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Perez, Sierra; Dalling, James; Fraterrigo, Jennifer (2021): Trelease and Brownfields Woods tree decay dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4547091_V1
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.
wood decay; carbon residence time; coarse woody debris; decomposition, temperate forests
Jianhao, Peng; Idoia, Ochoa (2021): Synthetic datasets for SimiC . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4996748_V1
This is the 5 states 5000 cells synthetic expression file we used for validation of SimiC, a single cell gene regulatory network inference method with similarity constraints. Ground truth GRNs are stored in Numpy array format, and expression profiles of all states combined are stored in Pandas DataFrame in format of Pickle files.
Numpy array; GRNs; Pandas DataFrame;
Detmer, Thomas (2021): Temperature, dissolved oxygen, and Secchi depth of Illinois Reservoirs. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1187851_V1
This data set describes temperature, dissolved oxygen, and secchi depth in 1-m interval profiles in the deepest point in 10 Illinois reservoirs between the years 1995 and 2016.
Water temperature; dissolved oxygen; secchi depth; climate change
planned publication date: 2022-09-29
Merrill, Loren; Jones, Todd; Brawn, Jeffrey; Ward, Michael (2022): Merrill et al. ECE-2021-05-00793.R1. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8719858_V1
Dataset associated with Merrill et al. ECE-2021-05-00793.R1 submission: Early life patterns of growth are linked to levels of phenotypic trait covariance and post-fledging mortality across avian species. Excel CSV files with all of the data used in analyses and file with descriptions of each column.
canalization; developmental flexibility; early-life stress; nest predation; phenotypic correlation; trait covariance
Stern, Jessica; Herman, Brook D. ; Matthews, Jeffrey (2021): Data from determining vegetation metric robustness to environmental and methodological variables . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0938556_V1
We studied vegetation metric robustness to environmental (season, interannual, and regional) and methodological (observer) variables, as well as adequate sample size for vegetation metrics across four regions of the United States.
coefficients of conservatism; floristic quality assessment; restoration; vegetation metric;
Clark, Lindsay V.; Mays, Wittney; Lipka, Alexander E.; Sacks, Erik J. (2021): Dataset for evaluating the Hind/He statistic in polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4814898_V1
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.
Edmonds, Devin (2021): Data for Poison Frogs in U.S. Collections. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4717502_V1
The dataset shows all poison frogs (superfamily Dendrobatoidea) in private U.S. collections during 1990–2020. For each species and color morph, there is a date of arrival, the way it arrived in U.S. collections, and detailed notes related to its presence in the pet trade. A second sheet details 10 wildlife trade pathways identified for poison frogs. The data can be used to examine the amphibian pet trade.
pet trade; amphibians; Dendrobatidae
Zaharias, Paul; Grosshauser, Martin; Warnow, Tandy (2021): Data from "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8921156_V1
This repository includes datasets for the paper "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling" accepted for RECOMB2021 and submitted to Journal of Computational Biology. Each zipped file contains a README.
deep neural networks; heterotachy; GHOST; quartet estimation; phylogeny estimation
planned publication date: 2022-08-20
Jones, Todd; Ward, Michael (2022): Jones and Ward BEAS-D-21-00106R2. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4619552_V1
Dataset associated with Jones and Ward BEAS-D-21-00106R2 submission: Parasitic cowbird development up to fledging and subsequent post-fledging survival reflect life history variation found across host species. Excel CSV files and .inp file with data used in nest survival and Brown-headed Cowbird post-fledging analyses and file with descriptions of each column. The CSV file is setup for logistic exposure models in SAS or R and the .inp file is setup to be uploaded into program MARK for multi-state recaptures only analysis. Species included in the analyses: American Robin, Blue Grosbeak, Brown Thrasher, Blue-winged Warbler, Carolina Chickadee, Chipping Sparrow, Common Yellowthroat, Dickcissel, Eastern Bluebird, Eastern Phoebe, Eastern Towhee, Field Sparrow, Gray Catbird, House Wren, Indigo Bunting, Northern Cardinal, Red-winged Blackbird, Tree Swallow, Yellow-breasted Chat, and Yellow Warbler.
brood parasitism; cowbird; carryover effects; phenotypic plasticity; post-fledging; songbirds
von Haden, Adam C.; DeLucia, Evan H.; Yang, Wendy; Burnham, Mark (2021): Maize and Sorghum Establishment and Yield following Pre-Emergence Waterlogging. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8293871_V1
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.
Sorghum; Maize; Emergence; Yield; LAI
Long, Stephen Patrick; Acevedo-Siaca, Liana Gabriella (2021): Data for publication "Evaluating natural variation, heritability, and genetic advance of photosynthetic traits in rice (Oryza sativa)". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3427028_V1
1. Rice H2 - Destructive Harvest - These data are for the destructive harvest (above-ground biomass) of 30 diverse indica rice genotypes that were grown to evaluate natural variation as well as the heritability of photosynthesis-related traits. Traits measured include: plant height, leaf area, plant fresh and dry weights, and tiller number. 2. Rice H2 - ACi Response Summary - These data characterize the response of CO2 uptake to change in intercellular CO2 concentration in 30 diverse indica rice genotypes. These measurements were taken to evaluate natural variation and the heritability of photosynthesis-related traits in rice. 3. Rice H2 - Survey Style Gas Exchange Measurements - These data document steady-state survey style gas exchange measurements in 30 diverse indica rice genotypes. These measurements were taken to evaluate natural variation and the heritability of photosynthesis-related traits in rice.
photosynthesis, photosynthetic capacity, natural variation, heritability, food security, rice
Ferguson, John; Fernandes, Samuel; Monier, Brandon; Miller, Nathan; Allen, Dylan; Dmitrieva, Anna; Schmuker, Peter; Lozano, Roberto; Valluru, Ravi; Buckler, Edward; Gore, Michael; Brown, Patrick; Spalding, Edgar; Leakey, Andrew (2021): Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5565022_V2
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. *<b>Note:</b> new in this second version is that JPG images outputted from the nms files were added <b>Accessions_2016.zip</b> and <b>Accessions_2017.zip</b>: contain raw images produced by Optical Topometer (nms files) for all sorghum accessions. Images can be opened with Nanofocus μsurf analysis extended software (Oberhausen,Germany). <b>Accessions_2016_jpg.zip</b> and <b>Accessions_2017_jpg.zip</b>: contain jpg images outputted from the nms files and used in the machine learning phenotyping.
stomata; segmentation; water use efficiency
Miller, Jim; Czesny, Sergiusz; Dai, Qihong; Ellis, James; Iverson, Louis; Matthews, Jeff; Roswell, Charlie; Suski, Cory; Taft, John; Ward, Mike (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 6: Climate Change Impacts on Ecosystems, Supplement 6.1: Scientific and Common Species Names. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9049988_V1
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”.
Scientific names; Common names; Illinois species
Zuckermann, Federico (2021): Bacillus-based direct-fed microbial reduces the pathogenic synergy of a co-infection with Salmonella enterica serovar Choleraesuis and porcine reproductive and respiratory syndrome virus. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0439780_V1
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).
Shen, Chengze; Zaharias, Paul; Warnow, Tandy (2021): MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2419626_V1
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.
MAGUS;UPP;Multiple Sequence Alignment;PASTA;eHMMs
Gramig, Benjamin; Khanna, Madhu; Jain, Atul (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 4: Climate Change Impacts on Agriculture, Supplemental Materials. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8285949_V1
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.
Illinois; climate change; agriculture; impacts; adaptation; crop yield; ISAM; econometrics; days suitable for fieldwork
Iverson, Louis (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 6: Climate Change Impacts on Ecosystems, Supplemental Forest Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3459813_V1
Supplemental Forest Data for Chapter 6: Climate Change Impacts on Ecosystems in "An Assessment of the Impacts of Climate Change in Illinois"
Rozansky, Zachary; Larson, Eric; Taylor, Christopher (2021): Data for “Invasive virile crayfish (Faxonius virilis Hagen, 1870) hybridizes with native spothanded crayfish (Faxonius punctimanus Creaser, 1933) in the Current River watershed of Missouri, U.S.”. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7683513_V1
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.
invasive species; hybridization; crayfishes; streams; freshwater; Cambaridae; virile crayfish; spothanded crayfish; Missouri; Current River; Ozark National Scenic Riverways
Szydlowski, Daniel; Daniels, Melissa; Larson, Eric (2021): Data for Do rusty crayfish (Faxonius rusticus) invasions affect water clarity in north temperate lakes?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4293962_V1
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
chlorophyll a; crayfish; Faxonius rusticus; invasive species; lakes; LandSat; remote sening; rusty crayfish; Secchi disc; water clarity
Castro, Daniel; Sweedler, Jonathan (2021): High-Throughput Single-Organelle Dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5949772_V1
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.
Dense-core vesicle; High-throughput; Mass Spectrometry; MALDI; Organelle; Image-Guided; Atrial gland; red hemiduct; Lucent Vesicle
Xie, Jiayang; Fernandes, Samuel; Mayfield-Jones, Dustin; Erice, Gorka; Choi, Min; Lipka, Alexander; Leakey, Andrew (2021): Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8275554_V1
This dataset containes the images of B73xMS71 RIL population used in QTL linkage mapping for maize epidermal traits in year 2016 and 2017. 2016RIL_all_mns.rar and 2017RIL_all_mns.rar: contain raw images produced by Nanofocus lsurf Explorer Optical Topometer (Oberhausen, Germany) at 20X magnification with 0.6 numerical aperture. Files were processed in Nanofocus μsurf analysis extended software (Oberhausen,Germany). 2016RIL_all_TIF.rar and 2017RIL_all_TIF.rar: contain images processed from the Topology layer in each nms file to strengthen the edges of cell outlines, and used in downstream cell detection. 2016RIL_all_detection_result.rar and 2017RIL_all_detection_result.rar: contain images with epidermal cells predicted using the Mask R-CNN model. training data.rar: contain images used for Mask R-CNN model training and validation.
stomata; Mask R-CNN; cell segmentation; water use efficiency
Egan, Maximillian; Larsen, Ryan; Sadaghiani, Sepideh (2021): Dataset for "Safety and data quality of EEG recorded simultaneously with multi-band fMRI". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1484994_V1
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.
Simultaneous EEG-fMRI, Multi-band fMRI, Safety, Heating
Kraft, Mary L.; Yeager, Ashley N.; Weber, Peter K. (2021): NanoSIMS depth profiling data of an MDCK cell. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3927212_V1
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.
secondary ion mass spectrometry; NanoSIMS; depth profiling; MDCK cell; sphingolipids; cholesterol
Warnow , Tandy; Wedell, Eleanor (2021): Fragmentary Sequences for Variable-Sized RNAsim Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8788479_V1
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.
Fragmentary Sequences; RNAsim
Anderson, Nicholas L.; Harmon-Threatt, Alexandra N. (2021): Data for: Chronic contact with imidacloprid during development may decrease female solitary bee foraging ability and increase male competitive ability for mates. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2315056_V1
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.
neonicotinoid; imidacloprid; bee; movement