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Datasets
published: 2019-11-11
Molloy, Erin K.; Warnow, Tandy (2019): Data from: FastMulRFS: Statistically consistent polynomial time species tree estimation under gene duplication. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5721322_V1
This repository includes scripts and datasets for the paper, "FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models." Note: The results from estimating species trees with ASTRID-multi (included in this repository) are *not* included in the FastMulRFS paper. We estimated species trees with ASTRID-multi in the fall of 2019, but ASTRID-multi had an important bug fix in January 2020. Therefore, the ASTRID-multi species trees in this repository should be ignored.
keywords:
Species tree estimation; gene duplication and loss; statistical consistency; MulRF, FastRFS
published: 2020-04-02
Parker, Christine; Meador, Morgan; Hoover, Jeffrey (2020): Automatic & manual black fly (Diptera:Simuliidae) counts. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7202559_V1
Automatic and manual counts of black flies captured in Illinois.
keywords:
black flies; simuliids; ImageJ; count method
published: 2020-04-22
Reiley, Bryan (2020): Avian fitness consequences and habitat selection. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3482175_V1
Nest survival and Fledgling production data for Bell's Vireo and Willow Flycatcher nests.
keywords:
Bell's Vireo;Willow Flycatcher;habitat selection;fitness;
published: 2017-12-22
Scheidler, Andrew; Kinnett-Hopkins, Dominique; Learmonth, Yvonne; Motl, Robert; Lopez-Ortiz, Citlali (2017): Targeted ballet program mitigates ataxia and improves agility in moderate-to-advanced multiple sclerosis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6858418_V2
TBP assessment raw data files of pre- and post- motion capture velocity and center of pressure force plate data. Labels are self-explanatory. The .mat files refer to data exported from the force plate for the time-to-stabilization assessments while the .txt files are the data collected for smoothness of gait assessments. These files do not relate to one another and are from separate assessments. Version2's files are the result from using Python code Data_Bank_Cleaner.py on version1's. Please find more information in READ_ME_databank.txt.
keywords:
Multiple Sclerosis; Rehabilitation; Balance; Ataxia; Ballet; Dance; Targeted Ballet Program
published: 2020-04-20
Ferrer, Astrid (2020): Data for: Contribution of fungal and invertebrate communities to mass loss and wood depolymerization in tropical terrestrial and aquatic habitats. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1530066_V1
Supplemental data sets for the Manuscript entitled "Contribution of fungal and invertebrate communities to mass loss and wood depolymerization in tropical terrestrial and aquatic habitats"
keywords:
Coiba Island; wood decomposition; cellulose; hemicellulose; lignin breakdown; aquatic fungi
published: 2020-04-06
McCoy, Annette; Lopp, Christine; Kooy, Sarah; Migliorisi, Alessandro; Austin, Scott; Wilkins, Pamela (2020): Supplemental Data Normal Regression of the Internal Umbilical Remnant Structures in Standardbred Foals. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2680911_V1
Raw measurement data for umbilical remnants (umbilical vein, umbilical arteries and urachus) in support of Equine Veterinary Journal publication "Normal Regression of the Internal Umbilical Remnant Structures in Standardbred Foals."
keywords:
equine; umbilicus; ultrasound
published: 2020-03-14
Rhoads, Bruce ; Lindroth, Evan (2020): Bank Elevation Dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6100626_V1
Data on bank elevations determined from lidar data for the Upper Sangamon River, Illinois, the Mission River, Texas, and the White River in Indiana
keywords:
bank elevations, rivers, meandering, lowland
published: 2020-03-13
Sweet, Andrew; Johnson, Kevin; Cameron, Stephen (2020): Data from: Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2211060_V2
Data files associated with the assembly of mitochondrial minicircles from five species of parasitic lice. This includes data from four species in the genus Columbicola and from the human louse (Pediculus humanus). The files include FASTA sequences for all five species, reference sequences for read mapping approaches, resulting contigs produced by various assembly approaches, and alignments of human louse minicircles mapped to published sequences of the same species.
keywords:
mitochondria; FASTA; nucleotide sequences; alignment; Columbicola; Pediculus
published: 2020-06-01
Hoover, Jeffrey P; Davros, Nicole M; Schelsky, Wendy; Brawn, Jeffry D (2020): Hoover et al AUK-19-093 Illinois Data Bank Local conspecific density does not influence reproductive output in a secondary cavity-nesting songbird. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6382488_V1
Dataset associated with Hoover et al AUK-19-093 submission: Local conspecific density does not influence reproductive output in a secondary cavity-nesting songbird. Excel CSV with all of the data used in analyses. Description of variables YEARS: year ORDINAL_DATE: number for what day of the year it is with 1 January = 1,……30 December = 365 SITE: acronym for each study site BOX: unique nest box identifier on each study site TREAT: designates whether nest box was in a high- or low- nest box density area within each study site ACTUAL_NO_NEIGHBORS: number of pairs of warblers using a nest box within 200 m of a given pair’s nest box CLUTCH_SIZE: number of warbler eggs in nest at the onset of incubation PROWN: number of warbler nestlings once eggs have hatched PROWF: number of warbler nestlings that fledged out of the nest box HATCH_SUCCESS: proportion of eggs in the nest that hatched FLEDG_SUCCESS: proportion of the nestlings that fledged from the nest box HATCH_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no hatching failure FLEDG_SUCCESS2: binary category where “0” indicates there was some, and “1” indicates there was no nestling failure (i.e. nestling death) BHCO_PARASIT2: binary category where “0” indicates no cowbird parasitism, and “1” indicates there was cowbird parasitism BHCOE: number of cowbird eggs in clutch BHCOF: number of cowbird nestlings that fledged from the nest PAIRID: unique number that identifies a male and female warbler that are together at a nest box and this number is the same in a subsequent nesting attempt or year if the same male and female are together again FEMALE_ID: unique identifier for each female which represents her leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg FEM_AGE: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird FEMALE_BREEDING_ATTEMPT: “1” indicates first, “2” indicates second,……..breeding attempt within a given year SECOND_ATTEMPT: for any female that fledged a brood in a given year, binary category where “0” represents that they did not, and “1” indicates that they did attempt a second brood that year F_TOT_PROWF: total reproductive output (number of warbler fledglings produced) for a given female in a given year MALE_ID: unique identifier for each male which represents his leg band combination. Each letter represents a band with letters preceding the hyphen being on the right leg and after the hyphen the left leg MALE_AGE2: binary category where “0” indicates a 1-year-old bird and “1” indicates a >1-year-old bird Provisioning_rate: total number of food provisions per nestling per hour by male and female warbler combined BROOD_MASS: average nestling mass (g) for the brood BROOD_TARSUS: average nestling tarsus length (mm) for the brood Brood_condition: unit-less index of nestling condition that uses the residuals of the BROOD_MASS/BROOD_TARSUS relationship A period (“.”) represents where data were not collected, not available, or because individual nest or female did not qualify for consideration of a category assignment. An empty cell represents no data available for this particular cell.
keywords:
conspecific density; density dependence; food limitation; hatching success; nestling body condition; nestling provisioning; Prothonotary Warbler; reproductive output
published: 2020-02-27
Clem, Scott; Sparbanie, Taylor; Luro, Alec; Harmon-Threatt, Alexandra (2020): Data for: Anthophilous hover flies (Diptera: Syrphidae) may visually discriminate neonicotinoid insecticides in sucrose solution: a choice experiment. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0490928_V1
These data were collected for an experiment examining effects of neonicotinoid (clothianidin) presence on hover fly (Diptera: Syrphidae) behavior. Hover flies of two species (Eristalis arbustorum and Toxomerus marginatus) were offered a choice to feed on artificial flowers laced with sucrose solution that was either contaminated (CLO) or not contaminated (CON) with clothianidin. Two different concentrations of clothianidin in 0.5 M sucrose solution were tested: 2.5 ppb and 150 ppb. We conducted four sets of 10 trials, each trial set examining a different combination of species and clothianidin dose. Across 6 hours of video for each trial we recorded 1) number of visits to each flower that resulted in feeding, and 2) amount of time spent feeding during each visit. We found that while neither species fed significantly longer on either of the solutions, E. arbustorum appeared to avoid flowers with clothianidin particularly at high rates. In the paper, we attribute this avoidance response, partially, to hover fly-visible spectral differences between the two flower choices and discuss potential implications for field and lab-based studies. In the enclosed zip file we have included all data for this project and code scripts from R. * Note: Data folder contains 4 files (instead of 6 as mentioned in Readme): e.tenax_photoreceptors.csv; hoverfly_data_UPDATE.csv; number_visits_UPDATE.csv; and Original 2018 hover fly choice test data_Clem2020.xlsx
keywords:
Syrphidae; hoverfly; Eristalis; Toxomerus; Choice Experiment; Neonicotinoid; Clothianidin
published: 2020-01-31
Bradshaw, Therin M.; Blake-Bradshaw, Abigail G.; Fournier, Auriel M.V.; Lancaster, Joseph D. ; O'Connell, John; Jacques, Christopher N.; Eicholtz, Michael W.; Hagy, Heath M (2020): Marsh bird occupancy of wetlands managed for waterfowl in the Midwestern USA - Analysis Inputs. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5152821_V1
Data inputs, and scripts for the analysis detailed in Bradshaw et al, published in PlosONE 2020.
keywords:
Marsh birds; wetlands
published: 2020-02-05
Zahniser, James; Dietrich, Christopher (2020): NEXUS data file for phylogenetic analysis of Deltocephalinae (Hemiptera: Cicadellidae) . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7290912_V1
The Delt_Comb.NEX text file contains the original data used in the phylogenetic analyses of Zahniser & Dietrich, 2013 (European Journal of Taxonomy, 45: 1-211). 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 nine lines of the file indicate the file type (Nexus), that 152 taxa were analyzed, that a total of 3971 characters were analyzed, the format of the data, and specification for two symbols used in the dataset. There are four datasets separated into blocks, one each for: 28S rDNA gene, Histone H3 gene, morphology, and insertion/deletion characters scored based on the alignment of the 28S rDNA dataset. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the publication using this dataset. A text file, Delt_morph_char.txt, is available here that states the morphological characters and characters states that were scored in the Delt_Comb.NEX dataset. The original DNA sequence data are available from NCBI GenBank under the accession numbers indicated in publication. Chromatogram files for each sequencing read are available from the first author upon request.
keywords:
phylogeny; DNA sequence; morphology; parsimony analysis; Insecta; Hemiptera; Cicadellidae; leafhopper; evolution; 28S rDNA; histone H3; bayesian analysis
published: 2020-02-01
Williams, Benjamin R.; Benson, Thomas J. (2020): Habitat Use of Spring Migrating Dabbling Ducks in the Wabash River Valley. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7017235_V1
This data describes habitat use, availability, landscape level influences, and daily movement of dabbling ducks in the Wabash River Valley of southeastern Illinois and southwestern Indiana. It contains triangulated locations of individual ducks, associated habitat assignments of those locations, flood survey data to determine water availability, and randomly generated points to assess landscape level questions.
keywords:
waterfowl; ducks; dabbling; mallard; teal; habitat
published: 2020-01-28
Miao, Guofang; Guan, Kaiyu (2020): Sun-induced chlorophyll fluorescence of two Nebraska maize sites in 2017. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5893373_V1
This dataset includes two data files that provide the time series (Jul. - Sep. 2017) data of sun-induced chlorophyll fluorescence (SIF_760) collected under sunny conditions at two maize sites (one rainfed and the other irrigated) in Nebraska in 2017. Data contain 392 SIF_760 records at the rainfed site and 707 records at the irrigated site. The timestamp uses local standard time. Data are available for the sunny conditions from 8 am to 5 pm (corresponding to 9 am to 6 pm local time) throughout the study period.
keywords:
sun-induced chlorophyll fluorescence (SIF); maize; gross primary production(GPP); light use efficiency(LUE); SIF yield
published: 2019-12-10
Yang, Pan; Zhao, Qiankun; Cai, Ximing (2019): Land productivity and land availability for growing bioenergy crop in the Contiguous US. Center for Advanced Bioenergy and Bioproducts Innovation (CABBI). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4584681_V1
The dataset consists of two types of data: the estimate of land productivity (the maximum productivity, MP) and the estimate of land that has low productivity for any major crops planted in the Contiguous United States and then may be available for growing bioenergy crops (the marginal land, ML). All data items are in GeoTiff format, under the World Geodetic System (WGS) 84 project, and with a resolution of 0.0020810045 degree (~250 m). The MP values are calculated based on machine learning model estimated yields of major crops in the CONUS, and its expected value (MP_mean.tif), and associated uncertainty (MP_IDP.tif). The ML availability data have two versions: a deterministic version and a version with uncertainty. The deterministic MLs are determined as the land pixels with expected MP values falling in the range defined in the following criteria, and the MLs with uncertainty are determined as the probability that the MP value of a land pixel falls in the range defined in the following criteria: Criteria_____Description S1________ Current crop and pasture land with MP <= P50 S2________ Current crop and pasture land with MP <= P25 S3________ S1 + current grass and shrub land with P25 < MP < P50 S4________ S2 + current grass and shrub land with P10 < MP < P25 Economic__ Current crop and pasture land with potential profitability < 0 Here P10, P25 and P50 are the 10th, 25th and 50th percentile of crop MP values
keywords:
Land productivity;marginal land;land use
published: 2019-12-03
de Moya, Robert (2019): Feather Louse Orthology set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0440388_V1
This is the data set associated with the manuscript titled "Extensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event." Included are the gene alignments used for phylogenetic analyses and the cophylogenetic input files.
keywords:
phylogenomics, cophylogenetics, feather lice, birds
published: 2019-12-03
de Moya, Robert (2019): Heteroptera Transcriptome Set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7784896_V1
These are the alignments of transcriptome data used for the analysis of members of Heteroptera. This dataset is analyzed in "Deep instability in the phylogenetic backbone of Heteroptera is only partly overcome by transcriptome-based phylogenomics" published in Insect Systematics and Diversity.
keywords:
Heteroptera; Hemiptera; Phylogenomics; transcriptome
published: 2019-11-18
Zhang, Chuanyi; Ochoa, Idoia (2019): VCF files used for VEF: a Variant Filtering tool based on Ensemble methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9401259_V1
VCF files used to analyze a novel filtering tool VEF, presented in the article "VEF: a Variant Filtering tool based on Ensemble methods".
keywords:
VCF files; filtering; VEF
published: 2019-10-18
Smith, Rebecca (2019): Spatial and Temporal Invasion Dynamics of Aedes albopictus (Diptera: Culicidae) in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7540359_V1
Supporting secondary data used in a manuscript currently in submission regarding the invasion dynamics of the asian tiger mosquito, Aedes albopictus, in the state of Illinois
keywords:
albopictus;mosquito
published: 2019-07-04
Rapti, Zoi (2019): Control of bacterial infections via antibiotic-induced proviruses . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9721455_V1
Software (Matlab .m files) for the article: Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses. The files can be used to reproduce the analysis and figures in the article.
keywords:
Matlab codes; antibiotic-induced dynamics
published: 2019-09-05
Yang, Ning; Gao, Jiarong; Lewis, Fred; Yau, Peter; Collins, James; Sweedler, Jonathan; Newmark, Phillip (2019): Data for A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1599850_V1
The data set here include data from NMR, LC-MS/MS, MALDI-MS, H/D exchange MS experiments used in paper "A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection".
published: 2019-08-29
de Moya, Robert (2019): Bemisia tabaci ortholog set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5333299_V1
This is the published ortholog set derived from whole genome data used for the analysis of members of the B. tabaci complex of whiteflies. It includes the concatenated alignment and individual gene alignments used for analyses (Link to publication: https://www.mdpi.com/1424-2818/11/9/151).
published: 2019-07-04
Sashittal, Palash; El-Kebir, Mohammed (2019): SharpTNI Results. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9734610_V1
Results generated using SharpTNI on data collected from the 2014 Ebola outbreak in Sierra Leone.
published: 2019-08-15
Smith, Rebecca (2019): Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7539223_V1
Simulation data related to the paper "Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study"
keywords:
paratuberculosis;simulation;dairy
published: 2019-08-30
Allen, Maximilian (2019): Wisconsin Bobcat Harvest Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2501832_V1
This dataset includes the data from an analysis of bobcat harvest data with particular focus on the relationship between catch-per-unit-effort and population size. The data relate to bobcat trapper and hunter harvest metrics from Wisconsin and include two RDS files which can be open in the software R using the readRDS() function.
keywords:
bobcat; catch-per-unit-effort; CPUE; harvest; Lynx rufus; wildlife management; trapper; hunter