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published: 2021-04-22
 
All code in Matlab .m scripts or functions (version R2019b) Affiliated with article “Temperate and chronic virus competition leads to low lysogen frequency” published in the Journal of Theoretical Biology (2021) Codes simulate and plot the solutions of an Ordinary Differential Equations model and generate bifurcation diagrams.
published: 2021-04-19
 
Dataset compiled by Yushu Xia and Michelle Wander for the Soil Health Institute. Data were recovered from peer reviewed literature reporting results for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) in terms of their relative response to management where soils under grassland cover, no-tillage, cover crops, residue return and organic amendments were compared to conventionally managed controls. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, and “fluorescein diacetate hydrolysis”, together with one or more of the following: “management practice”, “tillage”, “cover crop”, “residue”, “organic fertilizer”, or “manure”. Records were tabulated to compare SQI abundance in soil maintained under a control and soil aggrading practice with the intent to contribute to SQI databases that will support development of interpretive frameworks and/or algorithms including pedo-transfer functions relating indicator abundance to management practices and site specific factors. Meta-data include the following key descriptor variables and covariates useful for development of scoring functions: 1) identifying factors for the study site (location, year of initiation of study and year in which data was reported), 2) soil textural class, pH, and SOC, 3) depth and timing of soil sampling, 4) analytical methods for SQI quantification, 5) units used in published works (i.e. equivalent mass, concentration), 6) SQI abundances, and 7) statistical significance of difference comparisons. *Note: Blank values in tables are considered unreported data.
keywords: Soil health promoting practices; Soil quality indicators; β-glucosidase; fluorescein diacetate hydrolysis; Permanganate oxidizable carbon; Greenhouse gas emissions; Scoring curves; Soil Management Assessment Framework
published: 2021-04-11
 
This dataset contains RNASim1000, Cox1-Het datasets as well as analyses of RNASim1000, Cox1-Het, and 1000M1(HF).
keywords: phylogeny estimation; maximum likelihood; RAxML; IQ-TREE; FastTree; cox1; heterotachy; disjoint tree mergers; Tree of Life
published: 2021-05-14
 
- The aim of this research was to evaluate the novel dietary fiber source, miscanthus grass, in comparison to traditional fiber sources, and their effects on the microbiota of healthy adult cats. Four dietary treatments, cellulose (CO), miscanthus grass fiber (MF), a blend of miscanthus fiber and tomato pomace (MF+TP), or beet pulp (BP) were evaluated.<br /><br />- The study was conducted using a completely randomized design with twenty-eight neutered adult, domesticated shorthair cats (19 females and 9 males, mean age 2.2 ± 0.03 yr; mean body weight 4.6 ± 0.7 kg, mean body condition score 5.6 ± 0.6). Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br />- Filenames are composed of animal name identifier, diet (BP= beet pulp; CO= cellulose; MF= miscanthus grass fiber; TP= blend of miscanthus fiber and tomato pomace).
keywords: cats; dietary fiber; fecal microbiota; miscanthus grass; nutrient digestibility; postbiotics
published: 2021-05-07
 
- The objective of this study was to evaluate macronutrient apparent total tract digestibility (ATTD), gastrointestinal tolerance, and fermentative end-products in extruded, canine diets. <br />- Five diets were formulated to be isocaloric and isonitrogenous with either garbanzo beans (GBD), green lentils (GLD), peanut flour (PFD), dried yeast (DYD), or poultry by-product meal (CON) as the primary protein sources. Ten adult, intact, female beagles (mean age: 4.2 ± 1.1 yr, mean 28 weight: 11.9 ± 1.3 kg) were used in a replicated, 5x5 Latin square design with 14 d periods. Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br />- Filenames are composed of animal name identifier, diet (CON=control; DY= dried yeast; GB= garbanzo beans; GL= green lentils; PF= peanut flour) and period replicate number (P1, P2, P3, P4, and P5).
keywords: Dog; Digestibility; Legume; Microbiota; Pulse; Yeast
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: 2021-04-05
 
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: 2021-03-31
 
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: 2021-03-10
 
The PhytoplasmasRef_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the phylogenetic analyses of Trivellone et al. (Ecology and Evolution, in review). The 27 sequences (21 phytoplasma reference strains and 6 phytoplasmas strains from the present study) were aligned using the Muscle algorithm as implemented in MEGA 7.0 with default settings. The final dataset contains 952 positions of the F2n/R2 fragment of the 16S rRNA gene. The data analyses are further described in the cited original paper.
keywords: Hemiptera; Cicadellidae; Mollicutes; Phytoplasma; biorepository
published: 2021-03-08
 
These are abundance dynamics data and simulations for the paper "Higher-order interaction between species inhibits bacterial invasion of a phototroph-predator microbial community". In this V2, data were converted in Python, in addition to MATLAB and more information on how to work with the data was included in the Readme.
keywords: Microbial community; Higher order interaction; Invasion; Algae; Bacteria; Ciliate
published: 2021-03-08
 
In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves and high light transmission through the canopy are henceforth referred to as ‘erectophile’ and those with low leaf erectness, ‘planophile’. In the final year of the study, bundle sheath leakiness in erectophile and planophile accessions was also compared.
keywords: Sorghum; Photosynethic Performance; Leaf Inclination
published: 2021-03-05
 
Datasets that accompany Beilke, Blakey, and O'Keefe 2021 publication (Title: Bats partition activity in space and time in a large, heterogeneous landscape; Journal: Ecology and Evolution).
keywords: spatiotemporal; chiroptera
published: 2021-03-05
 
Adey_Larson_Behavior.csv: Results of behavioral assays for rusty crayfish Faxonius rusticus collected from six lakes in Vilas County, Wisconsin in summer 2018. Crayfish_ID is an individual crayfish ID or identifier that matches to individuals in Adey_Larson_Isotope. Collection is how organisms were collected (trapped = baited trapping, snorkel = by hand). Lake is the study lake crayfish were collected from. Length is crayfish carapace length in mm. CPUE is crayfish catch-per-unit effort from baited trapping in that lake during summer 2018. Shelter_Occupancy, Exploration, Feeding_Snail, Feeding_Detritus, Feeding_Crayfish, and Aggressiveness are behavioral assay scores for individual crayfish. Shelter_Occupancy is frequency of observation intervals (12 maximum) in which crayfish were observed in shelter over a 12 hour period. Exploration is time for crayfish to explore a new area measured in seconds (maximum possible time 1200 seconds or 20 minutes). Feeding_Snail, Feeding_Detritus, and Feeding_Crayfish is the time for crayfish to take a food item (snail, detritus, or snail in the presence of another crayfish) measured in seconds (maximum possibe time 1200 seconds or 20 minutes). Aggressiveness is the response to an approach with a novel object scored as a fast retreat (-2), slow retreat (-1), no visible response (0), approach without threat display (1), approach with threat display (2), interaction with closed chelae (3), or interaction with open chelae (4). Three repeated aggressiveness measures were made per individual (Aggresiveness1, Aggresiveness2, Aggresiveness3), which were summed for inclusion in subsequent analyses (Aggresiveness_Sum). More detailed behavioral assay methods can be found in Adey 2019 Masters thesis. Adey_Larson_Isotope.csv: Stable isotope (13C, 15N) values for rusty crayfish Faxonius rusticus and snail or mussel primary consumers from six lakes in Vilas County, Wisconsin collected during summer 2018. Crayf is an individual crayfish ID or identifier that matches to the same individual crayfish in Adey_Larson_Behavior. Lake is the study lake. Collection is how organisms were collected (trapped = baited trapping, snorkel = by hand). Sample type indicates whether isotope values are for crayfish, snail, or mussel. d13C and d15N are stable isotope values.
keywords: individual specialization; intraspecific competition; behavior; diet; stable isotopes; crayfish; invasive species; limnology; Faxonius rusticus
published: 2021-02-26
 
These data were used in the survival and cause-specific mortality analyses of translocated nuisance American black bear in Wisconsin published in Animal Conservation (Bauder, J.M., N.M. Roberts, D. Ruid, B. Kohn, and M.L. Allen. Accepted. Lower survival of nuisance American black bears (Ursus americanus) is not due to translocation. Animal Conservation). Included are CSV files including each bear's capture history and associated covariates and meta-data for each CSV file. Also included is an example R script of how to conduct the analyses (this R script is also included as supporting information with the published paper).
keywords: black bear; survival; translocation; nuisance wildlife management
published: 2021-02-25
 
Total nitrogen leaching rates were calculated over the Mississippi Atchafalaya River Basin (MARB) using an integrated economic-biophysical modeling approach. Land allocation for corn production and total nitrogen application rates were calculated for crop reporting districts using the Biofuel and Environmental Policy Analysis Model (BEPAM) for 5 RFS2 policy scenarios. These were used as input in the Integrated BIosphere Simulator-Agricultural Version (Agro-IBIS) and the Terrestrial Hydrologic Model with Biogeochemistry (THMB) to calculate the nitrogen loss. Land allocation and total nitrogen application simulations were simulated for the period 2016-2030 for 303 crop reporting districts (https://www.nass.usda.gov/Data_and_Statistics/County_Data_Files/Frequently_Asked_Questions/county_list.txt). The final 2030 values are reported here. Both are stored in csv files. Units for land allocation are million ha and nitrogen application are million kg. The nitrogen leaching rates were modeled with a spatial resolution of 5' x 5' using the North American Datum of 1983 projection and stored in NetCDF files. The 30-year average is calculated over the last 30 years of the 45 years being simulated. Leaching rates are calculated in kg-N/ha.
keywords: nitrogen leaching, bioethanol, bioenergy crops
published: 2021-02-16
 
Data from census of peer-reviewed papers discussing nosZ and published from 2013 to 2019. These data were reported in the manuscript titled, "Beyond denitrification: the role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions" published in Global Change Biology as an Invited Report.
keywords: atypical nosZ; Clade II nosZ; denitrification; nitrous oxide; N2O reduction; non-denitrifier; nosZ; nosZ-II; nosZ Clade II; soil N2O emissions
published: 2021-02-15
 
The file contains biomass and count data of food items encountered in the digestive tract of collected green-winged teal from the Illinois River Valley during spring 2016-2018. The file also contains biomass of food items collected from core samples collected at sites where the green-winged teal were collected. Together, the consumed and availability food data are used to calculate diet selection. The data also contains information on the teal, collection, sites, and other covariates used in analysis. Lastly, the dataset contains biomass of food items collected in medium (#35) and small (#60) sieves for 2018 core samples.
keywords: Anas crecca; food selection; green-winged teal; Illinois River Valley; moist-soil plants; spring migration; stopover ecology
published: 2021-08-28
 
Metabolite identifications and profiles of liver samples from 22 day old male and female pigs from gilt that exposed to porcine reproductive and respiratory syndrome virus (P) or not (C) that were weaned at 21 days of age (W) or not (N). Profiles were obtained by University of Illinois Carver Metabolomics Center. Spectrum for each sample was acquired using a gas chromatography mass spectrometry system consisting of an Agilent 7890 gas chromatograph, an Agilent 5975 MSD, and an HP 7683B auto sampler.
keywords: gas chromatography; mass spectrometry; maternal immune activation; weaning; liver
published: 2021-03-15
 
Dataset associated with "Hiding in plain sight: genetic confirmation of putative Louisiana Fatmucket Lampsilis hydiana in Illinois" as submitted to Freshwater Mollusk Biology and Conservation by Stodola et al. Images are from cataloged specimens from the Illinois Natural History Survey (INHS) Mollusk Collection in Champaign, Illinois that were used for genetic research. File names indicate the species as confirmed in Stodola et al. (i.e., Lampsilis siliquoidea or Lampsilis hydiana) followed by the INHS Mollusk Collection catalog number, followed by the individual specimen number, followed by shell view (interior or exterior). If no specimen number is noted in the file name, there is only one specimen for that catalog number. For example: Lsiliquoidea_46515_1_2_3_exterior. Images were created by photographing specimens on a metric grid in an OrTech Photo-e-Box Plus with a Nikon D610 single lens reflex camera using a 60mm lens. Post-processing of images (cropping, image rotation, and auto contrast) occurred in Adobe Photoshop and saved as TIFF files using no image compression, interleaved pixel order, and IBM PC Byte Order. One additional partial lot, INHS Mollusk Catalog No. 37059 (shown with both interior and exterior view in one image), is included for reference but was not genetically sequenced. A .csv file contains an index of all specimens photographed. SPECIES: species confirmed using genetic analyses GENE: cox1 or nad1 mitochondrial gene ACCESSION: GenBank accession number INHS CATALOG NO: Illinois Natural History Survey Mollusk Collection Catalog number WATERBODY: waterbody where specimen was collected PUTATIVE SPECIES: species determination based on morphological characters prior to genetic analysis Phylogenetic sequence data (.nex files) were aligned using BioEdit (Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95-98.). Pertinent methodology for the analysis are contained within the manuscript submittal for Stodola et al. to Freshwater Mollusk Biology and Conservation. In these files, "N" is a standard symbol for an unknown base.
keywords: Lampsilis hydiana; Lampsilis siliquoidea; unionid; Louisiana Fatmucket; Fatmucket; genetic confirmation
published: 2021-01-25
 
Dataset associated with Zenzal et al. Oikos submission: Retreat, detour, or advance? Understanding the movements of birds confronting the Gulf of Mexico. https://doi.org/10.1111/oik.07834 Four CSV files were used for analysis and are related to the following subsections under the “Statistics” heading in the “Materials and Methods” section of the journal article: 1. Departing the Edge = “AIC Analysis.csv” 2. Comparing Retreating to Advancing = “Advance and Retreat Analysis.csv” and “Wind Data at Departure.csv” 3. Food Abundance = “Fruit Data.csv” and “Arthropod Data.csv” <b>Description of variables:</b> Year: the year in which data were collected. Departure: the direction in which an individual departed the Bon Secour National Wildlife Refuge. “North” indicates an individual that departed ≥315° or <45°; “Circum” indicates an individual that departed east (45 – 134°) or west ( 225 – 314°); “Trans” indicates an individual that departed south (135 – 224°). Age: the age of an individual at capture. Individuals were aged as hatch year (HY) or after hatch year (AHY) according to Pyle (1997; see related article for full citation). Fat: the fat score of an individual at capture. Individuals were scored on a 6-point scale ranging from 0-5 following Helms and Drury (1960; see related article for full citation). Species: the standardized four letter alphabetic code used as an abbreviation for English common names of North American Birds. SWTH: Catharus ustulatus; REVI: Vireo olivaceus; INBU: Passerina cyanea; WOTH: Hylocichla mustelina; RTHU: Archilochus colubris. FTM_SD: stopover duration or number of days between first capture and departure from automated radio telemetry system coverage at the Bon Secour National Wildlife Refuge. TMB_SD: stopover duration or number of days between first and last detection from automated radio telemetry systems north of Mobile Bay, AL, USA. Mean speed north (km/hr): the northbound travel speed of individuals retreating from the Bon Secour National Wildlife Refuge by determining the time when the signal strength indicated the bird was directly east or west of the automated telemetry system and dividing the amount of time it took for an individual to move in an assumed straight path between the Refuge systems and those north of Mobile Bay, AL, USA. Mean speed south (km/hr): the southbound travel speed of individuals advancing from north of Mobile Bay, AL, USA by determining the time when the signal strength indicated the bird was directly east or west of the automated telemetry system and dividing the amount of time it took for an individual to move in an assumed straight path between the Refuge systems and those north of Mobile Bay, AL, USA. LN_FTM_DEP_TIME: the natural log of departure time from the Bon Secour National Wildlife Refuge. Departure time is defined as the number of hours before or after civil twilight. LN_TMB_DEP_TIME: the natural log of departure time from north of Mobile Bay, AL, USA. Departure time is defined as the number of hours before or after civil twilight. Paired_FTM_DEP_TIME: the departure time or number of hours before or after civil twilight from Bon Secour National Wildlife Refuge. Paired_TMB_DEP_TIME: the departure time or number of hours before or after civil twilight from north of Mobile Bay, AL, USA. Wind Direction: the direction from which the wind originated at the Bon Secour National Wildlife Refuge on nights when individuals were departing. “N” indicates winds from the north (≥315° or <45°); “E” indicates winds from the east (45 – 134°); “W” indicates winds from the west ( 225 – 314°); “S” indicates winds from the south (135 – 224°). Wind Speed (m/s): the wind speed on nights when individuals were departing the Bon Secour National Wildlife Refuge. Group: the direction the bird was traveling under specific wind conditions. Northbound individuals traveled north from Bon Secour National Wildlife Refuge. Southbound individuals traveled south from habitats north of Mobile Bay, AL, USA. Fruit: weekly mean number of ripe fruit per meter. Site: the site from which the data were collected. FTM is located within the Bon Secour National Wildlife Refuge. TMB is located within the Jacinto Port Wildlife Management Area. DOY: number indicating day of year (i.e., 1 January = 001….31 December = 365). Arthropod Biomass: estimated mean arthropod biomass from each sampling period. <b>Note:</b> Empty cells indicate unavailable data where applicable.
keywords: migratory birds; migration; automated telemetry; Gulf of Mexico
published: 2021-01-23
 
Data sets from "Comparing Methods for Species Tree Estimation With Gene Duplication and Loss." It contains data simulated with gene duplication and loss under a variety of different conditions.
keywords: gene duplication and loss; species-tree inference;
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: 2021-06-08
 
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
published: 2021-05-13
 
Data files and R code to replicate the econometric analysis in the journal article: B Chen, BM Gramig and SD Yun. “Conservation Tillage Mitigates Drought Induced Soybean Yield Losses in the US Corn Belt.” Q Open. https://doi.org/10.1093/qopen/qoab007
keywords: R, Conservation Tillage, Drought, Yield, Corn, Soybeans, Resilience, Climate Change