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Illinois Data Bank Dataset Search Results

Dataset Search Results

published: 2022-09-19
 
Data characterize zooplankton in Shelbyville Reservoir, Illinois, United States of America. Zooplankton were sampled with a conical zooplankton net (0.5m diameter mouth) when water was deeper than 2 m and by grab sample when water was shallower. Zooplankton samples were concentrated and subsampled with a Hensen-Stempel pipette following protocols described in Detmer et al. (2019). Zooplankton were identified to the lowest feasible taxonomic unit according to Pennak (1989) and Thorp and Covich (2001) and were enumerated in a 1 mL Sedgewick-Rafter cell. Subsamples were analyzed until at least 200 individuals were enumerated from each site.were counted across for each of the three main taxonomic groups (cladocerans, copepods, and rotifers). Given the variation in zooplankton concentrations at each site, this process often lead to far more than 200 individuals being counted (x̄ = 269, min = 200, max = 487). A summary of the sample size from each site can be found in Supplementary Table S2. Abundances were corrected for volume of water filtered. For rare taxa (< 20 individuals per sample), all individuals were measured for length. For abundant taxa, length measurements were collected on the first 20 organisms of each abundant taxon encountered in a subsample. Dry mass was calculated from equations for microcrustaceans, rotifers, and Chaoborus sp. (Rosen ,1981; Botrell et al., 1976; Dumont and Balvay, 1979).
keywords: Reservoir; Zooplankton
published: 2022-10-13
 
The text file contains the original DNA nucleotide sequence data used in the phylogenetic analyses of Xue et al. (in review), comprising the 13 protein-coding genes and 2 ribosomal gene subunits of the mitochondrial genome. The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 30 taxa (species) and 13078 characters, indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes (version 3.2.6) beginning near the end of the file. The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the Methods section of the submitted manuscript. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the individual mitochondrial genes and for different codon positions of the protein-coding genes used for analyses in the programs MrBayes and IQ-Tree (version 1.6.8) (Table S2). Full citations for references listed in Table S1 can be found by searching GenBank using the corresponding accession number. The supplemental tables will also be linked to the article upon publication at the journal website.
keywords: Hemiptera; phylogeny; mitochondrial genome; morphology; leafhopper
published: 2022-03-31
 
This dataset contains our bi-hourly temperature recordings from 40 rocket box style artificial roosts of 5 designs deployed in Indiana and Kentucky, USA from April through September 2019. This dataset also includes our endothermic and faculatively heterothermic daily energy expenditure datasets used in our bioenergetic analysis, which were calculated from the bi-hourly rocket box temperature data. Lastly, we include our overheating counts dataset which summarizes daily overheating events (i.e., temperatures > 40 Celsius) in each rocket box style bat box over the course of the study period, these daily summaries were also calculated from the bi-hourly rocket box temperature recordings.
keywords: artificial roost; bat box; microcllimate; temperature
published: 2022-08-31
 
This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes". Please refer to that publication for details about methodologies used to generate these data and for the experimental design. For this verison 2, we added specific gross nitrogen mineralization rates (ugN/gOM/d), microbial biomass carbon (ugC/gdw), microbial biomass nitrogen (ugN/gdw) and microbial biomass C:N ratios to the newest version of the data set. Additionally, we updated values for gross nitrogen mineralization, microbial NO3 assimilation and microbial NH4 assimilation to reflect slight changes in data processing. Those changes are reflected in "220829_All data_repository.csv". "220829_nitrogen_mineralization_readme.txt " is updated readme for the new file. The other 2 files begin with “220426_” are older version and same as in V1.
keywords: Nitrogen cycling; Ectomycorrhizal fungi; Arbuscular mycorrhizal fungi; Nitrogen fertilization; Gross mineralization
published: 2024-01-01
 
These data were used to make a predictive model of when ornate box turtles (Terrapene ornata) are likely to be above ground and at risk from fire. The data were generated using shell temperatures, soil temperatures at 0.35 m deep from known overwintering sites, and the spring and fall soil temperature inversion dates during 2019–2022 to infer if 26 individual radio-tracked turtles were above or below ground at three sites in Illinois.
keywords: turtle; conservation; controlled burn; fire management; ectotherm; hibernation; brumation; reptile
published: 2021-09-03
 
All of the files in this dataset pertain to the evaluation of a novel statistic, Hind/He, for distinguishing Mendelian loci from paralogs. They are derived from a RAD-seq genotyping dataset of diploid and tetraploid Miscanthus sacchariflorus.
published: 2021-10-15
 
Information on the location, dimensions, time of treefall or death, decay state, wood nutrient, wood pH and wood density data, and soil moisture, slope, distance from forest edge and soil nutrient data associated with the publication "Interspecific wood trait variation predicts decreased carbon residence time in changing forests" authored by Sierra Perez, Jennifer Fraterrigo, and James Dalling. ** <b>Note:</b> Blank cells indicate that no data were collected.
keywords: wood decay; carbon residence time; coarse woody debris; decomposition, temperate forests
published: 2021-10-22
 
This dataset includes the source data for Figures 1-4 and supplementary figures 1-10 for the manuscript "Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase".
published: 2022-01-30
 
This dataset contains temperature measurements in four different bat box designs deployed in central Indiana, USA from May to September 2018. Hourly environmental data (temperature, solar radiation, and wind speed) are also included for days and hours sampled. Bat box temperature data were used as inputs in a free program, GNU Octave, to assess design performance with respect to suitability indices for endothermic metabolism and pup development. Scripts are included in the dataset.
keywords: bats;thermal refuge;reproduction;conservation;bat box;microclimate
published: 2022-02-11
 
Upon treatment removal, spontaneous and random reactivation of latently infected T cells remains a major barrier toward curing HIV. Due to its stochastic nature, fluctuations in gene expression (or “noise”) can bias HIV reactivation from latency, and conventional drug screens for mean gene expression neglect compounds that modulate noise. Here we present a time-lapse fluorescence microscopy image set obtained from a Jurkat T-cell line, infected with a minimal HIV gene circuit, treated with 1,806 small molecule compounds, and imaged for 48 hours. In addition, the single-cell time-dependent reporter dynamics (single-cell gene expression intensity and noise trajectories) extracted from the image dataset are included. Based on this dataset, a total of 5 latency promoting agents of HIV was found through further experimentation in Lu et al., PNAS 2021 (doi: 10.1073/pnas.2012191118). For a detailed description of the dataset, please refer to the readme file.
keywords: HIV; latency; drug screen; fluorescence microscopy; time-lapse; microscopy; single-cell data; noise; gene expression fluctuation;
published: 2022-02-11
 
The Culex_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the haplotype analyses of Trivellone et al. (Frontiers in Public Health, under review). The 492 sequences (from specimens of Culex pipiens complex collected in different habitat types using a BG-sentinel traps) were aligned using PASTA v1.8.5 under default settings. The final dataset contains 686 positions of the cytochrome c oxidase subunit I (COI) mitochondrial gene. The data analyses are further described in the cited original paper.
keywords: Culex; Culicidae; COI; mosquito surveillance, species assemblages
published: 2021-06-24
 
This dataset contains EEG and Temperature data acquired from inside the bore of an MRI scanner during scanning with two different types of fMRI sequences: single-band and and multi-band. The EEG data were acquired from the heads of adult humans undergoing scanning, and can be used to assess differences in EEG data quality due to sequence type. The temperature data were acquired from a watermelon phantom and can be used to assess heating differences due to sequence type.
keywords: Simultaneous EEG-fMRI, Multi-band fMRI, Safety, Heating
published: 2021-05-10
 
UAV-based high-resolution multispectral time-series orthophotos utilized to understand the relation between growth dynamics, imagery temporal resolution, and end-of-season biomass productivity of biomass sorghum as bioenergy crop. Sensor utilized is a RedEdge Micasense flown at 40 meters above ground level at the Energy Farm- UIUC in 2019.
keywords: Unmanned aerial vehicles; High throughput phenotyping; Machine learning; Bioenergy crops
published: 2021-04-06
 
These datasets contain modeling files and GIS data associated with a risk assessment study for the Cambrian-Ordovician sandstone aquifer system in Illinois from predevelopment (1863) to the year 2070. Modeling work was completed using the Illinois Groundwater Flow Model, a regional MODFLOW model developed for water supply planning in Illinois, as a base model. The model is run using the graphical user interface Groundwater Vistas 7.0. The development and technical details of the base Illinois Groundwater Flow Model, including hydraulic property zonation, boundary conditions, hydrostratigraphy, solver settings, and discretization, are described in Abrams et al. (2018). Modifications to this base model (the version presented here) are described in Mannix et al. (2018), Hadley et al. (2020) and Abrams and Cullen (2020). Modifications include removal of particular multi-aquifer wells to improve calibration, changing Sandwich Fault Zone properties to achieve calibration at production wells within and near the fault zone, and the incorporation of demand scenarios based on a participatory modeling project with the Southwest Water Planning Group. The zipped folder of model files contains MODFLOW input (package) files, Groundwater Vistas files, and a head file for the entire model run. The zipped folder of GIS data contains rasters of: simulated drawdown in the St. Peter sandstone from predevelopment to 2018, simulated drawdown in the Ironton-Galesville sandstone from predevelopment to 2018, simulated head difference between the St. Peter and Ironton-Galesville sandstone units in 2018, simulated head above the top of the St. Peter sandstone for the years 2029, 2050, and 2070, and simulated head above the top of the Ironton-Galesville sandstone for the years 2029, 2050, and 2070. Raster outputs were derived directly from the simulated heads in the Illinois Groundwater Flow Model. Rasters are clipped to the 8 county northeastern Illinois region (Cook, DuPage, Grundy, Kane, Kendall, Lake, McHenry, and Will counties). Well names, historic and current head targets, and spatial offsets for the Illinois Groundwater Flow Model are available upon request via a data license agreement. Please contact authors to set this up if needed.
keywords: groundwater; aquifer; sandstone aquifer; risk assessment; depletion; Illinois; MODFLOW; modeling
published: 2021-06-14
 
Chronic contact exposure to realistic soil concentrations (0, 7.5, 15, and 100 ppb) of the neonicotinoid pesticide imidacloprid had species- and sex-specific effects on adult bee movement characteristics, but not on adult female bee brain development. This dataset contains two data files. The first contains information about adult bee movement characteristics for female Osmia lignaria and female and male Megachile rotundata over a 10-minute trial (total distance traveled and average movement speed). The second contains information about female Osmia lignaria and Megachile rotundata adult brain morphology. Detected effects included: female Osmia lignaria adults moved faster as they aged in the 0 and 7.5 ppb, but not in the 15 or 100 ppb, groups; young male Megachile rotundata adults moved more quickly (7.5 and 100 ppb) and farther (100 ppb) when treated with imidacloprid compared to the control group (0 ppb); and, while there was no impact of imidacloprid on adult female neuropil:Kenyon cell volume (N:K), N:K decreased with Osmia ligaria adult age and increased with Megachile rotundata adult age.
keywords: neonicotinoid; imidacloprid; bee; movement
published: 2021-06-16
 
Thank you for using these datasets. These RNAsim aligned fragmentary sequences were generated from the query sequences selected by Balaban et al. (2019) in their variable-size datasets (https://doi.org/10.5061/dryad.78nf7dq). They were created for use for phylogenetic placement with the multiple sequence alignments and backbone trees provided by Balaban et al. (2019). The file structures included here also correspond with the data Balaban et al. (2020) provided. This includes: Directories for five varying backbone tree sizes, shown as 5000, 10000, 50000, 100000, and 200000. These directory names are also used by Balaban et al. (2019), and indicate the size of the backbone tree included in their data. Subdirectories for each replicate from the backbone tree size labelled 0 through 4. For the smaller four backbone tree sizes there are five replicates, and for the largest there is one replicate. Each replicate contains 200 text files with one aligned query sequence fragment in fasta format.
keywords: Fragmentary Sequences; RNAsim
published: 2021-08-20
 
In 2020, early-season extreme precipitation events occurred following the planting of Sorghum bicolor (L.) Moench and Zea mays L. in central Illinois that caused ponding. Following the first rainfall event 50m transects were established to assess the waterlogging effects on seedling emergence and crop yields. Soil moisture, emergence, stem and tiller count, LAI, and yield were measured at various points in the season along these transects.
keywords: Sorghum; Maize; Emergence; Yield; LAI
published: 2021-02-25
 
Total nitrogen leaching rates were calculated over the Mississippi Atchafalaya River Basin (MARB) using an integrated economic-biophysical modeling approach. Land allocation for corn production and total nitrogen application rates were calculated for crop reporting districts using the Biofuel and Environmental Policy Analysis Model (BEPAM) for 5 RFS2 policy scenarios. These were used as input in the Integrated BIosphere Simulator-Agricultural Version (Agro-IBIS) and the Terrestrial Hydrologic Model with Biogeochemistry (THMB) to calculate the nitrogen loss. Land allocation and total nitrogen application simulations were simulated for the period 2016-2030 for 303 crop reporting districts (https://www.nass.usda.gov/Data_and_Statistics/County_Data_Files/Frequently_Asked_Questions/county_list.txt). The final 2030 values are reported here. Both are stored in csv files. Units for land allocation are million ha and nitrogen application are million kg. The nitrogen leaching rates were modeled with a spatial resolution of 5' x 5' using the North American Datum of 1983 projection and stored in NetCDF files. The 30-year average is calculated over the last 30 years of the 45 years being simulated. Leaching rates are calculated in kg-N/ha.
keywords: nitrogen leaching, bioethanol, bioenergy crops
published: 2021-05-14
 
This document contains the Supplemental Materials for Chapter 4: Climate Change Impacts on Agriculture from the report "An Assessment of the Impacts of Climate Change in Illinois" published in 2021.
keywords: Illinois; climate change; agriculture; impacts; adaptation; crop yield; ISAM; econometrics; days suitable for fieldwork
published: 2021-03-10
 
The PhytoplasmasRef_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the phylogenetic analyses of Trivellone et al. (Ecology and Evolution, in review). The 27 sequences (21 phytoplasma reference strains and 6 phytoplasmas strains from the present study) were aligned using the Muscle algorithm as implemented in MEGA 7.0 with default settings. The final dataset contains 952 positions of the F2n/R2 fragment of the 16S rRNA gene. The data analyses are further described in the cited original paper.
keywords: Hemiptera; Cicadellidae; Mollicutes; Phytoplasma; biorepository
published: 2021-05-14
 
Please cite as: Jim Miller, Sergiusz Czesny, Qihong Dai, James Ellis, Louis Iverson, Jeff Matthews, Charles Roswell, Cory Suski, John Taft, and Mike Ward. 2021. “Climate Change Impacts on Ecosystems: Scientific and Common Species Names”.
keywords: Scientific names; Common names; Illinois species
published: 2021-05-14
 
Supplemental Forest Data for Chapter 6: Climate Change Impacts on Ecosystems in "An Assessment of the Impacts of Climate Change in Illinois"
published: 2021-04-19
 
Dataset compiled by Yushu Xia and Michelle Wander for the Soil Health Institute. Data were recovered from peer reviewed literature reporting results for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) in terms of their relative response to management where soils under grassland cover, no-tillage, cover crops, residue return and organic amendments were compared to conventionally managed controls. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, and “fluorescein diacetate hydrolysis”, together with one or more of the following: “management practice”, “tillage”, “cover crop”, “residue”, “organic fertilizer”, or “manure”. Records were tabulated to compare SQI abundance in soil maintained under a control and soil aggrading practice with the intent to contribute to SQI databases that will support development of interpretive frameworks and/or algorithms including pedo-transfer functions relating indicator abundance to management practices and site specific factors. Meta-data include the following key descriptor variables and covariates useful for development of scoring functions: 1) identifying factors for the study site (location, year of initiation of study and year in which data was reported), 2) soil textural class, pH, and SOC, 3) depth and timing of soil sampling, 4) analytical methods for SQI quantification, 5) units used in published works (i.e. equivalent mass, concentration), 6) SQI abundances, and 7) statistical significance of difference comparisons. *Note: Blank values in tables are considered unreported data.
keywords: Soil health promoting practices; Soil quality indicators; β-glucosidase; fluorescein diacetate hydrolysis; Permanganate oxidizable carbon; Greenhouse gas emissions; Scoring curves; Soil Management Assessment Framework
published: 2021-05-09
 
Raw data and its analysis collected from a trial designed to test the impact of providing a Bacillus-based direct-fed microbial (DFM) on the syndrome resulting from orally infecting pigs with either Salmonella enterica serotype Choleraesuis (S. Choleraesuis) alone, or in combination with an intranasal challenge, three days later, with porcine reproductive and respiratory syndrome virus (PRRSV).
keywords: excel file
published: 2020-10-15
 
This dataset consists of various input data that are used in the GAMS model. All the data are in the format of .inc which can be read within GAMS or Notepad. Main data sources include: acreage data (acre), crop budget data ($/acre), crop yield data (e.g. bushel/acre), Soil carbon sequestration data (KgCO2/ha/yr). Model details can be found in the "Assessing the Additional Carbon Savings with Biofuel" and GAMS model package. ## File Description (1) GAMS Model.zip: This includes all the input files and scripts for running the model (2) Table*.csv: These files include the data from the tables in the manuscript (3) Figure2_3_4.csv: This contains the data used to create the figures in the manuscript (4) BaselineResults.csv: This includes a summary of the model results. (5) SensitivityResults_*.csv: Model results from the various sensitivity analyses performed (6) LUC_emission.csv: land use change emissions by crop reporting district for changes of pasturelands to annual crops.
keywords: Biogenic carbon intensity; Corn ethanol; Economic model; Dynamic optimization; Anticipated baseline approach; Life cycle carbon intenisty