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published: 2021-07-12
This dataset contains the images of a photoperiod sensitive sorghum accession population used for a GWAS/TWAS study of leaf traits related to water use efficiency in 2016 and 2017. Raw images were produced by Optical topometry (nms files).
keywords: stomata; segmentation; water use efficiency
published: 2021-06-28
This dataset contains 1) the cleaned version of 11 CRW datasets, 2) RNASim10k dataset in high fragmentation and 3) three CRW datasets (16S.3, 16S.T, 16S.B.ALL) in high fragmentation.
keywords: MAGUS;UPP;Multiple Sequence Alignment;PASTA;eHMMs
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: 2021-05-09
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: 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: 2021-03-31
This archive contains the datasets used in the paper "Recursive MAGUS: scalable and accurate multiple sequence alignment". - 16S.3, 16S.T, 16S.B.ALL - HomFam - RNASim These can also be found at https://sites.google.com/eng.ucsd.edu/datasets/alignment/pastaupp
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: 2021-05-14
Please cite as: Menglin Liu and Benjamin M. Gramig. "Survey of Cover Crop, Conservation Tillage and Nutrient Management Practice Usage in Illinois and 2020 Fall Covers for Spring Savings Crop Insurance Discount Program Participation." Report to the Illinois Department of Agriculture and Fall Covers for Spring Savings working group. Center for the Economics of Sustainability and Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign. 2021. https://doi.org/10.13012/B2IDB-5222984_V1
keywords: cover crops; Illinois; 2020; conservation tillage; nutrient management practices; farmer survey; NLRS
published: 2021-04-05
West Nile virus data, aggregated by 55 1-km hexagons, within the NWMAD jurisdiction Cook County, IL. The data incorporates deidentified human illness, mosquito infection and abundance, socio-economic data, and other abiotic and biotic predictors by epi-weeks 18-38 for the years 2005-2016.
keywords: WNV; modeling
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: 2021-05-14
Supplemental Forest Data for Chapter 6: Climate Change Impacts on Ecosystems in "An Assessment of the Impacts of Climate Change in Illinois"
published: 2021-04-30
This repository includes scripts and datasets for the paper, "Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy" submitted to Bioinformatics.
keywords: BAli-Phy;Bayesian co-estimation;multiple sequence alignment
published: 2021-05-17
Please cite as: Wuebbles, D., J. Angel, K. Petersen, and A.M. Lemke, (Eds.), 2021: An Assessment of the Impacts of Climate Change in Illinois. The Nature Conservancy, Illinois, USA. https://doi.org/10.13012/B2IDB-1260194_V1 Climate change is a major environmental challenge that is likely to affect many aspects of life in Illinois, ranging from human and environmental health to the economy. Illinois is already experiencing impacts from the changing climate and, as climate change progresses and temperatures continue to rise, these impacts are expected to increase over time. This assessment takes an in-depth look at how the climate is changing now in Illinois, and how it is projected to change in the future, to provide greater clarity on how climate change could affect urban and rural communities in the state. Beyond providing an overview of anticipated climate changes, the report explores predicted effects on hydrology, agriculture, human health, and native ecosystems.
keywords: Climate change; Illinois; Public health; Agriculture; Environment; Water; Hydrology; Ecosystems
published: 2021-07-21
This dataset contains 1 CSV file: RozanskyLarsonTaylorMsat.csv which contains microsatellite fragment lengths for Virile and Spothanded Crayfish from the Current River watershed of Missouri, U.S., and complimentary data, including assignments to species by phenotype and COI sequence data, GenBank accession numbers for COI sequence data, study sites with dates of collection and geographic coordinates, and Illinois Natural History Survey (INHS) Crustacean Collection lots where specimens are stored.
keywords: invasive species; hybridization; crayfishes; streams; freshwater; Cambaridae; virile crayfish; spothanded crayfish; Missouri; Current River; Ozark National Scenic Riverways
published: 2021-06-25
Data associated with the manuscript "Do rusty crayfish invasions affect water clarity in north temperate lakes?" by Daniel K. Szydlowski, Melissa K. Daniels, and Eric R. lARSON
keywords: chlorophyll a; crayfish; Faxonius rusticus; invasive species; lakes; LandSat; remote sening; rusty crayfish; Secchi disc; water clarity
published: 2021-07-15
The dataset contains the high-throughput matrix-assisted laser desorption/ionization mass spectrometry XmL files for the atrial gland and red hemiduct of Aplysia californica.
keywords: Dense-core vesicle; High-throughput; Mass Spectrometry; MALDI; Organelle; Image-Guided; Atrial gland; red hemiduct; Lucent Vesicle
has sharing link
planned publication date: 2021-09-01
Bigheaded Carp have spread throughout the Mississippi River basin since the 1970s. Little has stopped the spread as carp have the ability to pass through locks and dams, and they are currently approaching the Great Lakes. However, the location of the leading edge in the Illinois River has stalled for over a decade, even though there is no barrier preventing further advancement towards the Great Lakes. Defining why carp are not moving towards the Great Lakes is important for predicting why they might advance in the future. The aim of this study was to test the hypothesis that anthropogenic contaminants in the Illinois River may be playing a role in preventing further upstream movement of Bigheaded Carp. Ninety-three livers were collected from carp at several locations between May and October of 2018. Liver samples were analyzed using gas chromatography-mass spectrometry in a targeted metabolite profiling approach. Livers from carp at the leading edge had differences in energy use and metabolism, and suppression of protective mechanisms relative to downstream fish; differences were consistent across time. This body of work provides evidence that water quality is linked to carp movement in the Illinois River. As water quality in this region continues to improve, consideration of this impact on carp spread is essential to protect the Great Lakes. The data shared here contains the raw data from the fish collection.
keywords: water quality; metabolites; range expansion; energy; contaminants
published: 2021-07-10
This dataset containes the images of B73xMS71 RIL population used in QTL linkage mapping for maize epidermal traits in year 2016 and 2017. Raw images produced by Optical topometry (nms files) were processed to strengthen the edges of cell outlines and were transformed into TIFs. All images with epidermal cells predicted using the Mask R-CNN model were shown. Images used for model training and validation were attached as well.
keywords: stomata; Mask R-CNN; cell segmentation; water use efficiency
published: 2021-07-09
The data are original electron micrographs from the lab of the late Dr. Burt Endo of the USDA. These data were digitized from photographic prints and glass plate negatives at 600 DPI as 16 bit TIFF files. This second version added 10 new ZIP files from the Endo data collection. "Endo folder database.xlsx" is updated to reflect the addition. Information in "ReadmeFile name formatting.docx" remains the same as in V1.
keywords: nematode; ultrastructure; Endo; electron microscopy
planned publication date: 2022-01-01
The file “Fla.fasta”, comprising 10526 positions, is the concatenated amino acid alignments of 51 orthologues of 182 bacterial strains. It was used for the maximum likelihood and maximum parsimony analyses of Flavobacteriales. Bacterial species names and strains were used as the sequence names, host names of insect endosymbionts were shown in brackets. The file “16S.fasta” is the alignment of 233 bacterial 16S rRNA sequences. It contains 1455 positions and was used for the maximum likelihood analysis of flavobacterial insect endosymbionts. The names of endosymbiont strains were replaced by the name of their hosts. In addition to the species names, National Center for Biotechnology Information (NCBI) accession numbers were also indicated in the sequence names (e.g., sequence “Cicadellidae_Deltocephalinae_Macrostelini_Macrosteles_striifrons_AB795320” is the 16S rRNA of Macrosteles striifrons (Cicadellidae: Deltocephalinae: Macrostelini) with a NCBI accession number AB795320). The file “Sulcia_pep.fasta” is the concatenated amino acid alignments of 131 orthologues of “Candidatus Sulcia muelleri” (Sulcia). It contains 41970 positions and presents 101 Sulcia strains and 3 Blattabacterium strains. This file was used for the maximum likelihood analysis of Sulcia. The file “Sulcia_nucleotide.fasta” is the concatenated nucleotide alignment corresponding to the sequences in “Sulcia_pep.fasta” but also comprises the alignment of 16S rRNA. It has 127339 positions and was used for the maximum likelihood and maximum parsimony analyses of Sulcia. Individual gene alignments (16S rRNA and 131 orthologues of Sulcia and Blattabacterium) are deposited in the compressed file “individual_gene_alignments.zip”, which were used to construct gene trees for multispecies coalescent analysis. The names of Sulcia strains were replaced by the name of their hosts in “Sulcia_pep.fasta”, “Sulcia_nucleotide.fasta” and the files in “individual_gene_alignments.zip”. In all the alignment files, gaps are indicated by “-”.
keywords: endosymbiont, “Candidatus Sulcia muelleri”, Auchenorrhyncha, coevolution
published: 2016-05-16
This dataset contains the protein sequences and trees used to compare Non-Ribosomal Peptide Synthetase (NRPS) condensation domains in the AMB gene cluster and was used to create figure S1 in Rojas et al. 2015. Instead of having to collect representative sequences independently, this set of condensation domain sequences may serve as a quick reference set for coarse classification of condensation domains.
keywords: NRPS; biosynthetic gene cluster; antimetabolite; Pseudomonas; oxyvinylglycine; secondary metabolite; thiotemplate; toxin
published: 2021-06-24
This dataset consists of the secondary ion mass spectrometry (SIMS) depth profiling data that was collected with a Cameca NanoSIMS 50 instrument from a 10 micron by 10 micron region on a Madin-Darby canine kidney (MDCK) cell that had been metabolically labeled so most of its sphingolipids and cholesterol contained the rare nitrogen-15 oxygen-18 isotopes, respectively.
keywords: secondary ion mass spectrometry; NanoSIMS; depth profiling; MDCK cell; sphingolipids; cholesterol
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: 2021-06-14
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: 2021-06-08
Dataset associated with Jones and Ward JAE-2020-0031.R1 submission: Pre-to post-fledging carryover effects and the adaptive significance of variation in wing development for juvenile songbirds. Excel CSV files with data used in analyses and file with descriptions of each column. The flight ability variable in this dataset was derived from fledgling drop tests, examples of which can be found in the related dataset: Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1.
keywords: fledgling; wing development; life history; adaptive significance; post-fledging; songbirds