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CC BY (161)
Wang, Shaowen; Lyu, Fangzheng; Wang, Shaohua; Catlet, Charles; Padmanabhan, Anand; Soltani, Kiumars (2021): Data for Integrating CyberGIS and Urban Sensing for Reproducible Streaming Analytics. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0286574_V1
Increasingly pervasive location-aware sensors interconnected with rapidly advancing wireless network services are motivating the development of near-real-time urban analytics. This development has revealed both tremendous challenges and opportunities for scientific innovation and discovery. However, state-of-the-art urban discovery and innovation are not well equipped to resolve the challenges of such analytics, which in turn limits new research questions from being asked and answered. Specifically, commonly used urban analytics capabilities are typically designed to handle, process, and analyze static datasets that can be treated as map layers and are consequently ill-equipped in (a) resolving the volume and velocity of urban big data; (b) meeting the computing requirements for processing, analyzing, and visualizing these datasets; and (c) providing concurrent online access to such analytics. To tackle these challenges, we have developed a novel cyberGIS framework that includes computationally reproducible approaches to streaming urban analytics. This framework is based on CyberGIS-Jupyter, through integration of cyberGIS and real-time urban sensing, for achieving capabilities that have previously been unavailable toward helping cities solve challenging urban informatics problems. The files included in this dataset functions as follows: 1) Spatial_interpolation.ipynb is a python based Jupyter notebook that enables users to conduct spatial interpolation with AoT data; 2) Urban_Informatics.ipynb is a Jupyter notebook that helps to explore the AoT dataset; 3) chicago-complete.weekly.2019-09-30-to-2019-10-06.tar includes all the high-frequency urban sensing data from AoT sensors from 2019 September 30th to 2019 October 6th collected in Chicago, US; 4) sensors.csv is a processed dataset including information about the temperature in Chicago, and it is used in Spatial_interpolation.ipynb.
CyberGIS; Urban informatics; Array of Things
Stern, Jessica; Herman, Brook D. ; Matthews, Jeffrey (2021): Data from determining vegetation metric robustness to environmental and methodological variables . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0938556_V1
We studied vegetation metric robustness to environmental (season, interannual, and regional) and methodological (observer) variables, as well as adequate sample size for vegetation metrics across four regions of the United States.
coefficients of conservatism; floristic quality assessment; restoration; vegetation metric;
Zaharias, Paul; Grosshauser, Martin; Warnow, Tandy (2021): Data from "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8921156_V1
This repository includes datasets for the paper "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling" accepted for RECOMB2021 and submitted to Journal of Computational Biology. Each zipped file contains a README.
deep neural networks; heterotachy; GHOST; quartet estimation; phylogeny estimation
Clark, Lindsay V.; Mays, Wittney; Lipka, Alexander E.; Sacks, Erik J. (2021): Dataset for evaluating the Hind/He statistic in polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4814898_V1
All of the files in this dataset pertain to the evaluation of a novel statistic, Hind/He, for distinguishing Mendelian loci from paralogs. They are derived from a RAD-seq genotyping dataset of diploid and tetraploid Miscanthus sacchariflorus.
planned publication date: 2021-11-16
Prada, Cecilia M.; Turner, Benjamin L.; Dalling, James W. (2021): Seedling traits in oak and mix stands. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7636863_V1
Data from an a field experiment at El Velo, Chiriqui, Republic of Panama. Data contain information about functional traits of seedlings growing in different treatments including type of forest, nitrogen addition and organic matter.
Mycorrhiza; nitrogen; oak forest; Panama; plant-soil feedbacks, seedling growth
planned publication date: 2022-08-20
Jones, Todd; Ward, Michael (2022): Jones and Ward BEAS-D-21-00106R2. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4619552_V1
Dataset associated with Jones and Ward BEAS-D-21-00106R2 submission: Parasitic cowbird development up to fledging and subsequent post-fledging survival reflect life history variation found across host species. Excel CSV files and .inp file with data used in nest survival and Brown-headed Cowbird post-fledging analyses and file with descriptions of each column. The CSV file is setup for logistic exposure models in SAS or R and the .inp file is setup to be uploaded into program MARK for multi-state recaptures only analysis. Species included in the analyses: American Robin, Blue Grosbeak, Brown Thrasher, Blue-winged Warbler, Carolina Chickadee, Chipping Sparrow, Common Yellowthroat, Dickcissel, Eastern Bluebird, Eastern Phoebe, Eastern Towhee, Field Sparrow, Gray Catbird, House Wren, Indigo Bunting, Northern Cardinal, Red-winged Blackbird, Tree Swallow, Yellow-breasted Chat, and Yellow Warbler.
brood parasitism; cowbird; carryover effects; phenotypic plasticity; post-fledging; songbirds
Vargas, Fabio (2021): Mesospheric gravity wave activity estimated via airglow imagery, multistatic meteor radar, and SABER data taken during the SIMONe–2018 campaign. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8585682_V1
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".
airglow; meteor radar; gravity waves; momentum flux;
has sharing link
Suski, Cory; Curtis-Quick, Jocelyn (2021): Why the Stall? Using Metabolomics to Define the Lack of Upstream Movement of Invasive Bigheaded Carp in the Illinois River. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5190701_V1
Bigheaded Carp have spread throughout the Mississippi River basin since the 1970s. Little has stopped the spread as carp have the ability to pass through locks and dams, and they are currently approaching the Great Lakes. However, the location of the leading edge in the Illinois River has stalled for over a decade, even though there is no barrier preventing further advancement towards the Great Lakes. Defining why carp are not moving towards the Great Lakes is important for predicting why they might advance in the future. The aim of this study was to test the hypothesis that anthropogenic contaminants in the Illinois River may be playing a role in preventing further upstream movement of Bigheaded Carp. Ninety-three livers were collected from carp at several locations between May and October of 2018. Liver samples were analyzed using gas chromatography-mass spectrometry in a targeted metabolite profiling approach. Livers from carp at the leading edge had differences in energy use and metabolism, and suppression of protective mechanisms relative to downstream fish; differences were consistent across time. This body of work provides evidence that water quality is linked to carp movement in the Illinois River. As water quality in this region continues to improve, consideration of this impact on carp spread is essential to protect the Great Lakes. The data shared here contains the raw data from the fish collection.
water quality; metabolites; range expansion; energy; contaminants
Southey, Bruce; Rodriguez-Zas, Sandra (2021): Metabolics of weaning and maternal immune activation in 22 day old pigs. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9043394_V1
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.
gas chromatography; mass spectrometry; maternal immune activation; weaning; liver
Edmonds, Devin (2021): Data for Poison Frogs in U.S. Collections. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4717502_V1
The dataset shows all poison frogs (superfamily Dendrobatoidea) in private U.S. collections during 1990–2020. For each species and color morph, there is a date of arrival, the way it arrived in U.S. collections, and detailed notes related to its presence in the pet trade. A second sheet details 10 wildlife trade pathways identified for poison frogs. The data can be used to examine the amphibian pet trade.
pet trade; amphibians; Dendrobatidae
von Haden, Adam C.; DeLucia, Evan H.; Yang, Wendy; Burnham, Mark (2021): Maize and Sorghum Establishment and Yield following Pre-Emergence Waterlogging. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8293871_V1
In 2020, early-season extreme precipitation events occurred following the planting of Sorghum bicolor (L.) Moench and Zea mays L. in central Illinois that caused ponding. Following the first rainfall event 50m transects were established to assess the waterlogging effects on seedling emergence and crop yields. Soil moisture, emergence, stem and tiller count, LAI, and yield were measured at various points in the season along these transects.
Sorghum; Maize; Emergence; Yield; LAI
Long, Stephen Patrick; Acevedo-Siaca, Liana Gabriella (2021): Data for publication "Evaluating natural variation, heritability, and genetic advance of photosynthetic traits in rice (Oryza sativa)". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3427028_V1
1. Rice H2 - Destructive Harvest - These data are for the destructive harvest (above-ground biomass) of 30 diverse indica rice genotypes that were grown to evaluate natural variation as well as the heritability of photosynthesis-related traits. Traits measured include: plant height, leaf area, plant fresh and dry weights, and tiller number. 2. Rice H2 - ACi Response Summary - These data characterize the response of CO2 uptake to change in intercellular CO2 concentration in 30 diverse indica rice genotypes. These measurements were taken to evaluate natural variation and the heritability of photosynthesis-related traits in rice. 3. Rice H2 - Survey Style Gas Exchange Measurements - These data document steady-state survey style gas exchange measurements in 30 diverse indica rice genotypes. These measurements were taken to evaluate natural variation and the heritability of photosynthesis-related traits in rice.
photosynthesis, photosynthetic capacity, natural variation, heritability, food security, rice
Felix, Hanau; Hannes, Rost; Ochoa, Idoia (2021): mspack-data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1396774_V2
This data set contains mass spectrometry data used for the publication "mspack: efficient lossless and lossy mass spectrometry data compression".
mass-spectrometry data; compression; proteomics
Ferguson, John; Fernandes, Samuel; Monier, Brandon; Miller, Nathan; Allen, Dylan; Dmitrieva, Anna; Schmuker, Peter; Lozano, Roberto; Valluru, Ravi; Buckler, Edward; Gore, Michael; Brown, Patrick; Spalding, Edgar; Leakey, Andrew (2021): Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5565022_V2
This dataset contains the images of a photoperiod sensitive sorghum accession population used for a GWAS/TWAS study of leaf traits related to water use efficiency in 2016 and 2017. *<b>Note:</b> new in this second version is that JPG images outputted from the nms files were added <b>Accessions_2016.zip</b> and <b>Accessions_2017.zip</b>: contain raw images produced by Optical Topometer (nms files) for all sorghum accessions. Images can be opened with Nanofocus μsurf analysis extended software (Oberhausen,Germany). <b>Accessions_2016_jpg.zip</b> and <b>Accessions_2017_jpg.zip</b>: contain jpg images outputted from the nms files and used in the machine learning phenotyping.
stomata; segmentation; water use efficiency
Lotspeich-Yadao, Michael (2021): State of Illinois - Common Spatial Geodatabase for the Social Sciences. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4857915_V1
This geodatabase serves two purposes: 1) to provide State of Illinois agencies with a fast resource for the preparation of maps and figures that require the use of shape or line files from federal agencies, the State of Illinois, or the City of Chicago, and 2) as a start for social scientists interested in exploring how geographic information systems (whether this is data visualization or geographically weighted regression) can bring new meaning to the interpretation of their data. All layer files included are relevant to the State of Illinois. Sources for this geodatabase include the U.S. Census Bureau, U.S. Geological Survey, City of Chicago, Chicago Public Schools, Chicago Transit Authority, Regional Transportation Authority, and Bureau of Transportation Statistics.
State of Illinois; City of Chicago; Chicago Public Schools; GIS; Statistical tabulation areas; hydrography
Sabrina, Sadia; Lewis, Quinn; Rhoads, Bruce (2021): Data on Confluence Hydrodynamics from Large-scale Particle Velocimetry. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1079505_V1
This dataset contains data derived from large-scale particle velocimetry measurements obtained at the confluence of the Saline Branch and an unnamed tributary in Illinois. The data were collected using two cameras positioned about the confluence, one mounted on a cable and the other mounted on a tripod. A description of the content of the files can be found in Description of Files.rtf.
confluence; hydrodynamics; LSPIV; flow structure; stagnation
Proescholdt, Randi (2021): RISRS Retraction Review - Field Variation Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2070560_V1
This data comes from a scoping review associated with the project called Reducing the Inadvertent Spread of Retracted Science. The data summarizes the fields that have been explored by existing research on retraction, a list of studies comparing retraction in different fields, and a list of studies focused on retraction of COVID-19 articles.
retraction; fields; disciplines; research integrity
Xie, Jiayang; Fernandes, Samuel; Mayfield-Jones, Dustin; Erice, Gorka; Choi, Min; Lipka, Alexander; Leakey, Andrew (2021): Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8275554_V1
This dataset containes the images of B73xMS71 RIL population used in QTL linkage mapping for maize epidermal traits in year 2016 and 2017. 2016RIL_all_mns.rar and 2017RIL_all_mns.rar: contain raw images produced by Nanofocus lsurf Explorer Optical Topometer (Oberhausen, Germany) at 20X magnification with 0.6 numerical aperture. Files were processed in Nanofocus μsurf analysis extended software (Oberhausen,Germany). 2016RIL_all_TIF.rar and 2017RIL_all_TIF.rar: contain images processed from the Topology layer in each nms file to strengthen the edges of cell outlines, and used in downstream cell detection. 2016RIL_all_detection_result.rar and 2017RIL_all_detection_result.rar: contain images with epidermal cells predicted using the Mask R-CNN model. training data.rar: contain images used for Mask R-CNN model training and validation.
stomata; Mask R-CNN; cell segmentation; water use efficiency
Shen, Chengze; Zaharias, Paul; Warnow, Tandy (2021): MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2419626_V1
This dataset contains 1) the cleaned version of 11 CRW datasets, 2) RNASim10k dataset in high fragmentation and 3) three CRW datasets (16S.3, 16S.T, 16S.B.ALL) in high fragmentation.
MAGUS;UPP;Multiple Sequence Alignment;PASTA;eHMMs
Egan, Maximillian; Larsen, Ryan; Sadaghiani, Sepideh (2021): Dataset for "Safety and data quality of EEG recorded simultaneously with multi-band fMRI". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1484994_V1
This dataset contains EEG and Temperature data acquired from inside the bore of an MRI scanner during scanning with two different types of fMRI sequences: single-band and and multi-band. The EEG data were acquired from the heads of adult humans undergoing scanning, and can be used to assess differences in EEG data quality due to sequence type. The temperature data were acquired from a watermelon phantom and can be used to assess heating differences due to sequence type.
Simultaneous EEG-fMRI, Multi-band fMRI, Safety, Heating
Zuckermann, Federico (2021): Bacillus-based direct-fed microbial reduces the pathogenic synergy of a co-infection with Salmonella enterica serovar Choleraesuis and porcine reproductive and respiratory syndrome virus. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0439780_V1
Raw data and its analysis collected from a trial designed to test the impact of providing a Bacillus-based direct-fed microbial (DFM) on the syndrome resulting from orally infecting pigs with either Salmonella enterica serotype Choleraesuis (S. Choleraesuis) alone, or in combination with an intranasal challenge, three days later, with porcine reproductive and respiratory syndrome virus (PRRSV).
Miller, Jim; Czesny, Sergiusz; Dai, Qihong; Ellis, James; Iverson, Louis; Matthews, Jeff; Roswell, Charlie; Suski, Cory; Taft, John; Ward, Mike (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 6: Climate Change Impacts on Ecosystems, Supplement 6.1: Scientific and Common Species Names. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9049988_V1
Please cite as: Jim Miller, Sergiusz Czesny, Qihong Dai, James Ellis, Louis Iverson, Jeff Matthews, Charles Roswell, Cory Suski, John Taft, and Mike Ward. 2021. “Climate Change Impacts on Ecosystems: Scientific and Common Species Names”.
Scientific names; Common names; Illinois species
Smirnov, Vladimir (2021): Datasets used in "Recursive MAGUS: scalable and accurate multiple sequence alignment". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1048258_V1
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
Gramig, Benjamin; Khanna, Madhu; Jain, Atul (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 4: Climate Change Impacts on Agriculture, Supplemental Materials. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8285949_V1
This document contains the Supplemental Materials for Chapter 4: Climate Change Impacts on Agriculture from the report "An Assessment of the Impacts of Climate Change in Illinois" published in 2021.
Illinois; climate change; agriculture; impacts; adaptation; crop yield; ISAM; econometrics; days suitable for fieldwork
Urco Cordero, Juan M.; Kamalabadi, Farzad; Kamaci, Ulas; Harding, Brian J.; Frey, Harald U.; Mende, Stephen B.; Huba, Joe D.; England, Scott L.; Immel, Thomas J. (2021): Data for Conjugate photoelectron energy spectra derived from coincident FUV and radio measurements. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2215727_V1
Conjugate photoelectron energy spectra derived from coincident FUV and radio measurements. These are outputs of simulations from the semi-empirical SAMI2-PE (Varney et al. 2012) for the night of January 4, 2020.
Conjugate photoelectrons, SAMI2-PE, ICON