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The Biomass and Plant Functional Traits of Leymus chinensis Affected by Genotypic Diversity and Soil Nitrogen Addition through a Two-year Experiment, Tianjin, China, 2021-2023
In order to investigate the effects of soil nitrogen addition on the genotypic diversity of Leymus chinensis, 12 genotypes of Leymus chinensis were used as plant material and a two-factor experimental design was carried out in this study. Factor one was genotypic diversity of L. chinensis, including three levels: mono-genotype (G1), three genotypes (G3), and six genotypes (G6). Factor two was the soil nitrogen addition level, which included four levels: no nitrogen addition (N0), 2.5 g N/(m²·a) nitrogen application (N2.5), 5 g N/(m²·a) nitrogen application (N5), and 10 g N/(m²·a) nitrogen application (N10). Each treatment had 12 combinations as replicates, and 12 genotypes of L. chinensis were used. The frequency of each genotype was standardized across all treatment levels of genotypic diversity × soil nitrogen addition. The experiment commenced in September 2021 and soil nitrogen was applied every 2 months. Plants were cultivated in the experimental field at Nankai University, but were moved to a greenhouse for overwintering from November to February each year. During the experiment, there were no stresses or disturbances such as shading, drought, or insect feeding; weeds were regularly removed.
Effects of factorial nitrogen, phosphorus, and potassium with micronutrient addition and Host Community on Fungal Endophyte Diversity at Cedar Creek Ecosystem Reserve, Minnesota, USA, 2014
The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across a factorial nitrogen, phosphorus, and potassium addition experiment in Minnesota, USA. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition.
Soil and root-associated fungal response to nitrogen and phosphorus addition from grasslands worldwide: 2011-2012.
Ecosystems across the globe receive elevated inputs of nutrients, but the consequences of this for soil fungal guilds that mediate key ecosystem functions remain unclear. We found that nitrogen and phosphorus addition to 25 grasslands distributed across four continents promoted the relative abundance of fungal pathogens, suppressed mutualists, but did not affect saprotrophs. Structural equation models suggested that responses were often indirect and primarily mediated by nutrient-induced shifts in plant communities. Nutrient addition also reduced co-occurrences within and among fungal guilds, which could have important consequences for belowground interactions. Focusing only on plots that received no nutrient addition, soil properties influenced pathogen abundance globally, whereas plant community characteristics influenced mutualists, and climate influenced saprotrophs. These guild-level responses enhance our ability to predict soil functional responses to anthropogenic eutrophication and the associated longer-term responses of plant communities to this important global change factor.
Quarterly porewater salinity and conductivity measurements from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) Project
The Georgia Coastal Ecosystems LTER Seawater Addition Long-Term Experiment (SALTEx) is a large-scale field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. Thirty porewater well samples were collected every 2-3 months from all 30 treatment plots using a peristalsis pump. Salinity, conductivity and water temperature were measured from the samples using a handheld conductivity/salinity meter.
Effect of salt water intrusion on the distribution of invertebrates in a GA tidal freshwater marshes from the GCE Seawater Addition Long-Term Experiment (SALTEx) project.
To characterize the effect of persistent and episodic salt water intrusion on the distribution of common freshwater marsh invertebrates, we monitored the density of adult and juvenile fiddler crabs and snails. Prior to the start of salt water addition treatments, we collected data on the distribution of crabs and snails in all 30 experimental plots (6 replicates of 5 treatments: pressed salt water addition, pulsed salt water addition, fresh water addition, procedural control structure, and control no structure). In each experimental plot, we counted the number of adult and juvenile fiddler crab burrows and snails visible on the marshs surface in a 50cm x 75cm plot (juvenile fiddler crabs were counted in only half of this area) that was positioned in the Northeastern corner of each experimental plot. Initial data was collected in March 2014. A Bentho Torch was used to measure the concentrations of cyanobacteria, diatoms, and green algae on the marsh surface in 2015 and 2016.
SALTEx soil oxidation-reduction (redox) potential measurements from the GCE LTER Seawater Addition Long-Term Experiment (SALTEx) between July 2016 and March 2017
SALTEx (Seawater Addition Long-Term Experiment) is a field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots , each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. Response measurements include porewater chemistry, specifically concentrations of chloride, sulfate, sulfide, dissolved organic carbon (DOC), ammonium-N, nitrate/nitrite-N, dissolved reactive phosphorus, total phosphorus, total nitrogen, organic nitrogen, carbon:nitrogen ratio, organic-carbon:organic-nitrogen ratio, and pH.
Continuous groundwater well temperature, salinity and water level measurements at the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) site from May 2014 to February 2018
The Georgia Coastal Ecosystems LTER Seawater Addition Long-Term Experiment (SALTEx) is a large-scale field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. In order to characterize groundwater salinity, temperature, and plot flooding following experimental manipulation, unvented water pressure, temperature and conductivity were continuously measured in a PVC groundwater well installed at the SALTEx site. Measurements were made at the bottom of the well using a submerged Schlumberger CTD-Diver logger every 15 minutes from 30-May-2014 to 14-Feb-2018. In February 2016 a second CTD-Diver was deployed near the top of the well. Data were downloaded from the loggers using Diver Office communication software, then imported into MATLAB for post-processing, quality control and documentation. Raw, unvented pressure readings were corrected for atmospheric pressure and sensor height from the bottom of the well to generate corrected pressure readings, then water level, salinity and density were calculated from the measured variables using UNESCO algorithms. These data were collected as part of the Georgia Coastal Ecosystems LTER SALTEx project (http://gce-lter.marsci.uga.edu/public/app/send_project_eml.asp?id=73), and will be updated annually.
Porewater chemistry measurements from the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) from July 2017 through July 2019.
The Georgia Coastal Ecosystems LTER Seawater Addition Long-Term Experiment (SALTEx) is a large-scale field experiment designed to simulate saltwater intrusion in a tidal freshwater wetland to predict how chronic (Press) and acute (Pulse) salinization will affect this and other tidal freshwater ecosystems. The SALTEx experiment was initiated in 2012 and consists of 31 field plots, each 2.5 m on a side. There are three treatments (Press, Pulse, and Fresh) and two types of controls (with and without sides), each consisting of six replicates. The Press treatment plots receive regular (4 times each week) additions of a mixture of seawater and fresh river water. Pulse plots receive the same mixture of seawater and river water during September and October, which is historically a time of low flow in the river when natural saltwater intrusion occurs. The Fresh treatment plots receive regular additions of fresh river water. Treatment water is added during low tide to facilitate its infiltration into the soil, and all plots are inundated by astronomical tides at high tide. Response measurements include porewater chemistry, specifically concentrations of chloride, sulfate, sulfide, dissolved organic carbon (DOC), ammonium-N, nitrate/nitrite-N, dissolved reactive phosphorus, total phosphorus, total nitrogen, organic nitrogen, carbon:nitrogen (C:N) ratio, organic-carbon:organic-nitrogen ratio, and pH. Samples of source water were taken after collection (seawater, river water) or mixing (mixed seawater and river water in tanks) and analyzed for concentrations of dissolved reactive phosphorus, total phosphorus, ammonium-N, nitrate/nitrite-N, total nitrogen, organic nitrogen. Source water samples from 2016 and beyond also included measurements of dissolved organic carbon (DOC), carbon:nitrogen ratio, organic-carbon:organic-nitrogen ratio, chloride and sulfate.
Grasshopper counts and feeding damage at the GCE-LTER Seawater Addition Long-Term Experiment (SALTEx) in 2016
Grasshopper abundance and feeding damage were investigated at the Georgia Coastal Ecosystems (GCE) LTER Seawater Addition Long-Term Experiment (SALTEx) study area approximately monthly in 2016. We conducted visual surveys in each replicate plot and counted 3 species of grasshopper (Romalea, Leptysma, Orchelimum) and scored grasshopper feeding damage on 2 species of plants (Zizaniopsis, Pontederia).
Monthly Spartina alterniflora marsh vegetation data for additional sites along the Georgia coast used in the Belowground Ecosystem Resiliency Model
Study plots (1-m2) were established in three Spartina alterniflora-dominated marshes - 2 on Sapelo Island, Georgia, and 1 on Skidaway Island, Georgia, and sampled once each during May, July, August, September, and October of 2016. Nine replicate plots were placed in vegetated marsh along transects that spanned 3 Landsat-8 pixel footprints, with 3 plots per pixel foot print. In each plot, measurements included plant biomass, plant species, stem density, and height. Aboveground biomass was calculated using allometric relationships between plant height, flowering status and mass from plant clipping studies. During these surveys, destructive core sampling was also performed in the proximity of the plots (n = 1 per plot) to measure above and below ground biomass. Chlorophyll, foliar N, and Leaf Area Index measurements were taken in the proximity of the plots.
NGE01 Chronic Addition of Nitrogen Gradient Experiment (ChANGE): Assessing threshold responses of plant community composition and ecosystem processes at Konza Prairie
Chronic nutrient additions can lead to drastic shifts in the plant community through time, both within tallgrass prairie in other grassland ecosystems worldwide. Nutrient addition experiments have answered many questions about patterns of diversity loss and community shifts; however, the level of nutrients which must be added to cause community shifts is unknown. To date, all nitrogen (N) addition experiments at Konza have added 10 g m-2 (e.g., NutNet Plots; Phosphorus (P) Plots; Belowground Plots), yet current rates of N deposition are one-tenth of that level. Even predicted rates of future N deposition in grasslands are not expected to exceed 5 g m-2 by the year 2050 and will likely be around 2 g m-2 for most of the US. This mismatch begs the question will 10 g/m2 affect grasslands the same way 2 or 5 g m-2 will? There are two main goals for this long-term experiment (1) to identify the nutrient threshold needed to drive plant community change with nutrient additions, and (2) to determine what factors underlie those threshold responses (build up of nutrients, mycorrhizal loss, invertebrate herbivory). Konza ChANGE is part of a multi-site experiment spanning grasslands on two different continents: North America – tallgrass prairie (KNZ) and shortgrass steppe (SGS), and China – three sites in Inner Mongolia. By including multiple grasslands, we expand our ability to make generalizations about how grasslands are affected by N additions, and whether thresholds, if they exist, vary with precipitation, natural nutrient availability, and species identity/composition. Research Questions: (1) Do ecosystems have N tolerance thresholds above which community composition will change, and does that differ between grassland types (i.e. mesic and xeric grasslands)? (2) Does adding a large amount of nutrients in one season result in an equivalent community change as adding a small amount over multiple years? (For example does 5 g m-2 for 6 years create the same community change as
2007 Environmental Protection Agency (EPA) National Lakes Assessment dataset plus derived data and additional spatially explicit ancillary environmental data.
Lake water quality is known to be affected by local and regional drivers, including lake physical characteristics, hydrology, landscape position, land cover, land use, geology, and climate. Here, we demonstrate the utility of hypothesis testing within the landscape limnology conceptual framework using a random forest algorithm on large, national-scale, spatially explicit dataset, the United States Environmental Protection Agency 2007 National Lakes Assessment. For 1026 lakes, we tested the relative importance of water quality drivers across spatial scales, the importance of hydrologic connectivity in mediating water quality drivers, and how the importance of both spatial scale and connectivity differ across response variables for five important in-lake water quality metrics (total phosphorus, total nitrogen, dissolved organic carbon, turbidity, and conductivity).
Additional Daily Meteorological Data for Madison Wisconsin (1884-2010)
These data are in addition to "Madison Wisconsin Daily Meteorological Data 1869-current." Additional variables added include: daily cloud cover, wind, solar radiation, vapor pressure, dew point temperature, total atmospheric pressure, and average relative humidity for Madison, Wisconsin. In addition, the adjustment factors which were applied on a given date to calculate the adjusted parameters in "Madison Wisconsin Daily Meteorological Data 1869-current" are also included in these data. Raw data, in English units, were assembled by Douglas Clark - Wisconsin State Climatologist. Data were converted to metric units and adjusted for temporal biases by Dale M. Robertson. For adjustments applied to various parameters see Robertson, 1989 Ph.D. Thesis UW-Madison. Adjusted data represent the BEST estimated daily data and may be raw data. Data collected at Washburn observatory, 8-1-1883 to 9-30-1904. Data collected at North Hall, 10-1-1904 to 12-31-1947 Data collected at Truax Field (Admin BLDG), 1-1-1948 to 12-31-1959. Data collected at Truax Field, center of field, 1-1-1960 to Present. Much of the data after 1990 were obtained in digital form from Ed Hopkins, UW-Meteorology. Data starting in 2002-2005 were obtained from Sullivan at http://www.weather.gov/climate/index.php?wfo=mkx%20 ,then go to CF6 and download monthly data to Madison_sullivan_conversion. Relative humidity data was obtained from 1986 to 1995 from CD's at the State Climatologist's Office. Since Robertson (1989) adjusted all historical data to that collected prior to 1989; no adjustments were applied to the recent data except for wind and estimated vapor pressure. Wind after January 1997, and only wind from the southwest after November 2007, was extended by Dale M. Robertson and Yi-Fang "Yvonne" Hsieh, see methods. Estimated vapor pressure after April 2002 was updated by Yvonne Hsieh, see methods.
Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet NPP Quadrat Sampling at the Sevilleta National Wildlife Refuge, New Mexico
Two of the most pervasive human impacts on ecosystems are alteration of global nutrient budgets and changes in the abundance and identity of consumers. Fossil fuel combustion and agricultural fertilization have doubled and quintupled, respectively, global pools of nitrogen and phosphorus relative to pre-industrial levels. In spite of the global impacts of these human activities, there have been no globally coordinated experiments to quantify the general impacts on ecological systems. This experiment seeks to determine how nutrient availability controls plant biomass, diversity, and species composition in a desert grassland. This has important implications for understanding how future atmospheric deposition of nutrients (N, S, Ca, K) might affect community and ecosystem-level responses. This study is part of a larger coordinated research network that includes more than 40 grassland sites around the world. By using a standardized experimental setup that is consistent across all study sites, we are addressing the questions of whether diversity and productivity are co-limited by multiple nutrients and if so, whether these trends are predictable on a global scale.
Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet Seasonal Biomass and Seasonal and Annual NPP Data at the Sevilleta National Wildlife Refuge, New Mexico
Two of the most pervasive human impacts on ecosystems are alteration of global nutrient budgets and changes in the abundance and identity of consumers. Fossil fuel combustion and agricultural fertilization have doubled and quintupled, respectively, global pools of nitrogen and phosphorus relative to pre-industrial levels. In spite of the global impacts of these human activities, there have been no globally coordinated experiments to quantify the general impacts on ecological systems. This experiment seeks to determine how nutrient availability controls plant biomass, diversity, and species composition in a desert grassland. This has important implications for understanding how future atmospheric deposition of nutrients (N, S, Ca, K) might affect community and ecosystem-level responses. This study is part of a larger coordinated research network that includes more than 40 grassland sites around the world. By using a standardized experimental setup that is consistent across all study sites, we are addressing the questions of whether diversity and productivity are co-limited by multiple nutrients and if so, whether these trends are predictable on a global scale. Above-ground net primary production is the change in plant biomass, represented by stems, flowers, fruit and and foliage, over time and incoporates growth as well as loss to death and decomposition. To measure this change the vegetation variables, including species composition and the cover and height of individuals, are sampled twice yearly (spring and fall) at permanent 1m x 1m plots within each site. Volumetric measurements are made using vegetation data from permanent plots (SEV231, "Effects of Multiple Resource Additions on Community and Ecosystem Processes: NutNet NPP Quadrat Sampling") and regressions correlating species biomass and volume constructed using seasonal harvest weights from SEV157, "Net Primary Productivity (NPP) Weight Data."
Nitrogen addition alters plant competition directly more than indirectly through soil microbes.
Eutrophication, the excessive addition of nutrients to ecosystems, is a pervasive component of global environmental change that can alter community dynamics. Although nitrogen addition experiments have widely documented important declines in plant diversity and shifts in plant species composition, the underlying causes of these outcomes are widely debated. Nitrogen inputs may directly affect plant competition for light or soil water or may influence plant species indirectly by altering the composition of soil microbes. In a 28-year field nitrogen addition experiment, we tested whether nitrogen-induced changes to soil microbes could indirectly alter the outcome of competition between codominant foundation plant species. In the field, long-term addition of inorganic nitrogen slowed the competitive take-over of blue grama grass (Bouteloua gracilis) by black grama grass (B. eriopoda) and thereby stabilized the ecotone between two grassland ecosystems in central New Mexico, USA.
A uniaxial hysteretic superelastic constitutive model applied to additive manufactured lattices - data and postprocessing tools
<p>This data set contains all result data obtained during the implementation of an uniaxial hysteretic superelastic constitutive model and its application to additive manufactured lattices.</p> <p>Furthermore, it contains all ABAQUS .inp files, the implemented subroutine of the hysteretic superelastic constitutive model, diagrams generated from the data, as well as postprocessing tools for generating the diagrams.</p>
GREEN-VARAN additional regions resources
<p>Processed functional regions datasets to be used with GREEN-VARAN</p> <p>This repository contains the GRCh37 and GRCh38 files as indexed BED files. The GRCh38 version of UCNE and TAD were obtained by coordinate liftover.</p> <ul> <li>TFBS from ENCODE v3</li> <li>DNase hypersensitivity peaks from ENCODE v3</li> <li>UCNE (ultra-conserved non-coding elements) from https://ccg.epfl.ch/UCNEbase/</li> <li>TAD (topologically associating chromatin domains) from http://dna.cs.miami.edu/TADKB/</li> <li>Super enhancer from dbSuper at http://bioinfo.au.tsinghua.edu.cn/dbsuper/</li> </ul> <p>Please refer to the original datasets listed in related identifiers and references for eventual limits in use and distribution</p>
Chemical and Random Additive Noise Elimination (CRANE)
<p><strong>Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)</strong></p> <p><strong>Availability and implementation</strong></p> <p>The software is available on Github (<a href="https://github.com/CMRI-ProCan/CRANE">https://github.com/CMRI-ProCan/CRANE</a>). The datasets were obtained from ProteomeXchange (Identifiers—PXD002952 and PXD008651). Preliminary data and intermediate files are available via ProteomeXchange (Identifiers—PXD020529 and PXD025103).</p>
Additional evidence for a pulsar wind nebula in SN 1987A from multi-epoch X-ray data and MHD modelling
<p>This is a basic reproduction package for the paper "Additional evidence for a pulsar wind nebula in the hearth of sN 1987A from multi-epoch X-ray data and MHD modeling" by Greco et al. 2022. It aims to provide the most important data products to check and reproduce the main results of the paper.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.