational data at temperatures up to 20,000 K used in the paper: "Fate and detectability of rare gas hydride ions in Novae ejecta: A case study with Nova templates".</p>
The fate of sediment after a large earthquake
<p>This folder contains the Supplemental material related to Francis et al 2021; The fate of sediment after a large earthquake, Submitted to JGR Earth Surface<br> The folder contains 3 sub-folders and 2 excel spreadsheets.</p> <p>ChannelWidthSurveys - This folder contains the shape files of the 17 surveyed catchments and the jupyter notebook (ChannelDepositNotebook.ipynb) which is used to generate the Tributary channel deposit sediment budget.</p> <p>MassMovementInventory - This folder contains the shapefiles which are the basis of the mass movement sediment budget. More information on the origin and the attributes of these files can be found in Fan, X. et al. 2019. Two multi-temporal datasets that track the enhanced landsliding after the 2008 Wenchuan earthquake. Earth System Science Data 11(1), pp. 35–55. Available at: https://www.earth-syst-sci-data.net/11/35/2019/.</p> <p>MassBalanceFiles - This folder contains the jupyter notebook (MonteCarloSedimentBudgets.ipynb) which generates the sediment budget described in Francis et al 2021. The .txt and .csv files are the inputs and outputs of this notebook. See the notebook itself for more information on these files.</p> <p>TributaryChannelDepositSedimentBudget.xlsx - This file is the excel folder showing the processed results of ChannelDepositNotebook.ipynb. The file contains the final results and the processing methodology to allow the reader to reproduce the results.</p> <p>MassBudget.xlsx - This folder contains the final results of the sediment budget described in Francis et al, 2021. This excel file is made up of copying and pasting the output .txt files of MonteCarloSedimentBudgets.ipynb.</p>
Simulation outputs used in "Individual variation in dispersal, and its sources, shape the fate of pushed vs. pulled range expansions"
<p>Simulation outputs used in "Individual variation in dispersal, and its sources, shape the fate of pushed vs. pulled range expansions" (by Maxime Dahirel, Chloé Guicharnaud and Elodie Vercken)</p> <p>This is a copy for archiving purposes of the saved outputs from a NetLogo simulation model of range expansions, used in the analyses described in the following GitHub repository: https://github.com/mdahirel/pushed-pulled-2020-heritability-IBM (Zenodo archive: https://doi.org/10.5281/zenodo.5830993)</p> <p>This .csv file is the final output of the "generate_simulations" code in that repo, and feeds into in the "analyse_simulations" and "supplementary" codes. It is meant to be copied in the NetLogo_output folder of the aforementioned repo after download, in case one:</p> <p>- wants to check our analysis code</p> <p>- and does not want/ have time to re-run the simulations from scratch</p> <p>For any other information, including on the contents of the csv, please see the aforementioned repository</p> <p> </p>
Data from: Seed fate in ant-mediated dispersal: Seed dispersal effectiveness in the Ectatomma ruidum (Formicidae) - Zanthoyxlum ekmanii (Rutaceae) system
<p>Plants are often dispersal limited relying on passive or active agents to find suitable microhabitats for germination. Seeds of pioneer tree species, for example, require light gaps for growth but have short median dispersal distances and often do not provide a food reward to encourage animal dispersal. Zanthoxylum ekmanii seeds are frequently moved by ants but evaluating the effectiveness of ant-mediated seed removal requires knowledge of the species moving the seeds, how far they are moved, and the deposition site. To assess the effectiveness of ants as seed dispersers of Z. ekmanii, we utilized the seed dispersal effectiveness framework. We tracked the movement of seeds from caches on the forest floor, revealing that foragers of Ectatomma ruidum moved 32.8% of seeds an average first distance of 99.8 cm with 68.3% of those seeds taken into a colony. The quality of deposition location was assessed using a seedling emergence study where freshly germinated seeds were buried at different depths. Seedlings were primarily able to emerge from the shallowest depths. Wax castings of E. ruidum colonies demonstrated that seeds brought into the colony were deposited in chambers that had larvae present and experienced more damage than seeds unhandled by ants. Foragers, however, did not have a strong enough bite force to rupture Z. ekmanii seeds likely because their muscle morphology is not structured to maximize force generation. Overall, E. ruidum may help fine tune deposition location, incorporating seeds into the topsoil, though few seeds will likely emerge if soil bioturbation is low.</p>
Data supporting the study "The impact of molecular self-organisation on the atmospheric fate of a cooking aerosol proxy" by Milsom et al.
<p>Model and experimental data from the study "The impact of molecular self-organisation on the atmospheric fate of a cooking aerosol proxy" to be published in Atmospheric Chemistry and Physics. </p>
Mining minerals and critical raw materials from bittern: Understanding metal ions fate in saltwork ponds
<p>Seawater represents a potential resource for raw materials extraction. Although NaCl is the most representative mineral<br> extracted other valuable compounds such as Mg, Li, Sr, Rb and B and elements at trace level (Cs, Co, In, Sc, Ga and<br> Ge) are also contained in this “liquid mine”. Most of them are considered as Critical Raw Materials by the European<br> Union. Solar saltworks, providing concentration factors of up-to 20 to 40, offer a perfect platform for the development<br> of minerals and metal recovery schemes taking benefit of the concentration and purification achieved along the evaporation<br> saltwork ponds.<br> However, the geochemistry of these elements in this environment has not been yet thoroughly evaluated. Their knowledge<br> could enable the deployment of technologies capable to achieve the recovery of valuable minerals. The high ionic<br> strengths expected (0.5–7 mol/kg) and the chemical complexity of the solutions imply that only numerical geochemical<br> codes, as PHREEQC, and the use of Pitzer model to estimate the activity coefficients of the different species in solution<br> can be adopted to provide valuable description of the systems.<br> In the present work, for the first time, PHREEQC Pitzer code database was extended to include the target minor and<br> trace elements using Trapani saltworks (Sicily, Italy) as a case study system. The model was able to predict: i) the purity<br> in halite and the major impurities contained, mainly Ca,Mgand sulphate species; ii) the fate of minor components as B,<br> Sr, Cs, Co, Ge and Ga along the evaporation ponds. The results obtained pose a fundamental step in critical raw materials<br> mining from seawater brine, for process intensification and combination with desalination.</p>
Supplementary datasets for quantitative fate mapping
<p>Supplementary datasets for quantitative fate mapping:</p> <p>Dataset S1. All quantitative fate maps. Related to Figure 1. </p> <p>Dataset S2. inDelphi predicted mutant allele probabilities for hgRNAs in MARC1 mice and iPSC line. Related to Figure 4 and Figure 7. </p> <p>Dataset S3. Simulated phylogenies, single cell lineage barcodes, Phylotime reconstructed trees, fate map and set of MARC1 hgRNAs used for all experiments. Related to all Figures.</p>
Fig. 1 in The palm (Arecaceae) collections gathered by Bonpland and Humboldt in their American journey: origin and fate of the specimens and typifications
Fig. 1. – Representative palm specimens collected by Bonpland and Humboldt deposited in P-Bonpl. A. Bactris gasipaes Kunth; B. Ceroxylon andicolum Bonpl.; C. Corypha miraguama Kunth; D. Oreodoxa regia Kunth.
Fig. 4 in The palm (Arecaceae) collections gathered by Bonpland and Humboldt in their American journey: origin and fate of the specimens and typifications
Fig. 4. – Illustrations associated to the palms collected by Bonpland and Humboldt. A-B. Copper engravings produced by Turpin of the growth habit (A) and the male inflorescence (B) of Ceroxylon andicolum Bonpl. (Plantae Aequinoctiales 1: 1. 1805) based on original sketches drawn by Humboldt on site; C-D. Illustrations of Attalea amygdalina Kunth; grisaille deposited at P-Bonpl. (C) and coloured plate (D) published in the Nova genera 1: 319. 1816.
Fig. 7 in The palm (Arecaceae) collections gathered by Bonpland and Humboldt in their American journey: origin and fate of the specimens and typifications
Fig. 7. – Original descriptions of the royal Cuban Palm (Oreodoxa regia Humboldt & Bonpland ex Kunth). A. Entry 1276 in the "Journal Botanique" (MS 1332); B. Description of the species in Nova genera 1: 305. 1816.
Fig. 3 in The palm (Arecaceae) collections gathered by Bonpland and Humboldt in their American journey: origin and fate of the specimens and typifications
Fig. 3. – Representative palm specimens collected by Bonpland and Humboldt deposited in European herbaria. A. Mauritia flexuosa L. f. deposited at B; B. Ceroxylon andicolum Bonpl. deposited at FI; C. Corypha dulcis Kunth deposited at G; D. Corypha tectorum Kunth. deposited at M.
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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.