Dataset Search Results

This dataset includes mass spectrometry, library screening, and gas chromatography data used for creating a high-throughput screening in metabolic engineering.

The dataset consists of two types of data: the estimate of land productivity (the maximum productivity, MP) and the estimate of land that has low productivity for any major crops planted in the Contiguous United States and then may be available for growing bioenergy crops (the marginal land, ML). All data items are in GeoTiff format, under the World Geodetic System (WGS) 84 project, and with a resolution of 0.0020810045 degree (~250 m). The MP values are calculated based on machine learning model estimated yields of major crops in the CONUS, and its expected value (MP_mean.tif), and associated uncertainty (MP_IDP.tif). The ML availability data have two versions: a deterministic version and a version with uncertainty. The deterministic MLs are determined as the land pixels with expected MP values falling in the range defined in the following criteria, and the MLs with uncertainty are determined as the probability that the MP value of a land pixel falls in the range defined in the following criteria: Criteria_____Description S1________ Current crop and pasture land with MP <= P50 S2________ Current crop and pasture land with MP <= P25 S3________ S1 + current grass and shrub land with P25 < MP < P50 S4________ S2 + current grass and shrub land with P10 < MP < P25 Economic__ Current crop and pasture land with potential profitability < 0 Here P10, P25 and P50 are the 10th, 25th and 50th percentile of crop MP values

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.

This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.

These data represent the raw data from the paper “Evaluating the ability of wetland mitigation banks to replace plant species lost from destroyed wetlands” published in Journal of Applied Ecology in 2023 by Stephen C. Tillman and Jeffrey W. Matthews.

Matlab codes for the article "Phage-antibiotic synergy inhibited by temperate and chronic virus competition". Code can be used to reproduce the article figures, perform the parameter sensitivity analysis and simulate the model.

Supplemental data sets for the Manuscript entitled " Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats"

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.

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

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.

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.