Dataset Search

This dynamic photosynthesis model of soybean canopy is developed by Yu Wang (yuwangcn@illinois.edu), IGB, University of Illinois. If you want to know more details, please check the following publication Yu Wang, Steven J. Burgess, Elsa de Becker, Stephen P. Long. Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity? The Plant Journal.

This is the data used in the paper "Forecasting West Nile Virus with Graph Neural Networks: Harnessing Spatial Dependence in Irregularly Sampled Geospatial Data". A preprint may be found at https://doi.org/10.48550/arXiv.2212.11367 Code from the Github repository https://github.com/adtonks/mosquito_GNN can be used with the data here to reproduce the paper's results. v1.0.0 of the code is also archived at https://doi.org/10.5281/zenodo.7897830

This data set includes information used to determine patterns of mixing at three small confluences in East Central Illinois based on differences in the temperature or turbidity of the two confluent flows.

This dataset provides the raw data, code and related figures for the paper, "Channel Activation of CHSH Nonlocality"

This dataset contains all the datasets used in the study conducted for the research publication titled "Mapping dynamic human sentiments of heat exposure with location-based social media data". This paper develops a cyberGIS framework to analyze and visualize human sentiments of heat exposure dynamically based on near real-time location-based social media (LBSM) data. Large volumes and low-cost LBSM data, together with a content analysis algorithm based on natural language processing are used effectively to generate heat exposure maps from human sentiments on social media. ## What’s inside - A quick explanation of the components of the zip file * US folder includes the shapefile corresponding to the United State with County as spatial unit
 * Census_tract folder includes the shapefile corresponding to the Cook County with census tract as spatial unit * data/data.txt includes instruction to retrieve the sample data either from Keeling or figshare * geo/data20000.txt is the heat dictionary created in this paper, please refer to the corresponding publication to see the data creation process Jupyter notebook and code attached to this publication can be found at: https://github.com/cybergis/real_time_heat_exposure_with_LBSMD

Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and 50% majority-rule consensus trees generated from MrBayes analyses, using the NEXUS alignment files as inputs (fruit_dove_mrbayes_consensus.tre, fruit_dove_plus_cibois_data_mrbayes_consensus.tre).

This dataset inventories the availability of entrepreneurship and small business education, including co-curricular opportunities, in two-year colleges in the United States. The inventory provides a snapshot of activities at more than 1,650 public, not-for-profit, and private for-profit institutions, in 2014.

This dataset contains gamma-ray spectra templates for a source interdiction and uranium enrichment measurement task. This dataset also contains Keras machine learning models trained using datasets created using these templates.

This dataset contains transcribed entries from the "Prairie Directory of North America" (Adelman and Schwartz 2013) for the Tallgrass, Mixed Grass, and Shortgrass prairie regions of the united states. We identified the historical spatial extent of the Tallgrass, Mixed Grass, and Shortgrass prairie regions using Ricketts et al. (1999), Olson et al. (2001), and Dixon et al. (2014) and selected the counties entirely or partially within these boundaries from the USDA Forest Service (2022) file. The resulting lists of counties are included as separate files. The dataset contains information on publicly accessible grasslands and prairies in these regions including acreage and amenities like hunting access, restrooms, parking, and trails.

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.

These are the data sets associated with our publication "Field borders provide winter refuge for beneficial predators and parasitoids: a case study on organic farms." For this project, we compared the communities of overwintering arthropod natural enemies in organic cultivated fields and wildflower-strip field borders at five different sites in central Illinois. Abstract: Semi-natural field borders are frequently used in midwestern U.S. sustainable agriculture. These habitats are meant to help diversify otherwise monocultural landscapes and provision them with ecosystem services, including biological control. Predatory and parasitic arthropods (i.e., potential natural enemies) often flourish in these habitats and may move into crops to help control pests. However, detailed information on the capacity of semi-natural field borders for providing overwintering refuge for these arthropods is poorly understood. In this study, we used soil emergence tents to characterize potential natural enemy communities (i.e., predacious beetles, wasps, spiders, and other arthropods) overwintering in cultivated organic crop fields and adjacent field borders. We found a greater abundance, species richness, and unique community composition of predatory and parasitic arthropods in field borders compared to arable crop fields, which were generally poorly suited as overwintering habitat. Furthermore, potential natural enemies tended to be positively associated with forb cover and negatively associated with grass cover, suggesting that grassy field borders with less forb cover are less well-suited as winter refugia. These results demonstrate that semi-natural habitats like field borders may act as a source for many natural enemies on a year-to-year basis and are important for conserving arthropod diversity in agricultural landscapes.

Airglow images and Meteor radar data used in the paper "Mesospheric gravity wave activity estimated via airglow imagery, multistatic meteor radar, and SABER data taken during the SIMONe–2018 campaign".

Automatic and manual counts of black flies captured in Illinois.

The Allan Lab has published a Fluidigm pipeline online. This is the url: https://github.com/HPCBio/allan-fluidigm-pipeline. This url includes a tutorial for running the pipeline. However it does not have test datasets yet. This tarball hosted at the Illinois Data Bank is the dataset that completes the github tutorial. It includes inputs (custom database of tick pathogens and fluidigm raw reads) and output files (tables of samples with taxonomic classifications).

This dataset includes experimental data supporting the findings in the manuscript "Magnetostriction and Temperature Dependent Gilbert Damping in Boron Doped Fe80Ga20 Thin Films". It contains raw data for X-Ray diffraction, high resolution transmission electron microscopy, magnetic hysteresis loop measurement, magnetostriction measurement, and temperature dependent magnetic damping measurement.

This is the data set from the published manuscript 'Vertebrate scavenger guild composition and utilization of carrion in an East Asian temperate forest' by Inagaki et al.

Data extracted from Text, Tables and Figures of publications in summarizing crop responses to Free-Air CO2 Elevation (FACE)

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.

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.

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.

The data file contains a list of articles with PMIDs information, which were used in a project associated with the manuscript "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews".

The PDF describes the process and data used for the heuristic user evaluation described in the related article “<i>Evaluating an automatic data extraction tool based on the theory of diffusion of innovation</i>” by Linh Hoang, Frank Scannapieco, Linh Cao, Yingjun Guan, Yi-Yun Cheng, and Jodi Schneider (under submission).<br /> Frank Scannapieco assessed RobotReviewer data extraction performance on ten articles in 2018-02. Articles are included papers from an update review: Sabharwal A., G.-F.I., Stellrecht E., Scannapeico F.A. <i>Periodontal therapy to prevent the initiation and/or progression of common complex systemic diseases and conditions</i>. An update. Periodontol 2000. In Press. <br/> The form was created in consultation with Linh Hoang and Jodi Schneider. To do the assessment, Frank Scannapieco entered PDFs for these ten articles into RobotReviewer and then filled in ten evaluation forms, based on the ten Robot Reviewer automatic data extraction reports. Linh Hoang analyzed these ten evaluation forms and synthesized Frank Scannapieco’s comments to arrive at the evaluation results for the heuristic user evaluation.

This dataset includes microclimate species distribution models at a ~3 m2 spatial resolution and free-air temperature species distribution models at ~0.85 km2 spatial resolution for three plethodontid salamander species (Demognathus wrighti, Desmognathus ocoee, and Plethodon jordani) across Great Smoky Mountains National Park. We also include heatmaps representing the differences between microclimate and free-air species distribution models and polygon layers representing the fragmented habitat for each species' predicted range. All datasets include predictions for 2010, 2030, and 2050.

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.