Illinois Data Bank
Deposit Dataset
Find Data
Policies
Guides
Contact Us
Log in with NetID
University Library, University of Illinois at Urbana-Champaign
Toggle navigation
Illinois Data Bank
Deposit Dataset
Find Data
Policies
Guides
Contact Us
Log in with NetID
Displaying 226 - 250 of 335 in total
<
1
2
…
6
7
8
9
10
11
12
13
14
>
25 per page
50 per page
Show All
Clear Filters
Generate Report from Search Results
Subject Area
Life Sciences (335)
Social Sciences (0)
Physical Sciences (0)
Technology and Engineering (0)
Uncategorized (0)
Arts and Humanities (0)
Funder
Other (118)
U.S. National Science Foundation (NSF) (89)
U.S. Department of Energy (DOE) (38)
U.S. Department of Agriculture (USDA) (38)
U.S. National Institutes of Health (NIH) (25)
Illinois Department of Natural Resources (IDNR) (16)
U.S. Geological Survey (USGS) (4)
Illinois Department of Transportation (IDOT) (3)
U.S. National Aeronautics and Space Administration (NASA) (2)
U.S. Army (2)
Publication Year
2021 (66)
2020 (60)
2022 (56)
2019 (42)
2023 (40)
2018 (24)
2017 (19)
2024 (16)
2016 (12)
2025 (0)
2009 (0)
2011 (0)
2012 (0)
2014 (0)
2015 (0)
License
CC0 (211)
CC BY (111)
custom (13)
Datasets
published: 2020-11-18
Gardner, Allison; Allan, Brian (2020): Gardner Midwest Lyme Invasion Data 2020-11-18. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6050723_V2
These data obtained from the peer-reviewed literature and a public database depict the geographic expansion of the black-legged tick (Ixodes scapularis) and human cases of Lyme disease in the midwestern U.S. <b><i>Note</b></i>: There was an omission from the first version (V1) of the data set that required us to update the data. Specifically, we failed to include the data from the article "Caporale DA, Johnson CM, Millard BJ. 2005 Presence of Borrelia burgdorferi (Spirochaetales: Spirochaetaceae) in Southern Kettle Moraine State Forest, Wisconsin, and characterization of strain W97F51. J. Med. Entomol. 42, 457–472". In the second version (V2) of the data, this omission is corrected.
keywords:
Lyme disease; Borrelia burgdorferi; Ixodes scapularis; black-legged tick
published: 2020-11-14
Hoover, Jeffrey; Schelsky, Wendy (2020): Global warming effects on nesting in Prothonotary Warblers. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6482573_V1
Dataset includes temperature data (local average April daily temperatures), first egg dates and reproductive output of Prothonotary Warblers breeding in southernmost Illinois, USA. Also included are arrival dates for warblers returning to breeding grounds from wintering grounds, and global temperature anomaly data for comparison with local temperatures. These data were used in the manuscript entitled "Warmer April Temperatures on Breeding Grounds Promote Earlier Nesting in a Long-Distance Migratory Bird, the Prothonotary Warbler" published in Frontiers in Ecology and Evolution. A rich text file is included with explanations of each variable in the dataset.
keywords:
first egg dates; global warming; local temperature effects; long-distance migratory bird; prothonotary warbler; protonotaria citrea; reproductive output
published: 2020-11-06
Sashittal, Palash; Zhang, Chuanyi; El-Kebir, Mohammed (2020): Simulation Data for JUMPER: Discontinuous Transcript Assembly in SARS-CoV-2. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6667667_V1
This data contains bam files and transcripts in the simulated instances generated for the paper 'JUMPER: Discontinuous Transcript Assembly in SARS-CoV-2' submitted for RECOMB 2021. The folder 'bam' contained the simulated bam files aligned using STAR wile the reads were generated using the method polyester Note: in the readme file, close to the end of the document, please ignore this sentence: 'Those files can be opened by using [name of software].'
keywords:
transcript assembly; SARS-CoV-2; discontinuous transcription; coronaviruses
published: 2020-11-05
Miller, Andrew; Raudabaugh, Daniel (2020): Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6862941_V2
This version 2 dataset contains 34 files in total with one (1) additional file, called "Culture-dependent Isolate table with taxonomic determination and sequence data.csv". The remaining files (33) are identical to version 1. The following is the information about the new file and its variables: <b>Culture-dependent Isolate table with taxonomic determination and sequence data.csv</b>: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below: IsolateNumber : unique number identify each isolate cultured Time: season in which the sample was collected Location: the specific name of the location Habitat: type of habitat : either stream or peatland State: state in the USA in which the specific location is located Incubation_pH ID: pH of the medium during isolation of fungal cultures Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity) Sequence_quality: base call quality of the entire sequence used for blast analysis, if known %_coverage: sequence coverage reported from GenBank %_ID: sequence similarity reported from GenBank Life_style : ecological life style if known Phylum: phylogenetic phylum as indicated by Index Fungorum Subphylum: phylogenetic subphylum as indicated by Index Fungorum Class: phylogenetic class as indicated by Index Fungorum Subclass: phylogenetic subclass as indicated by Index Fungorum Order: phylogenetic order as indicated by Index Fungorum Family: phylogenetic Family as indicated by Index Fungorum ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5 Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software Note: blank cells mean no data is available or unknown.
keywords:
ITS1 forward reads; Illumina; peatlands; streams; bogs; fens
published: 2020-07-15
Molloy, Erin K. (2020): Data from: Supertree-like methods for genome-scale species tree estimation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4004605_V1
This repository includes scripts and datasets for Chapter 6 of my PhD dissertation, " Supertree-like methods for genome-scale species tree estimation," that had not been published previously. This chapter is based on the article: Molloy, E.K. and Warnow, T. "FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models." Bioinformatics, In press. https://doi.org/10.1093/bioinformatics/btaa444. The results presented in my PhD dissertation differ from those in the Bioinformatics article, because I re-estimated species trees using FastMulRF and MulRF on the same datasets in the original repository (https://doi.org/10.13012/B2IDB-5721322_V1). To re-estimate species trees, (1) a seed was specified when running MulRF, and (2) a different script (specifically preprocess_multrees_v3.py from https://github.com/ekmolloy/fastmulrfs/releases/tag/v1.2.0) was used for preprocessing gene trees (which were then given as input to MulRF and FastMulRFS). Note that this preprocessing script is a re-implementation of the original algorithm for improved speed (a bug fix also was implemented). Finally, it was brought to my attention that the simulation in the Bioinformatics article differs from prior studies, because I scaled the species tree by 10 generations per year (instead of 0.9 years per generation, which is ~1.1 generations per year). I re-simulated datasets (true-trees-with-one-gen-per-year-psize-10000000.tar.gz and true-trees-with-one-gen-per-year-psize-50000000.tar.gz) using 0.9 years per generation to quantify the impact of this parameter change (see my PhD dissertation or the supplementary materials of Bioinformatics article for discussion).
keywords:
Species tree estimation; gene duplication and loss; statistical consistency; MulRF, FastRFS
published: 2020-08-25
Allan, Brian; Fredericks, Lisa (2020): AllanLab fluidigm pipeline test dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0095812_V1
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).
keywords:
custom database of tick pathogens; fluidigm pipeline; fluidigm paired reads; fluidigm tutorial
published: 2020-08-31
Chen, Luoye; Khanna, Madhu; Debnath, Deepayan; Zhong, Jia; Ferin, Kelsie; VanLoocke, Andy (2020): BEPAM Model Code and CABBI Simulation Results for "The Economic and Environmental Costs and Benefits of the Renewable Fuel Standard". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9851670_V1
This dataset contains BEPAM model code and input data to replicate the outcomes for "The Economic and Environmental Costs and Benefits of the Renewable Fuel Standard". The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output.gms. (BEPAM-Social cost model-ERL.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.
keywords:
Social Cost of Carbon; Social Cost of Nitrogen; Cost-Benefit Analysis; Indirect Land-Use Change
published: 2020-11-01
Packard, Stephen; Spyreas, Greg (2020): Dramatic long-term restoration of an oak woodland due to multiple, sustained management treatments. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0887518_V1
A 30 year record of the vegetation in sample plots in a woodland in the Chicago area. The changes in these plots over time show how ecological restoration can yield dramatic results.
keywords:
woodland; ecological restoration; floristic quality; vegetation; plant ecology; ecological management
published: 2020-10-30
Warner, Genoa R; Pacyga, Diana; Strakovsky, Rita; Smith, Rebecca; James-Todd, Tamarra; Williams, Paige; Hauser, Russ; Meling, Daryl; Li, Lucas; Flaws, Jodi (2020): Phthalates and Hot Flashes SI. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9238850_V1
Supporting information for "Urinary Phthalate Metabolite Concentrations and Hot Flashes in Pre- and Perimenopausal Women from the Midlife Women’s Health Study." This file contains tables of the results of stratified analyses of the associations of hot flash outcomes with urinary phthalates metabolites by menopause status, race/ethnicity, body mass index, and depressive status. This file also contains supplementary HPLC methods for the analysis of phthalate metabolites.
keywords:
Hot flashes; menopause; phthalates; women
published: 2020-10-27
Kansara, Yogeshwar; Hoang, Linh (2020): Included Articles from Cochrane Reviews. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8212056_V2
The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".
keywords:
Cochrane reviews; automation; randomized controlled trial; RCT; systematic review
published: 2020-10-27
Kansara, Yogeshwar; Hoang, Linh; Dong, Xiaoru; Xie, Jingyi; Schneider, Jodi (2020): Sampled Cochrane Reviews Included RCTs Only. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3285089_V2
The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".
keywords:
Cochrane reviews; systematic reviews; randomized control trial; RCT; automation
published: 2020-10-16
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2020): Partial predation of a songbird nest by an Eastern Box Turtle (Terrapene carolina carolina) . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0684398_V1
Video footage of an Eastern Box Turtle (Terrapene carolina carolina) partially predating a Field Sparrow nest (Spizella pusilla) at 0845 h on the 31 of May 2020. Please note that the date on the video footage is incorrect due to user error, but the time is correct.
keywords:
nest predation; turtle; songbird; nest camera; Terrapene carolina carolina; Spizella pusilla;
published: 2020-10-15
Khanna, Madhu; Wang, Weiwei; Wang, Michael (2020): BEPAM Model Code and CABBI Simulation Results for "Assessing the Additional Carbon Savings with Biofuel". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4272529_V1
This dataset consists of various input data that are used in the GAMS model. All the data are in the format of .inc which can be read within GAMS or Notepad. Main data sources include: acreage data (acre), crop budget data ($/acre), crop yield data (e.g. bushel/acre), Soil carbon sequestration data (KgCO2/ha/yr). Model details can be found in the "Assessing the Additional Carbon Savings with Biofuel" and GAMS model package. ## File Description (1) GAMS Model.zip: This includes all the input files and scripts for running the model (2) Table*.csv: These files include the data from the tables in the manuscript (3) Figure2_3_4.csv: This contains the data used to create the figures in the manuscript (4) BaselineResults.csv: This includes a summary of the model results. (5) SensitivityResults_*.csv: Model results from the various sensitivity analyses performed (6) LUC_emission.csv: land use change emissions by crop reporting district for changes of pasturelands to annual crops.
keywords:
Biogenic carbon intensity; Corn ethanol; Economic model; Dynamic optimization; Anticipated baseline approach; Life cycle carbon intenisty
published: 2020-10-14
Dalling, James W.; Heineman, Katherine D. (2020): Multiple stem and environmental variables dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4045402_V1
Data on permanent plots at Fortuna and the Panama Canal Watershed, Republic of Panama, containing counts and percent of trees with one or more multiple stems >10cm diameter, with and without palms. Accompanying environmental data includes elevation, precipitation, soil type and soil chemical variables (pH, total N, NO3, NO4, resin P, mehlich Ca, K and Mg.
keywords:
multiple stems; resprouting; Panama Canal Watershed; Fortuna Forest Reserve
published: 2020-10-01
Acevedo-Siaca, Liana; Long, Stephen (2020): Photosynthetic Induction of Rice Flag Leaves. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3596430_V1
Raw gas exchange data for photosynthetic induction in 6 rice accession flag leaves. Photosynthetic induction and point measurements were made at ambient [CO2]. Two accessions (AUS 278 and IR64) were selected to screen in greater detail in which photosynthetic induction was measured at six [CO2].
published: 2020-09-25
Smirnov, Vladimir (2020): Data and results for: MAGUS: Multiple Sequence Alignment using Graph Clustering. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2643961_V1
This repository contains the datasets and corresponding results for the paper "MAGUS: Multiple Sequence Alignment using Graph Clustering". The Datasets.zip archive contains the ROSE, balibase, Gutell, and RNASim datasets used in our experiments. The Results.zip archive contains the outputs of running our methods against these datasets. Datasets used: ROSE: 10 simulated nucleotide model conditions from the SATe paper, each with 20 replicates, and with 1000 sequences per replicate. The ROSE datasets were originally taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/sate-i">https://sites.google.com/eng.ucsd.edu/datasets/alignment/sate-i</a> RNASim: This is a collection of simulated nucleotide datasets that were generated under a model of evolution that reflects selection due to RNA structural constraints. We sampled 20 subsets of 1000 sequences each, as well as 10 subsets of 10000 each, by randomly sampling from the original million-sequence RNASim dataset. Gutell: 16S.M, 16S.3, 16S.T, 16S.B.ALL: Four biological nucleotide datasets from the Comparative Ribosomal Website (CRW) with cleaned reference alignments from SATe. Since PASTA is restricted to datasets without sequence length heterogeneity, these were modified to remove sequences that deviate by more than 20% from the median length. The scrubbed datasets range from 740 to 24,246 sequences. The pre-screened 16S datasets were taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/16s23s">https://sites.google.com/eng.ucsd.edu/datasets/alignment/16s23s</a> BAliBASE: We use eight BAliBASE amino acid datasets used in the PASTA paper. As above, we remove outlier sequences, which leaves us with sizes ranging from 195 to 732 sequences. The pre-screened Balibase datasets were taken from <a href="https://sites.google.com/eng.ucsd.edu/datasets/alignment/pastaupp">https://sites.google.com/eng.ucsd.edu/datasets/alignment/pastaupp</a>
published: 2020-09-27
Long, Stephen (2020): Data used to construct Table1 and Figs. 2 and 4 in Ainsworth & Long (2020) 30 Years of Free Air Carbon Dioxide Enrichment (FACE): What Have We Learned About Future Crop Productivity and the Potential for Adaptation? Global Change Biology. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2432396_V1
Data extracted from Text, Tables and Figures of publications in summarizing crop responses to Free-Air CO2 Elevation (FACE)
keywords:
Free Air CO2 Elevation; FACE; wheat, rice, soybean, cassava;
published: 2020-09-18
Clark, Lindsay; Njuguna, Joyce; Jin, Xiaoli; Petersen, Karen; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens B.; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik (2020): RAD-seq genotypes for a Miscanthus sacchariflorus diversity panel. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8170405_V1
Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.
keywords:
variant call format (VCF); genotyping-by-sequencing (GBS); single nucleotide polymorphism (SNP); grass; genetic diversity; biomass
published: 2020-09-17
Refsland, Tyler; Knapp, Benjamin; Stephan, Kirsten; Fraterrigo, Jennifer (2020): Data for "Sixty-five years of fire manipulation reveals climate and fire interact to determine growth rates of Quercus spp". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6771049_V1
Data are from a long-term fire manipulation experiment in the Missouri Ozarks, USA. Data include the raw, annual ring-width increment (rwl), basal area increment (BAI), population-level annual growth resistance (Drs) and resilience (Drl) to drought, intrinsic water use efficiency values (WUEi) and oxygen isotopic composition of individual radial growth rings (δ18O) from southern red oak (Quercus falcata) and post oak (Q. stellata) trees. ---------------------- TITLE: Data for "Sixty-five years of fire manipulation reveals climate and fire interact to determine growth rates of Quercus spp." ---------------------- FILE OVERVIEW: This dataset contains four (4) CSV files as described below: Refsland_et_al_ECS20-0465_BAI.csv: annual basal area increment between 1948-2015 for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_DroughtIndices.csv: population-level drought resistance and resilience of trees during each target drought period Refsland_et_al_ECS20-0465_WUEi.csv: carbon isotope indicators of drought stress for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_d18Or.csv: oxygen isotope indicators of drought stress for trees across the fire manipulation experiment ---------------------- VARIABLE EXPLANATION: All the variables in those four files are explained as below: treeID: unique character string that identifies subject tree block: integer (1, 2) that identifies the study block plot: integer (1-12) that identifies the plot nested within each study block trt: character string (Annual, Control, Periodic) that identifies the fire treatment of a given plot species: character string (Quercus falcata, Quercus stellata) that identifies species of subject tree year: integer (1948-2015) that identifies the dated year of each tree ring rwl_mm: numerical value representing the annual tree ring-width, in mm bai_cm2: numerical value representing the annual basal area increment, in cm2 timeperiod: integer value (1953, 1964, 2007, 2012) representing the periods encompassing target dry and wet years Drs_2yr: numerical value representing the drought resistance, defined as the population-level annual growth of trees during drought years relative to pre-drought years for a given time period Drl_2yr: numerical value representing the drought resilience, defined as the population-level annual growth of trees following drought years relative to pre-drought years for a given time period stand_ba_m2ha: numerical value representing the total basal area of a given plot, in m2 per ha stand_density_stems_ha: numerical value representing the total stem density of a given plot, in stems per ha pool: numerical value (1-40) identifying the set of tree ring samples pooled for analysis. Samples were pooled by block, plot, year and species period: integer value (1953, 1964, 1980, 2007, 2012) representing the periods encompassing target dry and wet years type: character string (Dry, Wet) indicating the water availability of a given year d13C: numerical value representing the carbon isotopic composition of radial growth rings within a given sample pool, in per mil WUEi: numerical value representing the annual intrinsic water use efficiency of radial growth rings within a given sample pool d18O: numerical value representing the oxygen isotopic composition of radial growth rings within a given sample pool, in per mil
keywords:
climate change adaptation; drought; fire; nitrogen availability; oak-hickory; radial growth; resilience; resistance; stand density; temperate broadleaf forest; water stress
published: 2020-09-07
Chen, Luoye; Blanc-Betes, Elena; Hudiburg, Tara; Hellerstein, Daniel; Wallander, Steven; DeLucia, Evan; Khanna, Madhu (2020): BEPAM Model Code and CABBI Simulation Results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2224392_V2
This dataset contains BEPAM model code and input data to the replicate the results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land." The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output_0213-2020_Complete_daycent-agversion-[rental payment level]%_[biomass price].gms. (BEPAM-CRP model-Sep2020.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.
keywords:
Miscanthus; Switchgrass; soil carbon sequestration; greenhouse gas savings; rental payments; biomass price
published: 2020-10-01
Strickland, Lynette (2020): No choice mating trials and two choice mating trials in the polymorphic tortoise beetle, Chelymorpha alternans. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8972634_V1
These datasets were performed to assess whether color pattern phenotypes of the polymorphic tortoise beetle, Chelymorpha alternans, mate randomly with one another, and whether there are any reproductive differences between assortative and disassortative pairings.
keywords:
mate choice, color polymorphisms, random mating
published: 2020-07-15
Smirnov, Vladimir (2020): Vlad's Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6955387_V1
published: 2020-07-15
Legried, Brandon; Molloy, Erin K.; Warnow, Tandy; Roch, Sebastien (2020): Data from: Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2626814_V3
This repository includes scripts and datasets for the paper, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss."
keywords:
Species tree estimation; gene duplication and loss; identifiability; statistical consistency; quartets; ASTRAL
published: 2020-06-30
Chakraborty, Sulagna; Cristina Drumond Andrade , Flavia; Lee Smith, Rebecca (2020): Case Studies for 'An Interdisciplinary Approach to One Health: Course Design, Development and Delivery'. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0595759_V1
This file contains 13 unique case studies that were created for the One health: Infectious diseases course offered at the University of Illinois at Urbana-Champaign campus. The case studies are being made available as educational resources for other One health courses. Each case study is focused on a theme/topic which is associated with One health. These case studies were created using publicly available information and references have been provided for each case study.
keywords:
One health education; infectious diseases; case studies
published: 2020-02-12
Price, Edward; Spyreas, Greg; Matthews, Jeffrey (2020): Biotic homogenization of wetland vegetation in the conterminous United States driven by Phalaris arundinacea and anthropogenic disturbance. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7128075_V1
This is the dataset used in the Landscape Ecology publication of the same name. This dataset consists of the following files: NWCA_Int_Veg.txt NWCA_Reg_Veg.txt NWCA_Site_Attributes.txt NWCA_Int_Veg.txt is a site and plot by species matrix. Column labeled SITES consists of site IDs. Column labeled Plots consist of Plot ID numbers. All other columns represent species abundances (estimates of percent cover, summed across five plots). NWCA_Reg_Veg.txt is a site by species matrix of species abundances. Column labeled SITES consist of site IDs. All other columns represent species abundances (estimates of percent cover within individual plots). NWCA_Site_Attributes.txt is a matrix of site attributes. Column labeled SITES consist of site IDs. Column labeled AA_CENTER_LAT consist of latitudinal coordinates for the Assessment Area center point in decimal degrees. Column labeled AA_CENTER_LONG consist of longitudinal coordinates for the Assessment Area center point in decimal degrees. Column REFPLUS_NWCA represents disturbance gradient classes including MIN (minimally disturbed), L (least disturbed), I (intermediate), M (most disturbed). Column REFPLUS_NWCA2 represents revised disturbance gradient classes based on protocols described in the article. These revised classes were used for analysis. Column labeled STRESS_HEAVYMETAL represents heavy metal stressor classes, used to ascertain which wetlands were missing soil data. Classes in the STRESS_HEAVYMETAL column include Low, Moderate, High, and Missing. Sites with Missing STRESS_HEAVYMETAL classes were removed from analysis. More information about this dataset: All of the data used in this analysis was gathered from the National Wetlands Condition Assessment. Wetland surveys were conducted from 4/4/2011 to 11/2/2011. The entire National Wetlands Condition Assessment Dataset, which includes 3640 unique taxonomic identities of plants, can be found at: https://www.epa.gov/national-aquatic-resource-surveys/data-national-aquatic-resource-surveys
keywords:
Anthropogenic disturbance; β-Diversity; Biotic homogenization; Phalaris arundinacea; reed canary grass; Wetlands