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Above ground plant biomass and leaf area of moist acidic tussock tundra 1981 experimental site (MAT81), Arctic LTER, Toolik Lake, Alaska.1995.
Above ground plant biomass and leaf area were measured in a tussock tundra experimental site. The plots were set up in 1981 and have been harvested in previous years (See Shaver and Chapin Ecological Monographs, 61, 1991 pp.1-31).
Numbers of Eriophorum vaginatum inflorescences, both unclipped and clipped by small mammals, were counted in experimental small mammal exclosure plots, Arct LTER moist acidic tussock site, Toolik Field Station, Alaska, 1997 to 2015
Numbers of Eriophorum vaginatum inflorescences, both unclipped and clipped by small mammals, were counted in experimental plots. The plots are setup in moist acidic tussock tundra near Toolik Field Station, Alaska ((8 degrees 37' 27" N, 149 degrees 36' 27"W) and include fenced exclosures in both fertilized and unfertilized tundra.
Primary producer biomarker profiles of bulk carbon and nitrogen stable isotopes (SI), compound specific stable isotopes of carbon in essential amino acids (CSIA-EAA) and their fatty acid (FA) collected from the Beaufort Sea coastal lagoons,2021-2024
Within Stefansson Sound in Prudhoe Bay, AK various organic matter sources were collected to determine multiple biomarker baseline profiles (i.e., bulk carbon and nitrogen stable isotopes (SI), compound specific stable isotopes of carbon in essential amino acids (CSIA-EAA), fatty acids (FA)). Some organic matter sources were collected from Elson lagoon in Utqiaġvik, AK and Kaktovik and Jago lagoons in Kaktovik, AK to supplement low sample sizes in some organic matter source groups. Kelp, red algae, terrestrial plants, phytoplankton, and ice algae were collected in 2024 with some supplement samples collected in 2021 - 2023. Stable isotope values of δ13C and δ15N are reported as “del_13c” and “del_15n”, respectively. Individual fatty acids are reported as the percent relative to total fatty acids for 23 fatty acids: C11:0, C12:0, C14:0, C15:1, C15:0, C16:0, C16:1n7, C17:0, C17:1, C18:0, C18:1n9 trans, C18:2n6 cis, C18:1n7, C18:3n3, C20:0, C18:3n6, C20:4n6, C21:0, C22:0, C22:1n9, C23:0, C24:0, C22:6n3. Stable isotope values of δ13C are reported in the following essential amino acids: Valine (Val), Leucine (Leu), iLeu (isoleucine), Methionine (Met), Phenylalanine (Phe). Additionally, we used ice algal diatoms collected in the Arctic (landfast ice near Utqiaġvik, Alaska) and cultured in a laboratory setting at the University of Alaska Fairbanks to compare the CSIA-EAA fingerprints of field (composites) ice algal samples and isolate diatoms samples.
Plant biomass in mesic acidic tussock tundra, 1998 15Nitrogen controls, Toolik, Alaska.
Five or six quadrats (20cm x 20cm squares) along a line (block) were collected for plant biomass in mesic tussock tundra. In the lab each quadrat was separated into individual species, new and old aboveground and belowground biomass.
Above and below ground plant biomass in Arctic LTER's 1981 mesic acidic tussock tundra experimental site (MAT81) harvested in 2000, Arctic LTER, Toolik Lake, Alaska.
Above and below-ground plant biomass, including plant roots, was measured in Arctic LTER's moist acidic tussock tundra experimental site (MAT81). The plots were set up in 1981 and have been harvested in previous years (See Shaver and Chapin Ecological Monographs, 61(1), 1991 pp.1-31). This file contains the 2000 harvested biomass and percent carbon and nitrogen summaries for control and fertilized plots. Leaf area data for select species are available in Shaver, G. 2016. https://doi.org/10.6073/pasta/13915ef410067ef23bad0faff678319c
Above ground plant and below ground stem biomass in the Arctic LTER acidic tussock tundra experimental plots, 2002, Toolik Lake, Alaska.
Above ground plant and below ground stem biomass and their carbon and nitrogen content was measured in the Arctic LTER moist acidic tussock tundra experimental plots(MAT89). Treatments included control, nitrogen plus phosphorus amended plots for either 6 or 13 years and vole exclosure plots with or without amends of nitrogen and phosphorus. Note: The added Carbon and Nitrogen values were incorrectly added to the data sheet. A block of data was repeated for all treatments. In version 14 the values were corrected.
Air temperature and humidity, and soil temperature data from the Arctic LTER Moist Non-acidic Tussock Experimental plots (MNT97), Toolik Lake Field Station, Alaska, 1999-2025.
In 1999, a Campbell CR10x data logger was installed in block 2 of the Arctic LTER Toolik Moist Non-acidic Tussock Experimental plots(MNT97). The plots are located on a hillside near Toolik Lake (68 38' N, 149 36'W). Air temperature and relative humidity were measured at 3 meters (control), and inside the greenhouse, and fertilized greenhouse. Soil temperatures were measured with thermocouples placed in control, fertilized, greenhouse, and fertilized-greenhouse plots.
Late season thaw depth measured in the Arctic Long Term Ecological Research (ARC LTER) moist acidic tussock experimental plots at Toolik Field station, Alaska Arctic 1993 to 2025
Late season thaw depth was measured in the Arctic Long Term Ecological Research (ARC LTER) experimental plots (1981 Moist Acidic Tussock, 1989 Moist Acidic Tussock, 2006 Low Fertilization Moist Acidic Tussock, 1989 Moist Non-acidic Tussock, 1989 Moist Non-acidic Non-tussock and 1989 Wet Sedge tundra) at Toolik Lake, Alaska using a steel thaw probe. Note: for 2017-2018 only 1989 Moist Non-Acidic Tussock Tundra and 2006 Low fertilization Moist Acidic Tussock Tundra were measured. For other sites it has become difficult to distinguish rocks from frozen soil with a steel thaw probe. Starting in 2023 weekly thaw depth measurements were made throughout the growing season in the 2006 Low fertilization Moist Acidic Tussock Tundra experiment.
Soil biogeochemical variables collected on the Arctic Long Term Ecological Research (ARC LTER) experimental plots in moist acidic and dry heath tundra, Arctic LTER, Toolik Field Station, Alaska 2017.
**Note: Versions 1 and 2 had the wrong data files.** Soil nutrients (total Carbon and Nitrogen, inorganic nutrients (ammonium ion (NH4), nitrate anion (NO3-), phosphate anion (PO43-)); organic nutrients (extractable organic carbon (EOC), extractable total nitrogen (ETN), extractable organic phosphorus (EOP)), microbial biomass, and extracellular enzyme activity on soils sampled from the Arctic LTER Dry Heath (organic soils only) and Moist Acidic Tundra (organic and mineral soils) herbivore exclosures and control plots at Toolik Lake, AK in July 2017.
Above ground plant, belowground stem and root biomass in Arctic Long-term Ecological Research's 2006 moist acidic tussock tundra experimental sites, 2012, Toolik Lake, Alaska.
Above ground plant, belowground stem and root biomass was measured in moist acidic tussock tundra experimental sites established in 2006 by the Arctic Long-term Ecological Research site (ARC-LTER. Control plots and plots amended with three different levels of nitrogen(N) and phosphorus(P), F10 (10 g/m2 N and 5 g/m2 P); F5 (5 g/m2 N and 2.5 g/m2 P); F2 (2 g/m2 N and 1 g/m2 P), were sampled.
Concentration of gaseous sulfuric acid measured over the Southern Ocean in the austral summer of 2016/2017, during the Antarctic Circumnavigation Expedition (ACE).
<p><strong>Dataset abstract</strong></p> <p>The authors would highly appreciate being contacted if the data is used for any purpose.</p> <p>We measured sulfuric acid concentration in the gas phase with a nitrate chemical ionization mass spectrometer (we used an APi-HTOF mass spectrometer produced by Tofwerk AG coupled with a Chemical ionization inlet A70 produced by Airmodus). Sulfuric acid is detected in the mass spectrometer either as a deprotonated ion or as a cluster with the reagent ion (NO3-). The concentration is calculated as the area of these two peaks normalized to the concentration of the reagent ions (monomer, dimer and trimer) and multiplied by a calibration factor that was experimentally derived at Paul Scherrer Institute in the summer 2017, after the campaign. In the atmosphere, sulfuric acid is produced by the oxidation of sulfur dioxide that could have both a natural or anthropogenic origin (e.g. phytoplankton emission or fossil fuel combustion). Sulfuric acid in the atmosphere is responsible for a very large fraction of the newly formed particles, therefore it is important to have accurate measurements of this vapour in remote places like the Southern Ocean to better understand secondary aerosol sources and processes.</p> <p>The data have been cleaned from the influence of the exhaust of the research vessel. Temporal coverage is from January 22, 2017 to March 19, 2017. There are no data for the first leg of the expedition because the instrument was not on the ship. The instrument was operated during leg 4 but data has not been processed yet as they require additional work due to some instrumental issues that affects their quality. Data were collected with one-second time resolution but integrated to five minutes to increase the signal to noise ratio.</p> <p>Concentrations are reported as molecules per cubic centimeter. The lower limit of detection is in the ppq (part per quadrillion) range but was not determined exactly as it varies with the integration time and background noise.</p> <p><strong>Dataset contents</strong></p> <ul> <li>gas_sulfuric_acid_concentration_data.csv, data file, comma-separated values</li> <li>data_file_header.txt, metadata, text format</li> <li>README.txt, metadata, text format</li> <li>change_log.txt, metadata, text format</li> </ul> <p>Data that were missing or bad because of instrumental problems were simply removed from the file (no entry).</p> <p><strong>Change log</strong></p> <p>v1.1 - data files updated</p> <ul> <li>re-analysis of the raw data with an improved mass spectra peak fitting routine, a different calibration factor was also applied to the data following a more detailed analysis of the calibration experiment</li> <li>use updated, corrected GPS data</li> </ul> <p>v1.0 - initial release of dataset</p>
Concentration of gaseous methanesulfonic acid measured over the Southern Ocean in the austral summer of 2016/2017, during the Antarctic Circumnavigation Expedition (ACE).
<p><strong>Dataset abstract</strong></p> <p>The authors would highly appreciate being contacted if the data is used for any purpose.</p> <p>We measured methanesulfonic acid concentration in the gas phase with a nitrate chemical ionization mass spectrometer (we used an APi-HTOF mass spectrometer produced by Tofwerk AG coupled with a Chemical ionization inlet A70 produced by Airmodus). Methanesulfonic acid is detected in the mass spectrometer either as a deprotonated ion or as a cluster with the reagent ion (NO3-). The concentration is calculated as the area of these two peaks normalized to the concentration of the reagent ions (monomer, dimer and trimer) and multiplied by a calibration factor that was experimentally derived at Paul Scherrer Institute in the summer 2017, after the campaign.</p> <p>In the atmosphere, methanesulfonic acid is produced by the oxidation of dimethyl sulfide that is mostly emitted in the atmosphere by phytoplankton. Methanesulfonic acid can contribute to the growth of aerosol particles by condensation or aqueous phase processing in clouds. The data have been cleaned from the influence of the exhaust of the research vessel. Temporal coverage is from 22 January 2017 to 19 March 2017. There are no data for the first leg of the expedition because the instrument was not on the ship. The instrument was operated during leg 4 but data has not been processed yet as they require additional work due to some instrumental issues that affects their quality. Data were collected with one-second time resolution but integrated to five minutes to increase the signal-to-noise ratio.</p> <p>Concentrations are reported as molecules per cubic centimeter. The lower limit of detection is in the ppq (part per quadrillion) range but was not determined exactly as it varies with the integration time and background noise.</p> <p><strong>Dataset contents</strong></p> <ul> <li>gas_methanesulfonic_acid_concentration_data.csv, data file, comma-separated values</li> <li>data_file_header.txt, metadata, text format</li> <li>README.txt, metadata, text format</li> <li>change_log.txt, metadata, text format</li> </ul> <p>There are no null values in the file. Data that were missing or bad because of instrumental problems were simply removed from the file (no entry).</p> <p><strong>Change log</strong></p> <p>v1.1 - data files updated</p> <ul> <li>re-analysis of the raw data with an improved mass spectra peak fitting routine, a different calibration factor was also applied to the data following a more detailed analysis of the calibration experiment</li> <li>use updated, corrected GPS data</li> </ul> <p>v1.0 - initial release of dataset</p>
Data for: Techno-economic and environmental assessment of converting mixed prairie to renewable natural gas with co-product hydroxycinnamic acid, Iowa, USA, 2022-2023.
This dataset compiles model outputs, parameter sets, and documentation supporting a techno‑economic analysis (TEA) and life‑cycle assessment (LCA) of co‑digesting beef cattle manure with pretreated mixed prairie biomass to produce renewable natural gas (RNG), with hydroxycinnamic acids (HCA) and digestate‑derived biochar co‑products. It accompanies the study by Katherine Wild, Elmin Rahic, Lisa A Schulte Moore, and Mark Mba Wright "Techno-economic and environmental assessment of converting mixed prairie to renewable natural gas with co-product hydroxycinnamic acid," in Biofuels, Bioproducts, & Biorefining, 2024 (https://doi.org/10.1002/bbb.2710). The integrated simulation and assessment framework quantifies process performance, economics, and greenhouse‑gas intensity across five scenarios representing combinations of alkaline‑ethanol pretreatment for HCA extraction, liquid recirculation fractions, and biochar addition. This data collection includes: stream‑level mass flow/composition tables for each scenario; RNG, biochar, and HCA annual production summaries; literature‑based methane/biogas yield benchmarks; equipment‑level capital costs; TEA assumptions; emission‑factor inventories and displacement credits; and full sensitivity/uncertainty matrices for MFSP and GWP.
Soil nitrogen availability and acidity: effects on aboveground production and belowground carbon allocation in mid- and late-successional mixed temperate forests (2009-2021)
In 2011, an experimental nitrogen x pH manipulation study was initiated in mid- and late-successional mixed temperate forests in central New York, USA to disentangle the often-confounded roles of nitrogen (N) and soil pH in driving various ecosystem processes. This data package contains forest productivity (wood, litterfall, and aboveground net primary production), total belowground carbon flux (TBCF), and leaf litterfall and fine root chemistry (C and N concentration) data collected from all experimental plots. It also includes plot-level, species-weighted estimates of measured and modeled photosynthesis (Anet) for the late-successional stands. Wood production, litterfall production, and litterfall chemistry data were collected between 2009 and 2019. Aboveground net primary production data are reported for a pre-treatment interval (2009-2011) and the interval including years 6-9 of experimental treatment (2016-2019). All other properties were measured between years 9 and 11 of the experiment (2019-2021).
Hourly weather data from the Arctic LTER Moist Acidic Tussock Experimental plots from 2011 to present, Toolik Filed Station, North Slope, Alaska.
Hourly weather data from the LTER Moist Acidic Tussock Experimental plots. The station was installed in 1990 in block 2 of the Toolik LTER experimental moist acidic tussock plots. The plots are located on a hillside near Toolik Lake (68 38' N, 149 36'W). Global solar radiation, photosynthetic active radiation, unfrozen precipitation, air temperature, relative humidity, wind speed, and wind direction are measured at 3 meters. Additional sensors in greenhouses and shade houses plots measure air temperature, relative humidity and photosynthetic active radiation during the growing season. The sensors are read every minute and averaged or totaled every hour.
Relative percent cover of plant species in low nutrient LTER moist acidic tundra experimental plots (MAT06) established in 2006 for years 2008, 2010-2025, Arctic LTER Toolik Field Station Alaska.
Relative percent cover of plant species was measured in low nutrient LTER moist acidic tundra experimental plots (MAT06). Treatments include a gradient of nitrogen and phosphorus additions along with ammonium and nitrate alone.
Plant and root biomass, nitrogen, carbon, and phosphorus concentrations in a mesic acidic tussock tundra experimental site established in 1981(MAT81) and harvested in 2015, Arctic LTER, Toolik Lake, Alaska.
Plant and root biomass, nitrogen, carbon, and phosphorus were measured in 2015 in the Arctic LTER tussock tundra experimental site (MAT81). This site was established in 1981 and has been harvested in previous years (see Shaver and Chapin Ecological Monographs, 61(1), 1991, pp.1-31, https://doi.org/10.2307/1942997). Data tables include the biomass for each harvested quadrat and block summaries for percent carbon, nitrogen, and phosphorus for control and fertilized plots from the original 4-block design. New control plots, established in 2015, are in a separate data table and include biomass, percent carbon, nitrogen, and phosphorus for each quadrat.
Block summaries of biomass, carbon, nitrogen, and phosphorus allocation among tissue types, species, and plant functional types from Arctic LTER 1981 Moist Acidic Tussock (MAT81) long-term experiment harvests: 2000 and 2015, Toolik Lake Field Station, Alaska.
A complete accounting of biomass, C, N, and P allocation both among tissue types (leaves, stems, rhizomes, roots) and among species and plant functional types from Arctic LTER 1981 Moist Acidic Tussock (MAT81) long-term experiment’s untreated control plots and plots that were fertilized annually, harvested after 20 and 35 years, near Toolik Lake Field Station, Alaska. Data are gram per meter squared summarized by block.
Darwin: an amino acid sequence collection of complete proteomes from eukaryotes with different phylogenetic affinities (v. 03_2020_137)
<p><strong>Background</strong></p> <p>Every time we find an interesting gene in an organism of interest, the first question is often “how widely is this gene distributed in the eukaryotic kingdom?”. Naturally, one could use NCBI BLAST search against the non-redundant sequence database provided by GenBank to answer this question. However, it can be cumbersome to parse the results and assign them to taxonomic units. It is also not straightforward to get an overview of which eukaryotic groups are represented in the results. Top BLAST hits can be crowded with sequences from closely-related organisms making it difficult gain an overview of the overall distribution across eukaryotes. To streamline this process, we developed an in-house database of complete eukaryotic proteomes. We tagged each sequence with a eukaryotic group handle (two-character symbol) and combined them into a single data set searchable by standalone BLAST on one’s own computer. We named this data set “Darwin” to reflect the diverse nature of the sequences it contains. </p> <p><strong>Methods</strong></p> <p>We downloaded predicted proteomes in FASTA format from different sources such as GenBank, Joint Genome Institute (Depart of Energy, USA), Broad Institute (Massachusetts Institute of Technology, USA), Phytozome and a number of other specialized websites catering for a specific organism such as the Arabidopsis Information Resource (TAIR), or the Saccharomyces Genome Database (SGD). All the organisms we included in Darwin are listed in Table 1. To reduce redundancy, we took care not to include the same species more than once unless subspecies were known to show wide diversity. Each sequence header was tagged with a eukaryotic group handle composed of two-character symbols (based on Keeling <em>et al</em>., 2005). These handles clearly appear in BLAST output and can be parsed easily. We combined sequences from all proteomes into a single data set and named it “Darwin”.</p> <p><strong>Results</strong></p> <p>The current version of Darwin (v. 03_2020_137) contains 2,601,132 amino acid sequences from 137 eukaryotes (Table 1, Data file 1). The sizes of the proteomes were diverse, ranging from ~4000 sequences in some alveolates to 60,000-76,000 in plants. Darwin represents most of the supergroups of eukaryotic kingdom described in Keeling <em>et al.,</em> (2005) except those in Rhizaria whose genomes were not available at the time of data set construction. The data set contains larger numbers of proteomes from fungi and plants reflecting areas of interest in our group. </p> <p><strong>Conclusions</strong></p> <p>Darwin is provided as a text fasta file that can be formatted for BLAST searches on standalone computers. The results from the BLAST searches can be parsed to determine how widely a gene of interest is distributed among different eukaryotes. Simple counting of the eukaryotic group handles would also yield an overview of the distribution across taxa. Darwin is also useful for rapidly finding out whether a gene is missing in particular taxa.</p> <p><strong>Reference</strong></p> <p>Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, Roger AJ, Gray MW (2005) The tree of eukaryotes. <em>Trends Ecol. Evol.</em> <strong>20:</strong> 670-676</p>
Drug-drug interactions of irinotecan, 5-fluorouracil, folinic acid and oxaliplatin for improved colorectal carcinoma treatment
<p>Research records and experimental data of the study "Drug-drug interactions of irinotecan, 5-fluorouracil, folinic acid and oxaliplatin for improved colorectal carcinoma treatment"</p>
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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)
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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.