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Detmer, Thomas (2022): ShelbyvilleZooplankton. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2467544_V1
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).
has sharing link
planned publication date: 2023-09-01
Chakraborty, Sulagna; Steckler, Teresa; Gronemeyer, Peg; Mateus-Pinilla, Nohra; Smith, Rebecca (2023): Farmers’ knowledge, attitudes, and prevention practices regarding ticks and tickborne diseases in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3988796_V1
An online and paper knowledge, attitudes, and practices survey on ticks and tick-borne diseases (TBD) was distributed to farmers in Illinois during summer 2020 to spring 2022 (paper version titled Final Draft Farmer KAP_v.SoftCopy_Revised.docx). These are the raw data associated with that survey and the survey questions used (FarmerTickKAPdata.csv, data dictionary in Data Description.docx). We have added calculated values (columns 286 to end, code for calculation in FarmerKAPvariableCalculation.R), including: the tick knowledge score, TBD knowledge score, and total knowledge score, which are the sum of the total number of correct answers in each category, and score percent, which are the proportion of correct answers in each category.
ticks; survey; tick-borne disease; farmer
Beilke, Elizabeth; O'Keefe, Joy (2022): Data for Bats reduce insect density and defoliation in temperate forests: an exclusion experiment. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2455970_V1
Datasets that accompany Beilke and O'Keefe 2022 publication (Title: Bats reduce insect density and defoliation in temperate forests: an exclusion experiment; Journal: Ecology).
bats; defoliation; ecosystem services; forests, insectivory; insects; trophic cascades
Hartman, Jordan; Larson, Eric (2022): Data for Overlooked invaders? Ecological impacts of non-game, native transplant fishes in the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1161902_V1
Data associated with the manuscript "Overlooked invaders? Ecological impacts of non-game, native transplant fishes in the United States" by Jordan H. Hartman and Eric R. Larson
freshwater; non-game; native transplant; impacts; invasive species
Long, Stephen P.; Wang, Yu; Stutz, Samantha S. (2022): Data for Increased bundle sheath leakiness of CO2 during photosynthetic induction shows a lack of coordination between the C4 and C3 cycles. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1181155_V1
We developed a new application of isotopic gas exchange which couples a tunable diode laser absorption spectroscope (TDL) with a leaf gas exchange system, analyzing leakiness through induction of C4 photosynthesis on dark to high-light transitions. The youngest fully expanded leaf was measured on 40-45 day-old maize(B73) and sorghum (Tx430). Detail definition of each variable in raw Li-6400XT and Li-6800 (in "Original_data_AND_Data_processing_code.zip") is summarized in: <a href="https://www.licor.com/env/support/LI-6800/topics/symbols.html#const">https://www.licor.com/env/support/LI-6800/topics/symbols.html#const</a>
leakiness; bundle sheath leakage; C4 photosynthesis; photosynthetic induction; non-steady-state photosynthesis; carbon isotope discrimination; photosynthetic efficiency; corn
Jiang, Chongya; Guan, Kaiyu; Khanna, Madhu; Chen, Luoye; Peng, Jian (2022): Data for Assessing Marginal Land Availability Based on Land Use Change Information in the Contiguous United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6395937_V1
The availability of economically marginal land for energy crops is identified using the Cropland Data Layer and other soil, wind, climate data resources. All data are recognized on a 30m spatial resolution across the continental United States.
marginal land; biofuel production; remote sensing; land use change; Cropland Data Layer
Seyfried, Georgia; Midgley, Meghan; Phillips, Richard; Yang, Wendy (2022): Data for Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5586647_V2
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.
Nitrogen cycling; Ectomycorrhizal fungi; Arbuscular mycorrhizal fungi; Nitrogen fertilization; Gross mineralization
Souza-Cole, Ian; Ward, Michael; Rebecca, Mau; Jeffrey, Foster; Benson, Thomas (2022): Eastern Whip-poor-will abundance declines with urban land cover and increases with moth abundance in the American Midwest. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7745473_V1
Data in this publication were used to analyze the factors that influence the abundance of eastern whip-poor-wills in the Midwest and to describe the diet of this species. These data were collected in Illinois in 2019 and 2020. Procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 19006
eastern whip-poor-will; Antrostomus vociferus; abundance; moths; nightjars; Lepidoptera; metabarcoding
Pastrana-Otero, Isamar; Majumdar, Sayani; Kraft, Mary L. (2022): Raman spectra of individual, living hematopoietic stem and progenitor cells. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9950442_V1
This dataset contains Raman spectra, each acquired from an individual, living, primary murine cell belonging to one of the six most immature hematopoietic cell populations found in the body: hematopoietic stem cell (HSC), mutipotent progenitor 1 (MPP1), multipotent progenitor 2 (MPP2), multipotent progenitor 3 (MPP3), common lymphoid progenitor, common myeloid progenitor (CLP). These spectra are useful for identifying spectral signatures that are characteristic of each hematopoietic stem or early progenitor cell population. *NOTE: __MACOSX folder and files start with “._[file name]” found in "Raman spectra of single cells text files.zip" were created by the computer operation system, in unreadable format, which are not part of the data and can be removed/ignored when using the data.
Raman spectroscopy; single-cell spectrum; hematopoietic cell; hematopoietic stem cell; multipotent progenitor cell; common myeloid progenitor; common lymphoid progenitor
Seyfried, Georgia; Corrales, Adriana; Kent, Angela; Dalling, James; Yang, Wendy (2022): Soil data for Watershed-scale variation in potential fungal community contributions to ectomycorrhizal biogeochemical syndromes. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3532603_V1
This dataset contains soil chemical properties used to variation in soil fungal communities beneath Oreomunnea mexicana trees in the manuscript "Watershed-scale variation in potential fungal community contributions to ectomycorrhizal biogeochemical syndromes"
Acid-base chemistry; Ectomycorrhizal fungi; Exploration type; Nitrogen cycling; Nitrogen isotopes; Plant-soil (below-ground) interactions; Saprotrophic fungi; Tropical forest
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
has sharing link
Carson, Dawn; Kopsco, Heather; Gronemeyer, Peg; Mateus-Pinilla, Nohra; Smith, Genee; Sandstrom, Emma; Smith, Rebecca (2022): Knowledge, attitudes, and practices of Illinois medical professionals related to ticks and tick-borne disease. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0685545_V1
An online knowledge, attitudes, and practices survey on ticks and tick-borne diseases was distributed to medical professionals in Illinois during summer 2020 to fall 2021. These are the raw data associated with that survey and the survey questions used. Age, gender, and county of practice have been removed for identifiability. We have added calculated values (columns 165 to end), including: the tick knowledge score, TBD knowledge score, and total knowledge score, which are the sum of the total number of correct answers in each category, and score percent, which are the proportion of correct answers in each category; region, which is determined from the county of practice; TBD relevant practice, which separates the practice variable into TBD primary, secondary, and non-responders; and several variables which group categories.
ticks; medicine; tick-borne disease; survey
Hunninck, Louis; O'Keefe, Joy (2022): Bat activity and diversity in agricultural landscapes in Illinois, USA. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7792566_V1
This data set documents bat activity (counts per detector-night per phonic group) and bat diversity (number of bat species per detector-night) in relation to distance to the nearest forested corridor in a row crop agriculture dominated landscape and in relation to relative crop pest abundance. This data set was used to assess if bats were homogeneously distributed over a near-uninterrupted agricultural landscape and to assess the importance of forested corridors and the presence of pest species on their distribution across the landscape. Data was collected with 50 AudioMoth bat detectors along 10 transects, with each transect having 5 detectors. The transects started at a forest corridor and extended out for 4 km into uninterrupted row crop agriculture. Pest abundance was extrapolated from data collected in the same county during the same time as the study. Potentially important weather covariates were extracted from the nearest operational weather station.
bats; bat activity; biodiversity; agricultural pest
Shearer, David; Beilke, Elizabeth (2022): Data for Playing it by ear: gregarious sparrows recognize and respond to isolated wingbeat sounds and predator-based cues. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6676149_V1
Datasets that accompany Shearer and Beilke 2022 publication (Title: Playing it by ear: gregarious sparrows recognize and respond to isolated wingbeat sounds and predator-based cues.; Journal: Animal Cognition)
Vigilance; auditory detection; predator detection; predator-prey interaction; antipredator behavior
Parmar, Dharmeshkumar; Jia, Jin; Shrout, Joshua; Sweedler, Jonathan; Bohn, Paul (2022): Effect of Micro-patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0382919_V1
#### Details of Pseudomonas aeruginosa biofilm dataset #### ----------------*Folder Structure*------------------------------------- This dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in "MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip", each folder contains 3 sub-folders as listed below. 1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]: (1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h 2. StaticBiofilms [Static biofilms grown on mucin surface]: (1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones ----------------*File name*---------------------------------------------- Sample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below. *Example file name "Rep1-Stat-FRD1-mPat-48-FS"* ~ Each unit of information is separated by "-" ~Unit 1 - "Rep1" - Biological replicate ( Rep1, Rep2, and Rep3) ~Unit 2 - "Stat" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant) ~Unit 3 - "FRD1" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain) ~Unit 4 - "mPat" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface) ~Unit 5 - "48" - Sample time point (hours = 48, 72, 96) ~Unit 6 - "FS" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288)) ----------------*File structure*------------------------------------------ All MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix. ----------------*End of Information*--------------------------------------
mass spectrometry imaging (MSI); biofilm; antibiotic resistance; Pseudomonas aeruginosa; quorum sensing; rhamnolipids
Rahlin, Anastasia; Saunders, Sarah; Beilke, Stephanie (2022): Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1575830_V1
Dataset for "Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States" manuscript contains occupancy data for ten wetland bird species used in single-species occupancy models at four spatial scales and four wetland habitat types. Data were collected from 2017-2019 in NE Illinois and NW Indiana. Dataset includes wetland bird occupancy data, habitat parameter values for each survey location, and R code used to run analyses.
wetland birds; occupancy; emergent wetland; urbanization; Great Lakes region
Haselhorst, Derek; Moreno, J. Enrique; Tcheng, David K.; Punyasena, Surangi W. (2022): Images and annotated counts for aerial pollen samples from the Barro Colorado Island megaplot, Panama (1994 – 2010). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2176715_V1
This dataset includes images and annotated counts for 150 airborne pollen samples from the Center for Tropical Forest Science 50 ha forest dynamics plot on Barro Colorado Island, Panama. Samples were collected once a year from April 1994 to June 2010.
aerial pollen traps; automated pollen identification; Barro Colorado Island; convolutional neural networks; Neotropics; palynology; phenology
Androwski, Rebecca; Asad, Nadeem; Wood, Janet; Hofer, Allison; Locke, Steven; Smith, Cassandra; Rose, Becky; Schroeder, Nathan (2020): Data From: Mutually exclusive dendritic arbors in C. elegans neurons share a common architecture and convergent molecular cues. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0818023_V1
This dataset includes neuronal development of the Caenorhabditis elegans dauer and adult.
Nematode; Dendrite; Stress
Rapti, Zoi; Clifton, Sara (2022): Code for "Phage-antibiotic synergy inhibited by temperate and chronic virus competition". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9460305_V1
Matlab codes for the article "Phage-antibiotic synergy inhibited by temperate and chronic virus competition". Code can be used to reproduce the article figures, perform the parameter sensitivity analysis and simulate the model.
bacterium-phage-antibiotic model; ODEs; Matlab; sensitivity analysis
Rapti, Zoi; Rivera Quinones, Vanessa; Stewart Merrill, Tara (2022): Codes for the analysis of an eco-immunological disease-transmission mathematical model. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1686840_V1
MATLAB files for the analysis of an ODE model for disease transmission. The codes may be used to find equilibrium points, study transient dynamics, evaluate the basic reproductive number (R0), and simulate the model when parameters depend on the independent variables. In addition, the codes may be used to perform local sensitivity analysis of R0 on the model parameters.
Crawford, Reed D.; Dodd, Luke E.; Tillman, Frank E.; O'Keefe, Joy M. (2022): Data for Evaluating bat boxes: Design and placement alter bioenergetic costs and overheating risk. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3592866_V1
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.
artificial roost; bat box; microcllimate; temperature
Yan, Bin; Dietrich, Christopher; Yu, Xiaofei; Dai, Renhuai; Maofa, Yang (2022): Data files for phylogenetic analysis of Typhlocybinae (Hemiptera: Cicadellidae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8761342_V1
The files are plain text and contain the original data used in phylogenetic analyses of of Typhlocybinae (Bin, Dietrich, Yu, Meng, Dai and Yang 2022: Ecology & Evolution, in press). The three files with extension .phy are text files with aligned DNA sequences in the standard PHYLIP format and correspond to Matrix 1 (amino acid alignment), Matrix 2 (nucleotide alignment of first two codon positions of protein-coding genes) and Matrix 3 (nucleotide alignment of protein-coding genes plus 2 ribosomal genes) described in the Methods section. An additional text file in NEXUS format (.nex extension) contains the morphological character data used in the ancestral state reconstruction (ASCR) analysis described in the Methods. NEXUS is a standard format used by various phylogenetic analysis software. For more information on data file content, see the included "readme" files.
Hemiptera; phylogeny; mitochondrial genome; morphology; leafhopper
Trivellone, Valeria; Cao, Yanghui; Dietrich, Christopher (2022): Alternative approaches for uncovering phytoplasma biodiversity and vector associations. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9804959_V1
This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.
anchored hybrid enrichment; biodiversity, biorepository; nested PCR; Sanger sequencing
Xia, Yushu; Wander, Michelle; Kwon, Hoyoung (2021): County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3112432_V1
This dataset includes five files developed using the procedures described in the article 'Developing County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States' and Supplemental Information published in the Journal of Cleaner Production in 2021. Citation: Xia, Yushu, Hoyoung Kwon, and Michelle Wander. "Developing county-level data of nitrogen fertilizer and manure inputs for corn production in the United States." Journal of Cleaner Production 309 (2021): e126957. Brief method: The fertilizer and manure inputs for corn were generated with a top-down approach by assigning county-level total N inputs reported by USGS to different crops using state- and county-level survey data. The corn N needs were estimated using empirical extension-based equations coupled with soil and environmental covariates. The estimates of fertilizer N inputs were further refined for corn grain and silage production at the county level and gap-filling (using state-level averages) was carried out to generate final files for U.S. county-level N inputs. The dataset is provided in an alternative format in Google Earth Engine: https://code.earthengine.google.com/13a0078e7ee727bc001e045ad0e8c6fc
Corn; Nitrogen Fertilizer; Manure; Conterminous U.S.
Southey, Bruce; Rodriguez-Zas, Sandra L. (2022): Data for changes in neuropeptide prohormone genes among Cetartio-dactyla livestock and wild species associated with evolution and domestication. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2071917_V1
This dataset contain information for the paper "Changes in neuropeptide prohormone genes among Cetartio-dactyla livestock and wild species associated with evolution and domestication" Veterinary Sciences, MDPI. Protein sequences were predicted using GeneWise for 98 neuropeptide prohormone genes from publicly available genomes of 118 Cetartiodactyla species. All predictions (CetartiodactylaSequences2022.zip) were manually verified. Sequences were aligned within each prohormone using MAFFT (MDPImultalign2022.zip includes multiple sequence alignment of all species available for each prohormone). Phylogenetic gene trees were constructed using PhyML and the species tree was constructed using ASTRAL (MDPItree2022.zip). The data is released under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).
prohormone; neuropeptide; Cetartiodactyla; Cetartiodactyla; phylogenetics; gene tree; species tree