Dataset Search Results

This dataset contains MRI data and Imaris modeling analysis of CLARITY-cleared, immunostained tissue associated with a study that assessed the effects of lipid blends containing various levels of a hydrolyzed fat system on myelin development in healthy neonatal piglets. Data are from thirty-two piglets of mixed sexes across four diet treatment groups and includes a sow-fed reference group. MRI data (presented in Figure 2 of the associated article) consists of volumetric data from Voxel-Based Morphometry analysis in brain grey matter and white matter, as well as mean fractional anisotropy and mean orientation dispersion index data from Tract-Based Spatial Statistics analysis. Imaris data (presented in Figure 3 of the associated article) consists of twenty-one select output measures from 3D modeling analysis of PLP-stained prefrontal cortex tissue. All methods used for collection/generation/processing of data are described in the associated article: Louie AY, Rund LA, Komiyama-Kasai KA, Weisenberger KE, Stanke KL, Larsen RJ, Leyshon BJ, Kuchan MJ, Das T, Steelman AJ. A hydrolyzed lipid blend diet promotes myelination in neonatal piglets in a region and concentration-dependent manner. J Neurosci Res. 2023.

An online and paper knowledge, attitudes, and practices survey on ticks and tick-borne diseases (TBD) was distributed to farmers in Illinois during summer 2020 to spring 2022 (paper version titled Final Draft Farmer KAP_v.SoftCopy_Revised.docx). These are the raw data associated with that survey and the survey questions used (FarmerTickKAPdata.csv, data dictionary in Data Description.docx). We have added calculated values (columns 286 to end, code for calculation in FarmerKAPvariableCalculation.R), including: the tick knowledge score, TBD knowledge score, and total knowledge score, which are the sum of the total number of correct answers in each category, and score percent, which are the proportion of correct answers in each category.

An online knowledge, attitudes, and practices survey on ticks and tick-borne diseases was distributed to veterinary professionals in Southern and Central Illinois during summer and fall 2020. These are the raw data associated with that survey and the survey questions used. * NOTE: "age" and "gender" variables were removed from the data to protect participants.

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.

This repository includes scripts and datasets for the paper, "Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy" submitted to Bioinformatics.

Steady-state and dynamic gas exchange data for maize (B73), sugarcane (CP88-1762) and sorghum (Tx430)

Supplementary data tables for the dissertation "Hybridization dynamics and population genomics of a Manacus hybrid zone." This work focuses on the dynamics of hybridization over time in two species of tropical birds, the golden-collared manakin (Manacus vitellinus) and white-collared manakin (Manacus candei) comparing data from historical museum samples and contemporary wild-caught birds. Table A1 contains the sample metadata for the Manacus Restriction site-associated DNA sequencing dataset used in the dissertation with associated NCBI Biosample Accession numbers, Smithsonian Museum of Natural History number (where applicable), sample IDs, sampling site locations, and sample information of year the sample was taken, age, and sex. Table A6 contains phenotypic measurements of male plumage traits of manakins used in cline analyses to assess hybrid zone movement over time in historical and contemporary datasets, including beard length (mm), epaulet width (mm), tail length (mm), collar color (nm), and belly color (nm). Table A7 contains a summary of male plumage measurements across the hybrid zone. Table C1 contains a list of annotated protein coding genes in candidate regions of interest in Manacus genomes using outlier regions of genomic divergence, linkage disequilibrium, and enrichment of parental private alleles.

Video footage of an Eastern Box Turtle (Terrapene carolina carolina) partially predating a Field Sparrow nest (Spizella pusilla) at 0845 h on the 31 of May 2020. Please note that the date on the video footage is incorrect due to user error, but the time is correct.

High-speed X-ray videos of four E. abruptus specimens recorded at the Advanced Photron Source (Argonne National lab) in the Summer of 2018 and corresponding position data of landmarks tracked during the motion. See readme file for more details.

This dataset contains the amino acid and nucleotide alignments corresponding to the phylogenetic analyses of South et al. 2020 in Systematic Entomology. This dataset also includes the gene trees that were used as input for coalescent analysis in ASTRAL.

Video recorded by Louise Barker using a Cannon Powershot camera documents late-season combat behavior in Agkistrodon contortrix. Recorded in Beaufort County, North Carolina, 11.1 km SE of downtown Washington on 21 October 2020.

The dataset consists of results and various input data that are used in the GAMS model for the publication "Repeal of the Clean Power Plan: Social Cost and Distributional Implications". All the data are either excel files or in the .inc format which can be read within GAMS or Notepad. Main data sources include: agriculture, transportation and electricity data. Model details can be found in the paper and the GAMS model package.

Data sets from "Comparing Methods for Species Tree Estimation With Gene Duplication and Loss." It contains data simulated with gene duplication and loss under a variety of different conditions.

This is a general description of the datasets included in this upload; details of each dataset can be found in the individual README.txt in each compressed folder. We have: 1. ROSE-HF.tar.gz 2. ROSE-LF.tar.gz HF (high fragmentary): 50% of the sequences are made fragmentary, which have average lengths of 25% of the original lengths with a standard deviation of 60 bp. LF (low fragmentary): 25% of the sequences are made fragmentary, which have average lengths of 50% of the original lengths with a standard deviation of 60 bp. The seven ROSE datasets made fragmentary are: 1000L1, 1000L3, 1000L4, 1000M3, 1000S1, 1000S2 and 1000S4. "ROSE-HF.tar.gz" contains HF versions of the seven ROSE datasets. "ROSE-LF.tar.gz" contains LF versions of the seven ROSE datasets.

Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.

The Empoascini_morph_data.nex text file contains the original data used in the phylogenetic analyses of Xu et al. (Systematic Entomology, in review). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first nine lines of the file indicate the file type (Nexus), that 110 taxa were analyzed, that a total of 99 characters were analyzed, the format of the data, and specification for symbols used in the dataset to indicate different character states. For species that have more than one state for a particular character, the states are enclosed in square brackets. Question marks represent missing data.The pdf file, Appendix1.pdf, is available here and describes the morphological characters and character states that were scored in the dataset. The data analyses are described in the cited original paper.

This dataset includes neuronal development of the Caenorhabditis elegans dauer and adult.

In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves and high light transmission through the canopy are henceforth referred to as ‘erectophile’ and those with low leaf erectness, ‘planophile’. In the final year of the study, bundle sheath leakiness in erectophile and planophile accessions was also compared.

This repository includes scripts and datasets for the paper, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss."

This repository includes a simulated dataset and related scripts used for the paper "Moss: Accurate Single-Nucleotide Variant Calling from Multiple Bulk DNA Tumor Samples".

Supplemental data sets for the Manuscript entitled "Contribution of fungal and invertebrate communities to mass loss and wood depolymerization in tropical terrestrial and aquatic habitats"

Data inputs, and scripts for the analysis detailed in Bradshaw et al, published in PlosONE 2020.

This dataset includes images and annotated counts for 150 airborne pollen samples from the Center for Tropical Forest Science 50 ha forest dynamics plot on Barro Colorado Island, Panama. Samples were collected once a year from April 1994 to June 2010.

This dynamic photosynthesis model of soybean canopy is developed by Yu Wang (yuwangcn@illinois.edu), IGB, University of Illinois. If you want to know more details, please check the following publication Yu Wang, Steven J. Burgess, Elsa de Becker, Stephen P. Long. Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity? The Plant Journal.

Data files associated with the assembly of mitochondrial minicircles from five species of parasitic lice. This includes data from four species in the genus Columbicola and from the human louse (Pediculus humanus). The files include FASTA sequences for all five species, reference sequences for read mapping approaches, resulting contigs produced by various assembly approaches, and alignments of human louse minicircles mapped to published sequences of the same species.