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Illinois Data Bank Dataset Search Results
Dataset Search Results
published: 2024-10-08
Mersich, Ina; Bishop, Rebecca; Diaz Yucupicio, Sandra; Nobrega, Ana D.; Austin, Scott; Barger, Anne; Fick , Megan E.; Wilkins, Pamela (2024): Data for Decreased Circulating Red Cell Mass (Packed Cell Volume) Alters Viscoelastic and Traditional Plasma Coagulation Testing Results in Healthy Horses. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9153919_V1
Acepromazine was administered to healthy adult horses to induce transient anemia secondary to splenic sequestration. Data was collected at baseline (T0), 1 hour (T1) and 12 hours (T2) post acepromazine administration. Data collection included PCV, TP, CBC, fibrinogen, PT, PTT and viscoelastic coagulation profiles (VCM Vet) as well as ultrasonographic measurements of the spleen at all 3 time points.
keywords:
horse; coagulation; viscoelastic testing; anemia; acepromazine
published: 2024-10-07
Kole Aspray, Elise; Ainsworth, Elizabeth; McGrath, Jesse; McGrath, Justin; Montes, Christopher; Whetten, Andrew; Ort, Donald; Long, Stephen; Puthuval, Kannan; Mies, Timothy; Bernacchi, Carl; DeLucia, Evan; Dalsing, Bradley; Leakey, Andrew; Li, Shuai; Herriott, Jelena; Miglietta, Franco (2024): SoyFACE Fumigation Data Files. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3496460_V4
This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. This V4 contains new experimental data files, hourly fumigation files, and weather/ambient files for 2022 and 2023, since the original dataset only included files for 2001-2021. The MATLAB code has also been updated for efficiency, and explanatory files have been updated accordingly. Below are new changes in V4: - The "SoyFACE Plot Information 2001 to 2021" file is renamed to “SoyFACE ring information 2001 to 2023.xlsx”. Data for 2022 and 2023 were added. File contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - The "SoyFACE 1-Minute Fumigation Data Files" were updated to contain sub-folders for each year of the experiments (2001-2023), each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments ("SoyFACE Hourly Fumigation Data Files" folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments ("Hourly Weather and Ambient Data Files" folder which has also been updated to include 2022 and 2023 data). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - “Rings.xlsx” is new in this version. This file lists the rings and treatments used in each year of the SoyFACE experiments between 2001 and 2023 and is used in several of the MATLAB codes. - “CMI Weather Data Explanation.docx” is newly added. This file contains specific information about the processing of raw weather data, which is used in the hourly weather and ambient data files. - Files that were in RAR format in V3 are now updated and saved as ZIP format, including: Hourly Weather and Ambient Data Files.zip , SoyFACE 1-Minute Fumigation Data Files.zip , SoyFACE Hourly Fumigation Data Files.zip, and Matlab Files.zip. - The "Fumigation Target Percentages" file was updated to add data for 2022 and 2023. This file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The "Matlab Files" folder contains custom code (Aspray, E.K.) that was used to clean the "SoyFACE 1-Minute Fumigation Data" files and to generate the "SoyFACE Hourly Fumigation Data" and "Fumigation Target Percentages" files. Code information can be found in the various "Explanation" files. The Matlab code changes are as follows: 1. “Data_Issues_Finder.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 2. “Data_Issues_Finder_all.m” code is new. This code is the same as the “Data_Issues_Finder.m” code except that it identifies all CO2 and O3 repeats. In contrast, the “Data_Issues_Finder.m” code only identifies CO2 and O3 repeats that occur when the fumigation system is turned on. 3. “Target_Yearly.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 4. “HourlyFumCode.m” code is new. This code uses the “Rings.xlsx” file to gather ring and treatment information based on the contents of the file instead of the user needing to define these values explicitly. This code also defines a list of all ring folders for the year selected and runs the hourly code for each ring, instead of the user having to run the hourly code for each ring individually. Finally, the code generates two dialog boxes for the user, one which allows user to specify whether they want the hourly code to be run for 1-minute fumigation files or 1-minute ambient files, and another which allows user to specify whether they would like the hourly fumigation averages to be replaced with hourly ambient averages when the fumigation system is turned off. 5. “HourlyDataFun.m” code was changed to run either “HourlyData.m” code or “HourlyDataAmb.m” code, depending on user input in the first dialog box. 6. “HourlyData.m” code was changed to replace hourly fumigation averages with hourly ambient averages when the fumigation system is turned off, depending on user input in the second dialog box. 7. “HourlyDataAmb.m” code is new. This code is similar to “HourlyData.m” code but is used to calculate hourly averages for 1-minute ambient files instead 1-minute fumigation files. 8. “batch.m” code was changed to account for new function input variables in “HourlyDataFun.m” code, along with adding header columns for “FumOutput.xlsx” and “AmbOutput.xlsx” output files generated by “HourlyData.m” and “HourlyDataAmb.m” code. - Finally, the " * Explanation" files contain information about the column names, units of measurement, steps needed to use Matlab code, and other pertinent information for each data file. Some of them have been updated to reflect the current change of data.
keywords:
SoyFACE; agriculture; agricultural; climate; climate change; atmosphere; atmospheric change; CO2; carbon dioxide; O3; ozone; soybean; fumigation; treatment
published: 2024-08-12
Hartman, Jordan H; Davis, Mark A; Iacaruso, Nicholas J; Tiemann, Jeremy S; Larson, Eric R (2024): Data for Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7837995_V2
Data associated with the manuscript "Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies." by Jordan H. Hartman, Mark A. Davis, Nicholas J. Iacaruso, Jeremy S. Tiemann, Eric R. Larson. For this project, we sampled six locations in Michigan and Illinois for Eastern and Western Banded Killifish and primary consumers. Using stable isotope analysis we found that Eastern Banded Killifish had higher variance in littoral dependence and trophic position than Western Banded Killifish, but both stable isotope and gut content metabarcoding analyses revealed an overlap in the diet composition and trophic position between the subspecies. This dataset provides the sampling locations, accession numbers for gut content metabarcoding data from the National Center for Biotechnology Information Sequence Read Archive, the assignment of each family used in the gut content metabarcoding analysis as littoral, pelagic, terrestrial, or parasite. and the raw stable isotope data from University of California Davis.
keywords:
non-game fish; invasive species; imperiled species; stable isotope analysis; gut content metabarcoding
published: 2024-07-01
Edmonds, Devin; Andriantsimanarilafy, Raphali; Crottini, Angelica; Dreslik, Michael; Newton-Youens, Jade; Andoniana, Ramahefason; Christian, Randrianantoandro; Andreone, Franco (2024): Data and code for estimating population sizes, annual survival, and inferring absence of the frog Mantella cowanii. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0681943_V1
This data and code accompany the manuscript "Small population size and possible extirpation of the threatened Malagasy poison frog Mantella cowanii". The data were collected using photograph capture-recapture at three sites in the central highlands of Madagascar. In Part 1, the script implements robust design capture-mark-recapture models in program MARK through the RMark interface to estimate population sizes and annual survival probabilities. In Part 2, it estimates the number of surveys needed to infer absence at sites where we did not detect the frog.
keywords:
abundance; amphibian; capture-recapture
published: 2024-10-01
Li, Shengyun; Wu, Wen-Yen; Liao, Ling-Hsiu; Berenbaum, May (2024): Data for Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1147122_V1
This dataset is associated with the manuscript "Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment" This dataset includes 2 Excel files: 1) raw_data_bioassay.xlsx: this file contains the raw data for waxworm bioassay. There are 2 worksheets within this file: - LC50: raw data for measuring LC50 in the laboratory and field strain of Galleria mellonella. - RGR: Relative Growth Rate, raw data for measuring body weight of field strain of Galleria mellonella . 2) raw-data_RT-qPCR.xlsx: this file contains raw data (Ct value) of RT-qPCR.
keywords:
Apis mellifera; cytochrome P450; honey bee; pesticide; waxworm
published: 2024-09-16
Wu, Steven; Smith, Hannah (2024): Data on Controversies in Electric Vehicle Batteries. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9365647_V1
This dataset describes an analysis of research documents about the debate between hydrogen fuel cells and lithium-ion batteries within the context of electric vehicles. To create this dataset, we first analyzed news articles on the topic of sustainable development. We searched for related science using keywords in Google Scholar. We then identified subtopics and selected one specific subtopic: electric vehicles. We started to identify positions and players about electric vehicles [1]. Within electric vehicles, we started searching in OpenAlex for a topic of reasonable size (about 300 documents) related to a scientific or technical debate. We narrowed to electric vehicles and batteries, then trained a cluster model [2] on OpenAlex’s keywords to develop some possible search queries, and chose one. Our final search query (May 7, 2024) returned 301 document in OpenAlex: Title & abstract includes: Electric Vehicle + Hydrogen + Battery filter is Lithium-ion Battery Management in Electric Vehicle We used a Python script and the Scopus API to find missing abstracts and DOIs [3]. To identify relevant documents, we used a combination of Abstractkr [4] and manual screening. As a starting point for Abstractkr [4], one person manually screened 200 documents by checking the abstracts for “hydrogen fuel cells” and “battery comparisons”. Then we used Abstractkr [4] to predict the relevance of the remaining documents based on the title, abstract, and keywords. The settings we used were single screening, ordered by most likely to be relevant, and 0 pilot size. We set a threshold of 0.6 for the predictions. After screening and predictions, 176 documents remained
keywords:
controversy mapping; sustainable development; evidence synthesis; OpenAlex; Abstrackr; Scopus; meta-analysis; electric vehicle; hydrogen fuel cells; battery
published: 2024-09-28
Huang, Yijing (2024): tellurium_magneto_chiral_instability. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9143327_V1
The data and code provided in this dataset can be used to generate key plots in the manuscript. It is divided into four subfolders (B parallel/perpendicular to the tellurium c axis and field/ temperature dependence), each containing the raw data (saved in .mat format), the oscillator parameters obtained through linear prediction (saved in .mat format), and the plot-generating code (.m files). The code was written using MATLAB R2024a. To run the code, go to each folder, and run the .m file in that folder, which generates two plots.
published: 2024-09-26
Kamara, Shasta; Hay, Allison; Oller, Reagan; Suski, Cory (2024): Examining the consequences of angling tournament culling practices on Largemouth Bass Micropterus nigricans. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9108676_V1
This dataset is from a study of a simulated angling tournament livewell holding in June of 2023 on Largemouth Bass (Micropterus nigricans) on Clinton Lake, Illinois. Fish were collected via electrofishing, weighed, measured and assessed for physical injury prior to receiving a commercially available cull tag and being placed in a simulated livewell. After a six hour livewell holding period, fish were removed from the livewell assessed for physical injury and then assessed for reflex action mortality predictors prior to being placed in a net pen for 3 days of observation. This dataset includes, weights, total lengths, physical injury scores, and reflex action mortality predictor scores for Largemouth Bass and water quality parameters of livewells and the lake in net pens.
keywords:
sport fish conservation; fisheries management; high-grading; stringer
published: 2024-09-24
Sawyer, Elle; Kreps, Timothy; Lodge, David; Larson, Eric (2024): Rusty crayfish body size in Vilas County, Wisconsin lakes 1980-2020. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1143617_V1
Data at the lake summary and individual crayfish level that supports the manuscript Sawyer, E.K., Kreps, T. A., Lodge, D. M. and E.R. Larson. “Long-term declines in body size of the invasive rusty crayfish (Faxonius rusticus) in temperate lakes." Includes size measurements of 69,303 individual rusty crayfish (Faxonius rusticus) for 17 lakes of Vilas County, Wisconsin, United States collected between 1980 and 2020.
keywords:
body size; Faxonius rusticus; invasive species; non-native species; rusty crayfish; Wisconsin; Vilas County
published: 2024-09-19
Klimasmith, Isaac; Kent, Angela (2024): Propagule Pressure in Microbial Introductions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0907683_V1
The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. The dataset filed here includes the experimemtal datafile, and a RMarkdown file that includes all the code used in in both the modeling and anaylsis.
keywords:
microbial inoculants; invasion ecology; propagule pressure; agriculture; modeling
published: 2024-09-17
Cao, Yanghui; Dietrich, Christopher H.; Dmitriev, Dmitry A.; Kits, Joel H.; Xue, Qingquan; Zhang, Yalin (2024): Dataset title: Datasets, scripts and main output files for "Phylogeny, Biogeography and Morphological Evolution of the Treehopper-Like Leafhoppers (Hemiptera: Cicadellidae) Megophthalminae and Ulopinae". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1475719_V3
The following seven zip files are compressed folders containing the input datasets/trees, main output files and the scripts of the related analyses performed in this study. I. ancestral_microhabitat_reconstruction.zip: contains four files, including two input files (microhabitats.csv, timetree.tre) and a script (simmap_microhabitat.R) for ancestral states reconstruction of microhabitat by make.simmap implemented in the R package phytools v1.5, as well as the main output file (ancestral_microhabitats.csv). 1. ancestral_microhabitats.csv: reconstructed ancestral microhabitats for each node. 2. microhabitats.csv: microhabitats of the studies species. 3. simmap_microhabitat.R: the R script of make.simmap for ancestral microhabitat reconstruction 4. timetree.tre: dated tree used for ancestral state reconstruction for microhabitat and morphological characters II. ancestral_morphology_reconstruction.zip: contains six files, including an input file (morphology.csv) and a script (simmap_morphology.R) for ancestral states reconstruction of morphology by make.simmap implemented in the R package phytools v1.5, as well as four main output files(forewing_ancestral_state.csv, frontal_sutures_ancestral_state.csv, hind_wing_ancestral_state.csv, ocellus_ancestral_state.csv). 1. forewing_ancestral_state.csv: reconstructed ancestral states of the development of the forewing for each node. 2. frontal_sutures_ancestral_state.csv: reconstructed ancestral states of the development of frontal sutures for each node. 3. hind_wing_ancestral_state.csv: reconstructed ancestral states of the development of the hind wing for each node. 4. morphology.csv: the states of the development of ocellus, forewing, hing wing and frontal sutures for each studies species. 5. ocellus_ancestral_state.csv: reconstructed ancestral states of the development of the ocellus for each node. 6. simmap_morphology.R: the R script of make.simmap for ancestral state reconstruction of morphology III. biogeographic_reconstruction.zip: contains four files, including three input files (dispersal_probablity.txt, distributions.csv, timetree_noOutgroup.tre) used for a stratified biogeographic analysis by BioGeoBEARS in RASP v4.2 and the main output file (DIVELIKE_result.txt). 1. dispersal_probablity.txt: relative dispersal probabilities among biogeographical regions at different geological epochs. 2. distributions.csv: current distributions of the studied species. 3. DIVELIKE_result.txt: BioGeoBEARS result of ancestral areas based on the DIVELIKE model. 4. timetree_noOutgroup.tre: the dated tree with the outgroup lineage (Eurymelinae) excluded. IV. coalescent_analysis.zip: contains a folder and two files, including a folder (individual_gene_alignment) of input files used to construct gene trees, an input file (MLtree_BS70.tre) used for the multi-species coalescent analysis by ASTRAL v 4.10.5 and the main output file (coalescent_species_tree.tre). 1. coalescent_species_tree.tre: the species tree generated by the multi-species coalescent analysis with the quartet support, effective number of genes and the local posterior probability indicated. 2. individual_gene_alignment: a folder containing 427 FASTA files, each one represents the nucleotide alignment for a gene. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12. 3. MLtree_BS70.tre: 165 gene trees with the average SH-aLRT and ultrafast bootstrap values of ≥ 70%. This file was used to estimate the species tree by ASTRAL v 4.10.5. V. divergence_time_estimation.zip: contains five files, including two input files (treefile_rooted_noBranchLength.tre, treefile_rooted.tre) and two control files (baseml.ctl, mcmctree.ctl) used for divergence time estimation by BASEML and MCMCTREE in PAML v4.9, as well as the main output file (timetree_with95%HPD.tre). 1. baseml.ctl: the control file used for the estimation of substitution rates by BASEML in PAML v4.9. 2. mcmctree.ctl: the control file used for the estimation of divergence times by MCMCTREE in PAML v4.9. 3. timetree_with95%HPD.tre: dated tree with the 95% highest posterior density confidence intervals indicated. 4. treefile_rooted_noBranchLength.tre: the maximum likelihood tree based on the concatenated nucleotide dataset with calibrations for the crown and internal nodes. Branch length and support values were not indicated. 5. treefile_rooted.tre: the maximum likelihood tree based on the concatenated nucleotide dataset with a secondary calibration on the root age. Branch support values were not indicated. VI. maximum_likelihood_analysis_aa.zip: contains three files, including two input files (concatenated_aa_partition.nex, concatenated_aa.phy) used for the maximum likelihood analysis by IQ-TREE v1.6.12 and the main output file (MLtree_aa.tre). 1. concatenated_aa_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_aa.phy. This file partitions the 52,024 amino acid positions into 427 character sets. 2. concatenated_aa.phy: a concatenated amino acid dataset with 52,024 amino acid positions. Hyphens are used to represent gaps. This dataset was used for the maximum likelihood analysis. 3. MLtree_aa.tre: the maximum likelihood tree based on the concatenated amino acid dataset, with SH-aLRT values and ultrafast bootstrap values indicated. VII. maximum_likelihood_analysis_nt.zip: contains three files, including two input files (concatenated_nt_partition.nex, concatenated_nt.phy) used for the maximum likelihood analysis by IQ-TREE v1.6.12 and the main output file (MLtree_nt.tre). 1. concatenated_nt_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_nt.phy. This file partitions the 156,072 nucleotide positions into 427 character sets. 2. concatenated_nt.phy: a concatenated nucleotide dataset with 156,072 nucleotide positions. Hyphens are used to represent gaps. This dataset was used for the maximum likelihood analysis as well as divergence time estimation. 3. MLtree_nt.tre: the maximum likelihood tree based on the concatenated nucleotide dataset, with SH-aLRT values and ultrafast bootstrap values indicated. VIII. Taxon_sampling.csv: contains the sample IDs (1st column) which were used in the alignments and the taxonomic information (2nd to 6th columns).
keywords:
Anchored Hybrid Enrichment, Biogeography, Cicadellidae, Phylogenomics, Treehoppers
published: 2024-09-03
Bishop, Rebecca; Jonk, Kaitlyn M; Migliorisi, Alessandro; Austin, Scott M; Mullins, Emma C; Wilkins, Pamela (2024): Effect of phenylepherine-induced increased PCV on viscoelastic coagulation testing in horses. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0295993_V1
Healthy mares were administered phenylephrine to induce transient polycythemia secondary to splenic contraction. Data was collected at baseline (T0), 5 minutes (T1) and 2 hours (T2) post-phenylephrine infusion. Collected data included baseline CBC, chemistry, fibrinogen, and serum amyloid A; at each time point viscoelastic coagulation profiles (VCM Vet), traditional in-vitro coagulation profiles, and ultrasonographic measurements of the spleen were obtained.
keywords:
horse; coagulation; polycythemia; blood clotting; viscoelastic testing
published: 2024-08-29
Li, Shuai; Montes, Christopher; Aspray, Elise; Ainsworth, Elizabeth (2024): How do drought and heat affect the response of soybean seed yield to elevated O3? An analysis of 15 seasons of free-air O3 concentration enrichment (O3-FACE) studies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9394312_V1
Over the past 15 years, soybean seed yield response to season-long elevated O3 concentrations [O3] and to year-to-year weather conditions was studied using free-air O3 concentration enrichment (O3-FACE) in the field at the SoyFACE facility in Central Illinois. Elevated [O3] significantly reduced seed yield across cultivars and years. However, our results quantitatively demonstrate that weather conditions, including soil water availability and air temperature, did not alter yield sensitivity to elevated [O3] in soybean.
keywords:
drought, elevated O3, heat, O3-FACE, soybean, yield
published: 2022-10-10
Varela, Sebastian; Leakey, Andrew; Sacks, Erik (2022): UAV remote sensing imagery - Miscanthus trials 2020 - Energy Farm - UIUC . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5689586_V1
Aerial imagery utilized as input in the manuscript "Deep convolutional neural networks exploit high spatial and temporal resolution aerial imagery to predict key traits in miscanthus" . Data was collected over M. Sacchariflorus and Sinensis breeding trials at the Energy Farm, UIUC in 2020. Flights were performed using a DJI M600 mounted with a Micasense Rededge multispectral sensor at 20 m altitude around solar noon. Imagery is available as tif file by field trial and date (10). The post-processing of raw images into orthophoto was performed in Agisoft Metashape software. Each crop surface model and multispectral orthophoto was stacked into an unique raster stack by date and uploaded here. Each raster stack includes 6 layers in the following order: Layer 1 = crop surface model, Layer 2 = Blue, Layer 3 = Green, Layer 4 = Red, Layer 5 = Rededge, and Layer 6 = NIR multispectral bands. Msa raster stacks were resampled to 1.67 cm spatial resolution and Msi raster stacks were resampled to 1.41 cm spatial resolution to ease their integration into further analysis. 'MMDDYYYY' is the date of data collection, 'MSA' is M. Sacchariflorus trial, 'MSI' is Miscanthus Sinensis trial, 'CSM' is crop surface model layer, and 'MULTSP' are the five multispectral bands.
keywords:
convolutional neural networks; miscanthus; perennial grasses; bioenergy; field phenotyping; remote sensing; UAV
published: 2024-08-13
Maffeo, Christopher; Chhabra, Hemani; Aksimentiev, Aleksei (2024): Scripts for computationally estimating the current in "A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6464580_V1
Scripts used to computationally estimate the current through a DNA nanopore, starting from an equilibrated oxDNA configuration, in association with the manuscript "A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport".
keywords:
DNA origami nanopore; Steric exclusion model; Ionic current
published: 2016-05-19
Donovan, Brian; Work, Dan (2016): New York City Taxi Trip Data (2010-2013). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/J8PN93H8
This dataset contains records of four years of taxi operations in New York City and includes 697,622,444 trips. Each trip records the pickup and drop-off dates, times, and coordinates, as well as the metered distance reported by the taximeter. The trip data also includes fields such as the taxi medallion number, fare amount, and tip amount. The dataset was obtained through a Freedom of Information Law request from the New York City Taxi and Limousine Commission. The files in this dataset are optimized for use with the ‘decompress.py’ script included in this dataset. This file has additional documentation and contact information that may be of help if you run into trouble accessing the content of the zip files.
keywords:
taxi;transportation;New York City;GPS
published: 2024-08-24
Jones, Todd; Llamas, Alfredo; Phillips, Jennifer (2024): Data for Jones et al. GCB-23-1273.R1. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6010827_V1
Dataset associated with Jones et al. GCB-23-1273.R1 submission: Phenotypic signatures of urbanization? Resident, but not migratory, songbird eye size varies with urban-associated light pollution levels. Excel CSV file with all of the data used in analyses and file with descriptions of each column.
keywords:
body size; demographics; eye size; phenotypic divergence; songbirds; sensory pollution; urbanization
published: 2021-05-10
Varela Quintela, Sebastian; Leakey, Andrew (2021): UAV-based multispectral time-series imagery of biomass sorghum - 2019. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0353090_V1
UAV-based high-resolution multispectral time-series orthophotos utilized to understand the relation between growth dynamics, imagery temporal resolution, and end-of-season biomass productivity of biomass sorghum as bioenergy crop. Sensor utilized is a RedEdge Micasense flown at 40 meters above ground level at the Energy Farm- UIUC in 2019.
keywords:
Unmanned aerial vehicles; High throughput phenotyping; Machine learning; Bioenergy crops
published: 2024-08-15
Gounder, Babu; Kadiyan, Lakshya; Sarker, Zafar Waziha (2024): Oil Spill Shell Data Set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9244463_V1
This study acquired publicly available Shell annual reports. Reports were selected for the years since the UN investigation in 2011, resulting in documents from 2012 to 2023.
keywords:
environmental justice; ethics of care; indigenous communities; Niger River Delta; oil spills
published: 2024-08-19
Ward, Michael; Stewart, Sarah; Benson, Thomas (2024): Whip-poor-will nesting success. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7835826_V1
Data on the nesting success and post-fledgling survival of Eastern Whip-poor-wills in central Illinois. Data was part of Sarah Stewart's MS project at the University of Illinois.
keywords:
bird nesting success; post-fledgling survival; eastern whip-poor-will
published: 2024-08-17
Storms, Suzanna; Leonardi-Cattolica, Antonio; Prezioso, Tara; Varga, Csaba; Wang, Leyi; Lowe, James (2024): Data for Influenza A virus shedding and reinfection during the post-weaning period in swine: longitudinal study of two nurseries. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0440849_V1
This dataset includes the RT-PCR shedding data and primers used for whole genome sequencing of Influenza A virus in swine. It also includes the GenBank accession numbers for all segments generated by Influenza A virus sequencing from nasal swab samples. Additionally, all nucleotide changes are listed by sample.
published: 2024-08-16
Halligan, Susannah; Schummer, Michael; Fournier, Auriel; Musni, Vergie; Davis, J. Brian; Downs, Cynthia; Lavretsky, Philip (2024): Morphological differences between wild and game-farm Mallards in North America. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3363781_V1
Dataset used for the paper entitled "Morphological differences between wild and game-farm Mallards in North America". Large-scale releases of domesticated, game-farm Mallards to supplement wild populations have resulted in wide-spread introgressive hybridization that changed the genetic constitution of wild populations in eastern North America. The resulting gene flow is well-documented between game-farm and wild Mallards, but the mechanistic consequences from such interactions remain unknown in North America. We provide the first study to characterize and investigate potential differences in morphology between genetically known, wild and game-farm Mallards in North America. We used nine morphological measurements to discriminate between wild and game-farm Mallards with 96% accuracy. Compared to their wild counterparts, game-farm Mallards had longer bodies and tarsi, shorter heads and wings, and shorter, wider, and taller bills. The nail on the end of the bill of game-farm Mallards was longer, and game-farm Mallard bills had a greater lamellae:bill length ratio than wild Mallards. Differences in body morphologies between wild and game-farm Mallards are consistent with an artificial, terrestrial life whereby game-farm Mallards are fed pelleted foods resulting in artificial selection for a more “goose-like” bill. We posit that 1) game-farm Mallards have diverged from their wild ancestral traits of flying and filter feeding towards becoming optimized to run and peck for food; 2) game-farm morphological traits optimized over the last 400 years in domestic environments are likely to be maladaptive in the wild; and 3) the introgression of such traits into wild populations is likely to reduce fitness. Understanding effects of game-farm Mallard introgression requires analysis of various game-farm × wild hybrid generations to determine how domestically-derived traits persist or diminish with each generation.
keywords:
Mallard; Game Farm; Morphology; Waterfowl; Duck
published: 2024-08-11
Curtis, Jeffrey H.; Riemer, Nicole; West, Matthew (2024): Data for Explicit stochastic advection algorithms for the regional scale particle-resolved atmospheric aerosol model WRF-PartMC (v1.0). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3847217_V2
This dataset contains all material required to produce the figures found within the manuscript submitted to Geoscientific Model Development entitled “Explicit stochastic advection algorithms for the regional scale particle-resolved atmospheric aerosol model WRF-PartMC (v1.0)”. The dataset consists of Python Jupyter notebooks and any applicable WRF-PartMC output. This dataset covers the three numerical examples of the manuscript, 1D advection by a uniform constant wind, a 2D rotational flow and a 3D time-evolving WRF simulated flow.
keywords:
Atmospheric chemistry; Atmospheric Science; Particle-resolved modeling; Numerical modeling; Advection;
published: 2024-05-23
Xing, Yuqing; Bae, Seokjin; Ritz, Ethan; Yang, Fan; Birol, Turan; Salinas , Andrea N. Capa ; Ortiz, Brenden R.; Wilson , Stephen D.; Wang, Ziqiang; Fernandes, Rafael M.; Madhavan, Vidya (2024): Data for manuscript entitled "Optical Manipulation of the Charge Density Wave state in RbV3Sb5". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4197245_V1
This dataset consists of all the figure files that are part of the main text and supplementary of the manuscript titled "Optical manipulation of the charge density wave state in RbV3Sb5". For detailed information on the individual files refer to the readme file.
keywords:
kagome superconductor; optics; charge density wave
published: 2024-08-06
Xing, Yuqing; Bae, Seokjin; Madhavan, Vidya (2024): Raw topographies for the study of magnetic field response of RbV3Sb5. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0274244_V1
This is the raw topographies (without linear background subtraction) related to the publication: https://www.nature.com/articles/s41586-024-07519-5