Dataset Search Results

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.

#### Details of Pseudomonas aeruginosa biofilm dataset #### ----------------*Folder Structure*------------------------------------- This dataset contains peak intensity tables extracted from mass spectrometry imaging (MSI) data using tools, SCiLS and MSI reader. There are 2 folders in "MSI-Data-Paeruginosa-biofilms-UIUC-DP-JVS-July2022.zip", each folder contains 3 sub-folders as listed below. 1. PellicleBiofilms-and-Supernatant [Pellicle biofilms collected from air-liquid interface and spend supernatant medium after 96 h incubation period]: (1) Full-Scan-Data-96h; (2) MSMS-data-from-C7-Quinolones-96h; and (3) MSMS-data-from-C9-Quinolones-96h 2. StaticBiofilms [Static biofilms grown on mucin surface]: (1) Full-Scan-Data; (2) MSMS-data-from-C7-Quinolones; and (3) MSMS-data-from-C9-Quinolones ----------------*File name*---------------------------------------------- Sample information is included in the file names for easy identification and processing. Attributes covered in file names are explained in the example below. *Example file name "Rep1-Stat-FRD1-mPat-48-FS"* ~ Each unit of information is separated by "-" ~Unit 1 - "Rep1" - Biological replicate ( Rep1, Rep2, and Rep3) ~Unit 2 - "Stat" - Sample type (Stat = Static Biofilm, Pel = Pellicle biofilm, Sup = Supernatant) ~Unit 3 - "FRD1" - Strain (FRD1 = Mucoid strain, PAO1C = Non-mucoid strain) ~Unit 4 - "mPat" - Type of mucin surface used (mPat = patterned mucin surface, mUni = uniform mucin surface) ~Unit 5 - "48" - Sample time point (hours = 48, 72, 96) ~Unit 6 - "FS" - Scan type used in MSI (FS = high resolution full-scan, 260 = targeted MS/MS of C7 quinolones (m/z 260), 288 = targeted MS/MS of C9 quinolones (m/z 288)) ----------------*File structure*------------------------------------------ All MSI data has been exported to CSV format. Each CSV files contains information about scan number, Coordinates (x,y,z), m/z values, extraction window (absolute), and corresponding intensities in the form of a matrix. ----------------*End of Information*--------------------------------------

This dataset contains re-estimated gene trees from the ASTRAL-II [1] simulated datasets. The re-estimated variants of the datasets are called MC6H and MC11H -- they are derived from the MC6 and MC11 conditions from the original data (the MC6 and MC11 names are given by ASTRID [2]). The uploaded files contain the sequence alignments (half-length their original alignments), and the re-estimated species trees using FastTree2. Note: - "mc6h.tar.gz" and "mc11h.tar.gz" contain the sequence alignments and the re-estimated gene trees for the two conditions - the sequence alignments are in the format "all-genes.phylip.splitted.[i].half" where i means that this alignment is for the i-th alignment of the original dataset, but truncating the alignment halving its length - "g1000.trees" under each replicate contains the newline-separated re-estimated gene trees. The gene trees were estimated from the above described alignments using FastTree2 (version 2.1.11) command "FastTree -nt -gtr" [1]: Mirarab, S., & Warnow, T. (2015). ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52. [2]: Vachaspati, P., & Warnow, T. (2015). ASTRID: accurate species trees from internode distances. BMC genomics, 16(10), 1-13.

These data were used in the survival and cause-specific mortality analyses of translocated nuisance American black bear in Wisconsin published in Animal Conservation (Bauder, J.M., N.M. Roberts, D. Ruid, B. Kohn, and M.L. Allen. Accepted. Lower survival of nuisance American black bears (Ursus americanus) is not due to translocation. Animal Conservation). Included are CSV files including each bear's capture history and associated covariates and meta-data for each CSV file. Also included is an example R script of how to conduct the analyses (this R script is also included as supporting information with the published paper).

These are abundance dynamics data and simulations for the paper "Higher-order interaction between species inhibits bacterial invasion of a phototroph-predator microbial community". In this V2, data were converted in Python, in addition to MATLAB and more information on how to work with the data was included in the Readme.

The compiled datasets include plot level observations of energy crops (miscanthus and switchgrass) from recent experimental field trials in the US including dry biomass yield, location, state, region, harvest year, growing season degree days (GDD), winter season heating degree days (HDD), growing season cumulative precipitation, annual nitrogen application rate, age of the pant when harvested, National Commodity Crop Productivity Index (NCCPI) values, and cultivar type (switchgrass) from various published and unpublished sources. The stata codes include estimation procedures for four different specifications, i.e., Model A includes deterministic effect without interaction terms; Model B includes deterministic effect with interaction terms (N2, age2, N × age, GDD2, precip2, N × NCCPI); Model C includes deterministic effect with interaction terms, study, and location random effect; Model D includes deterministic effect with interaction terms, harvest year augmented study, and location random effect.

This dataset includes structural MRI head scans of 32 piglets, at 28 days of age, scanned at the University of Illinois. The dataset also includes manually drawn brain masks of each of the piglets. The dataset also includes brain masks that were generated automatically using Region-Based Convolutional Neural Networks (Mask R-CNN), trained on the manually drawn brain masks.

This data set describes temperature, dissolved oxygen, and secchi depth in 1-m interval profiles in the deepest point in 10 Illinois reservoirs between the years 1995 and 2016.

These data and code are associated with a study on differences in the rate of hatching failure of eggs across 14 free-living grassland and shrubland birds. We used a device to measure the embryonic heart rate of eggs and found there was variation across species related to factors such as nest type and nest safety. This work is to be published in Ornithology.

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.

- 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).

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.

- The objective of this study was to evaluate macronutrient apparent total tract digestibility (ATTD), gastrointestinal tolerance, and fermentative end-products in extruded, canine diets. <br />- Five diets were formulated to be isocaloric and isonitrogenous with either garbanzo beans (GBD), green lentils (GLD), peanut flour (PFD), dried yeast (DYD), or poultry by-product meal (CON) as the primary protein sources. Ten adult, intact, female beagles (mean age: 4.2 ± 1.1 yr, mean 28 weight: 11.9 ± 1.3 kg) were used in a replicated, 5x5 Latin square design with 14 d periods. Total DNA from fresh fecal samples was extracted using Mo-Bio PowerSoil kits (MO BIO Laboratories, Inc., Carlsbad, CA). Amplification of the 292 bp-fragment of V4 region from the 16S rRNA gene was completed using a Fluidigm Access Array (Fluidigm Corporation, South San Francisco, CA). Paired-end Illumina sequencing was performed on a MiSeq using v3 reagents (Illumina Inc., San Diego, CA) at the Roy J. Carver Biotechnology Center at the University of Illinois. <br />- Filenames are composed of animal name identifier, diet (CON=control; DY= dried yeast; GB= garbanzo beans; GL= green lentils; PF= peanut flour) and period replicate number (P1, P2, P3, P4, and P5).

Twenty-two genotypes of C4 species grown under ambient and elevated O3 concentration were studied at the SoyFACE (40°02’N, 88°14’W) in 2019. This dataset contains leaf morphology, photosynthesis and nutrient contents measured at three time points. The results of CO2 response curves are also included.

This dataset includes supporting data for our article 'Assessing long-term impacts of cover crops on soil organic carbon in the central U.S. Midwestern agroecosystems'. The dataset contains carbon fluxes and SOC benefits from cover crops at six cover crop experiment sites in Illinois with three rotation systems: (1) without-cover-crop (maize-soybean rotations), (2) non-legume-preceding-maize (maize-annual ryegrass-soybean-annual ryegrass rotations), and (3) legume-preceding-maize (maize-cereal rye-soybean-hairy vetch rotations). <b>*NOTE:</b> there should be 13 files + 1 readme file, instead of 15 files as mentioned in readme.

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

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

All code in Matlab .m scripts or functions (version R2019b) Affiliated with article “Temperate and chronic virus competition leads to low lysogen frequency” published in the Journal of Theoretical Biology (2021) Codes simulate and plot the solutions of an Ordinary Differential Equations model and generate bifurcation diagrams.

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.

The file “Fla.fasta”, comprising 10526 positions, is the concatenated amino acid alignments of 51 orthologues of 182 bacterial strains. It was used for the maximum likelihood and maximum parsimony analyses of Flavobacteriales. Bacterial species names and strains were used as the sequence names, host names of insect endosymbionts were shown in brackets. The file “16S.fasta” is the alignment of 233 bacterial 16S rRNA sequences. It contains 1455 positions and was used for the maximum likelihood analysis of flavobacterial insect endosymbionts. The names of endosymbiont strains were replaced by the name of their hosts. In addition to the species names, National Center for Biotechnology Information (NCBI) accession numbers were also indicated in the sequence names (e.g., sequence “Cicadellidae_Deltocephalinae_Macrostelini_Macrosteles_striifrons_AB795320” is the 16S rRNA of Macrosteles striifrons (Cicadellidae: Deltocephalinae: Macrostelini) with a NCBI accession number AB795320). The file “Sulcia_pep.fasta” is the concatenated amino acid alignments of 131 orthologues of “Candidatus Sulcia muelleri” (Sulcia). It contains 41970 positions and presents 101 Sulcia strains and 3 Blattabacterium strains. This file was used for the maximum likelihood analysis of Sulcia. The file “Sulcia_nucleotide.fasta” is the concatenated nucleotide alignment corresponding to the sequences in “Sulcia_pep.fasta” but also comprises the alignment of 16S rRNA. It has 127339 positions and was used for the maximum likelihood and maximum parsimony analyses of Sulcia. Individual gene alignments (16S rRNA and 131 orthologues of Sulcia and Blattabacterium) are deposited in the compressed file “individual_gene_alignments.zip”, which were used to construct gene trees for multispecies coalescent analysis. The names of Sulcia strains were replaced by the name of their hosts in “Sulcia_pep.fasta”, “Sulcia_nucleotide.fasta” and the files in “individual_gene_alignments.zip”. In all the alignment files, gaps are indicated by “-”.

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.

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.

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.

This dataset contain information for the paper "Changes in neuropeptide prohormone genes among Cetartio-dactyla livestock and wild species associated with evolution and domestication" Veterinary Sciences, MDPI. Protein sequences were predicted using GeneWise for 98 neuropeptide prohormone genes from publicly available genomes of 118 Cetartiodactyla species. All predictions (CetartiodactylaSequences2022.zip) were manually verified. Sequences were aligned within each prohormone using MAFFT (MDPImultalign2022.zip includes multiple sequence alignment of all species available for each prohormone). Phylogenetic gene trees were constructed using PhyML and the species tree was constructed using ASTRAL (MDPItree2022.zip). The data is released under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0).

This dataset includes a total of 501 images of 42 fossil specimens of Striatopollis and 459 specimens of 45 extant species of the tribe Amherstieae-Fabaceae. These images were taken using Airyscan confocal superresolution microscopy at 630X magnification (63x/NA 1.4 oil DIC). The images are in the CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or in ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/microscope-software/zen/czi.html#microscope---image-data].