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published: 2021-08-24
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.
keywords:
deep neural networks; heterotachy; GHOST; quartet estimation; phylogeny estimation
published: 2021-08-20
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.
keywords:
Sorghum; Maize; Emergence; Yield; LAI
published: 2021-08-14
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.
keywords:
photosynthesis, photosynthetic capacity, natural variation, heritability, food security, rice
published: 2021-08-12
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.
keywords:
stomata; segmentation; water use efficiency
published: 2021-07-10
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.
keywords:
stomata; Mask R-CNN; cell segmentation; water use efficiency
published: 2021-06-24
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.
keywords:
Simultaneous EEG-fMRI, Multi-band fMRI, Safety, Heating
published: 2021-07-21
Rozansky, Zachary; Larson, Eric; Taylor, Christopher (2021): Data for “Invasive virile crayfish (Faxonius virilis Hagen, 1870) hybridizes with native spothanded crayfish (Faxonius punctimanus Creaser, 1933) in the Current River watershed of Missouri, U.S.”. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7683513_V1
This dataset contains 1 CSV file: RozanskyLarsonTaylorMsat.csv which contains microsatellite fragment lengths for Virile and Spothanded Crayfish from the Current River watershed of Missouri, U.S., and complimentary data, including assignments to species by phenotype and COI sequence data, GenBank accession numbers for COI sequence data, study sites with dates of collection and geographic coordinates, and Illinois Natural History Survey (INHS) Crustacean Collection lots where specimens are stored.
keywords:
invasive species; hybridization; crayfishes; streams; freshwater; Cambaridae; virile crayfish; spothanded crayfish; Missouri; Current River; Ozark National Scenic Riverways
published: 2021-06-25
Szydlowski, Daniel; Daniels, Melissa; Larson, Eric (2021): Data for Do rusty crayfish (Faxonius rusticus) invasions affect water clarity in north temperate lakes?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4293962_V1
Data associated with the manuscript "Do rusty crayfish invasions affect water clarity in north temperate lakes?" by Daniel K. Szydlowski, Melissa K. Daniels, and Eric R. lARSON
keywords:
chlorophyll a; crayfish; Faxonius rusticus; invasive species; lakes; LandSat; remote sening; rusty crayfish; Secchi disc; water clarity
published: 2021-07-15
Castro, Daniel; Sweedler, Jonathan (2021): High-Throughput Single-Organelle Dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5949772_V1
The dataset contains the high-throughput matrix-assisted laser desorption/ionization mass spectrometry XmL files for the atrial gland and red hemiduct of Aplysia californica.
keywords:
Dense-core vesicle; High-throughput; Mass Spectrometry; MALDI; Organelle; Image-Guided; Atrial gland; red hemiduct; Lucent Vesicle
published: 2016-05-16
Imker, Heidi (2016): Phylogenetic Analysis of the NRPS AmbE Condensation Domains for the L-2-amino-4-methoxy-trans-3-butenoic acid (AMB) Biosynthetic Pathway in Pseudomonas aeruginosa. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4602893_V1
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: 2021-06-28
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.
keywords:
MAGUS;UPP;Multiple Sequence Alignment;PASTA;eHMMs
published: 2021-06-24
Kraft, Mary L.; Yeager, Ashley N.; Weber, Peter K. (2021): NanoSIMS depth profiling data of an MDCK cell. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3927212_V1
This dataset consists of the secondary ion mass spectrometry (SIMS) depth profiling data that was collected with a Cameca NanoSIMS 50 instrument from a 10 micron by 10 micron region on a Madin-Darby canine kidney (MDCK) cell that had been metabolically labeled so most of its sphingolipids and cholesterol contained the rare nitrogen-15 oxygen-18 isotopes, respectively.
keywords:
secondary ion mass spectrometry; NanoSIMS; depth profiling; MDCK cell; sphingolipids; cholesterol
published: 2021-06-16
Warnow , Tandy; Wedell, Eleanor (2021): Fragmentary Sequences for Variable-Sized RNAsim Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8788479_V1
Thank you for using these datasets. These RNAsim aligned fragmentary sequences were generated from the query sequences selected by Balaban et al. (2019) in their variable-size datasets (https://doi.org/10.5061/dryad.78nf7dq). They were created for use for phylogenetic placement with the multiple sequence alignments and backbone trees provided by Balaban et al. (2019). The file structures included here also correspond with the data Balaban et al. (2020) provided. This includes: Directories for five varying backbone tree sizes, shown as 5000, 10000, 50000, 100000, and 200000. These directory names are also used by Balaban et al. (2019), and indicate the size of the backbone tree included in their data. Subdirectories for each replicate from the backbone tree size labelled 0 through 4. For the smaller four backbone tree sizes there are five replicates, and for the largest there is one replicate. Each replicate contains 200 text files with one aligned query sequence fragment in fasta format.
keywords:
Fragmentary Sequences; RNAsim
published: 2021-06-14
Anderson, Nicholas L.; Harmon-Threatt, Alexandra N. (2021): Data for: Chronic contact with imidacloprid during development may decrease female solitary bee foraging ability and increase male competitive ability for mates. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2315056_V1
Chronic contact exposure to realistic soil concentrations (0, 7.5, 15, and 100 ppb) of the neonicotinoid pesticide imidacloprid had species- and sex-specific effects on adult bee movement characteristics, but not on adult female bee brain development. This dataset contains two data files. The first contains information about adult bee movement characteristics for female Osmia lignaria and female and male Megachile rotundata over a 10-minute trial (total distance traveled and average movement speed). The second contains information about female Osmia lignaria and Megachile rotundata adult brain morphology. Detected effects included: female Osmia lignaria adults moved faster as they aged in the 0 and 7.5 ppb, but not in the 15 or 100 ppb, groups; young male Megachile rotundata adults moved more quickly (7.5 and 100 ppb) and farther (100 ppb) when treated with imidacloprid compared to the control group (0 ppb); and, while there was no impact of imidacloprid on adult female neuropil:Kenyon cell volume (N:K), N:K decreased with Osmia ligaria adult age and increased with Megachile rotundata adult age.
keywords:
neonicotinoid; imidacloprid; bee; movement
published: 2021-06-08
Todd, Jones; Michael, Ward (2021): Jones and Ward JAE-2020-0031.R1. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6218430_V1
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: 2021-05-21
Willson, James; Roddur, Mrinmoy Saha; Baqiao, Liu; Zaharias, Paul; Warnow, Tandy (2021): Data from: "Inferring Species Trees from Gene-Family with Duplication and Loss using Multi-Copy Gene-Family Tree Decomposition". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4050038_V1
Data sets from "Inferring Species Trees from Gene-Family with Duplication and Loss using Multi-Copy Gene-Family Tree Decomposition." It contains trees and sequences simulated with gene duplication and loss under a variety of different conditions. <b>Note:</b> - trees.tar.gz contains the simulated gene-family trees used in our experiments (both true trees from SimPhy as well as trees estimated from alignements). - sequences.tar.gz contains simulated sequence data used for estimating the gene-family trees as well as the concatenation analysis. - biological.tar.gz contains the gene trees used as inputs for the experiments we ran on empirical data sets as well as species trees outputted by the methods we tested on those data sets. - stats.txt list statistics (such as AD, MGTE, and average size) for our simulated model conditions.
keywords:
gene duplication and loss; species-tree inference; simulated data;
published: 2021-05-26
Wang, Yu; Chan, Kher Xing; Long, Stephen P. (2021): Data for Toward a Dynamic Photosynthesis Model to Guide the Yield Improvement in C4 Crops. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2694900_V1
Steady-state and dynamic gas exchange data for maize (B73), sugarcane (CP88-1762) and sorghum (Tx430)
keywords:
C4 plants; gas exchange
published: 2021-05-14
Liu, Menglin; Gramig, Benjamin (2021): Survey of Cover Crop, Conservation Tillage and Nutrient Management Practice Usage in Illinois and 2020 Fall Covers for Spring Savings Crop Insurance Discount Program Participation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5222984_V1
Please cite as: Menglin Liu and Benjamin M. Gramig. "Survey of Cover Crop, Conservation Tillage and Nutrient Management Practice Usage in Illinois and 2020 Fall Covers for Spring Savings Crop Insurance Discount Program Participation." Report to the Illinois Department of Agriculture and Fall Covers for Spring Savings working group. Center for the Economics of Sustainability and Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign. 2021. https://doi.org/10.13012/B2IDB-5222984_V1
keywords:
cover crops; Illinois; 2020; conservation tillage; nutrient management practices; farmer survey; NLRS
published: 2021-05-14
Cattai de Godoy, Maria (2021): Miscanthus grass as a novel functional fiber source in extruded feline diets . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3595148_V1
- 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: 2021-05-14
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.
keywords:
Illinois; climate change; agriculture; impacts; adaptation; crop yield; ISAM; econometrics; days suitable for fieldwork
published: 2021-05-14
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”.
keywords:
Scientific names; Common names; Illinois species
published: 2021-05-14
Iverson, Louis (2021): An Assessment of the Impacts of Climate Change in Illinois, Chapter 6: Climate Change Impacts on Ecosystems, Supplemental Forest Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3459813_V1
Supplemental Forest Data for Chapter 6: Climate Change Impacts on Ecosystems in "An Assessment of the Impacts of Climate Change in Illinois"
published: 2020-10-28
Curtis, Amanda; Tiemann, Jeremy; Douglass, Sarah; Davis, Mark; Larson, Eric (2020): Data for: High stream flows dilute environmental DNA (eDNA) concentrations and reduce detectability. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1591542_V1
We studied we examined the role of stream flow on environmental DNA (eDNA) concentrations and detectability of an invasive clam (Corbicula fluminea), while also accounting for other abiotic and biotic variables. This data includes the eDNA concentrations, quadrat estimates of clam density, and abiotic variables.
keywords:
Corbicula; detection probability; eDNA; invasive species; lotic; occupancy modeling
published: 2021-05-13
Chen, Bowen; Gramig, Benjamin; Yun, Seong (2021): Data for Conservation Tillage Mitigates Drought Induced Soybean Yield Losses in the US Corn Belt. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9179636_V1
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
published: 2021-05-12
Clem, Scott; Harmon-Threatt, Alexandra (2021): Raw data and code for the paper "Field borders provide winter refuge for beneficial predators and parasitoids: a case study on organic farms". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8470827_V2
These are the data sets associated with our publication "Field borders provide winter refuge for beneficial predators and parasitoids: a case study on organic farms." For this project, we compared the communities of overwintering arthropod natural enemies in organic cultivated fields and wildflower-strip field borders at five different sites in central Illinois. Abstract: Semi-natural field borders are frequently used in midwestern U.S. sustainable agriculture. These habitats are meant to help diversify otherwise monocultural landscapes and provision them with ecosystem services, including biological control. Predatory and parasitic arthropods (i.e., potential natural enemies) often flourish in these habitats and may move into crops to help control pests. However, detailed information on the capacity of semi-natural field borders for providing overwintering refuge for these arthropods is poorly understood. In this study, we used soil emergence tents to characterize potential natural enemy communities (i.e., predacious beetles, wasps, spiders, and other arthropods) overwintering in cultivated organic crop fields and adjacent field borders. We found a greater abundance, species richness, and unique community composition of predatory and parasitic arthropods in field borders compared to arable crop fields, which were generally poorly suited as overwintering habitat. Furthermore, potential natural enemies tended to be positively associated with forb cover and negatively associated with grass cover, suggesting that grassy field borders with less forb cover are less well-suited as winter refugia. These results demonstrate that semi-natural habitats like field borders may act as a source for many natural enemies on a year-to-year basis and are important for conserving arthropod diversity in agricultural landscapes.
keywords:
Natural enemy; wildflower strips; conservation biological control; semi-natural habitat; field border; organic farming