Datasets

Dataset associated with Jones et al. ECY22-0118.R3 submission: Ontogenetic effects of brood parasitism by the Brown-headed Cowbird on host offspring. Excel CSV files with all of the data used in analyses and file with descriptions of each column.

This dataset contains the behavioral, metabolic, and capture data which is reported within the manuscript Data for Capture is predicted by behavior and size, not metabolism, in Muskellunge

Datasets that accompany Beilke, Haulton, and O'Keefe 2022 publication (Title: Foliage-roosting eastern red bats select for features associated with management in a central hardwood forest; Journal: Forest Ecology and Management).

This dataset consists of all the files that are part of the manuscript titled "Evidence for a robust sign-changing s-wave order parameter in monolayer films of superconducting Fe(Se,Te)/Bi2Te3". For detailed information on the individual files refer to the readme file.

This dataset is the raw data including SEM, TEM, PINEM images and FDTD simulation as well as pairwise interaction calculation results.

The Membracoidea_morph_data_Final.nex text file contains the original data used in the phylogenetic analyses of Dietrich et al. (Insect Systematics and Diversity, 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 complete taxon names corresponding to the 131 genus names listed under “BEGIN TAXA” are listed in Table 1 in the included PDF file “Taxa_and_characters”; the 229 morphological characters (names abbreviated under under “BEGIN CHARACTERS” are fully explained in the list of character descriptions following Table 1 in the same PDF). The data matrix follows “MATRIX” and gives the numerical values of characters for each taxon. Question marks represent missing data. The lists of characters and taxa and details on the methods used for phylogenetic analysis are included in the submitted manuscript.

The text file contains the original DNA nucleotide sequence data used in the phylogenetic analyses of Xue et al. (in review), comprising the 13 protein-coding genes and 2 ribosomal gene subunits of the mitochondrial genome. 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 six lines of the file identify the file as NEXUS, indicate that the file contains data for 30 taxa (species) and 13078 characters, indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes (version 3.2.6) beginning near the end of the file. The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the Methods section of the submitted manuscript. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the individual mitochondrial genes and for different codon positions of the protein-coding genes used for analyses in the programs MrBayes and IQ-Tree (version 1.6.8) (Table S2). Full citations for references listed in Table S1 can be found by searching GenBank using the corresponding accession number. The supplemental tables will also be linked to the article upon publication at the journal website.

Aerial imagery utilized as input in the manuscript "Deep convolutional neural networks exploit high spatial and temporal resolution aerial imagery to predict key traits in miscanthus" . Data was collected over M. Sacchariflorus and Sinensis breeding trials at the Energy Farm, UIUC in 2020. Flights were performed using a DJI M600 mounted with a Micasense Rededge multispectral sensor at 20 m altitude around solar noon. Imagery is available as tif file by field trial and date (10). The post-processing of raw images into orthophoto was performed in Agisoft Metashape software. Each crop surface model and multispectral orthophoto was stacked into an unique raster stack by date and uploaded here. Each raster stack includes 6 layers in the following order: Layer 1 = crop surface model, Layer 2 = Blue, Layer 3 = Green, Layer 4 = Red, Layer 5 = Rededge, and Layer 6 = NIR multispectral bands. Msa raster stacks were resampled to 1.67 cm spatial resolution and Msi raster stacks were resampled to 1.41 cm spatial resolution to ease their integration into further analysis. 'MMDDYYYY' is the date of data collection, 'MSA' is M. Sacchariflorus trial, 'MSI' is Miscanthus Sinensis trial, 'CSM' is crop surface model layer, and 'MULTSP' are the five multispectral bands.

One of the newest types of multimedia involves body-connected interfaces, usually termed haptics. Haptics may use stylus-based tactile interfaces, glove-based systems, handheld controllers, balance boards, or other custom-designed body-computer interfaces. How well do these interfaces help students learn Science, Technology, Engineering, and Mathematics (STEM)? We conducted an updated review of learning STEM with haptics, applying meta-analytic techniques to 21 published articles reporting on 53 effects for factual, inferential, procedural, and transfer STEM learning. This deposit includes the data extracted from those articles and comprises the raw data used in the meta-analytic analyses.

3DIFICE: 3-dimensional Damage Imposed on Frame structures for Investigating Computer vision-based Evaluation methods This dataset contains 1,396 synthetic images and label maps with various types of earthquake damage imposed on reinforced concrete frame structures. Damage includes: cracking, spalling, exposed transverse rebar, and exposed longitudinal rebar. Each image has an associated label map that can be used for training machine learning algorithms to recognize the various types of damage.

Dataset associated with Merrill et al. ECE-2021-05-00793.R1 submission: Early life patterns of growth are linked to levels of phenotypic trait covariance and post-fledging mortality across avian species. Excel CSV files with all of the data used in analyses and file with descriptions of each column.

Data in this publication were used to examine the effects of environmental and temporal covariates on detection probability, and the effects of habitat and landscape level covariates on occupancy and within season turnover of Black-billed Cuckoos and Yellow-billed Cuckoos. Data were collected between 2019-2020 in northern Illinois, USA. Procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 19086.

Simulated sequences provide a way to evaluate multiple sequence alignment (MSA) methods where the ground truth is exactly known. However, the realism of such simulated conditions often comes under question compared to empirical datasets. In particular, simulated data often does not display heterogeneity in the sequence lengths, a common feature in biological datasets. In order to imitate sequence length heterogeneity, we here present a set of data that are evolved under a mixture model of indel lengths, where indels have an occasional chance of being promoted to long indels (emulating large insertion/deletion events, e.g., domain-level gain/loss). This dataset is otherwise (e.g., in GTR parameters) analogous to the 1000M condition as presented in the SATe paper (doi: 10.1126/science.1171243) but with 5000 sequences and simulated with INDELible (http://abacus.gene.ucl.ac.uk/software/indelible/). For more information, see README.txt. For the INDELible control files, see https://github.com/ThisBioLife/5000M-234-het.

Data from an a field survey at Nikko National Park in central Japan. Data contain information about deer carcass, environment of sites, and vertebrate scavenging.

Data characterize zooplankton in Shelbyville Reservoir, Illinois, United States of America. Zooplankton were sampled with a conical zooplankton net (0.5m diameter mouth) when water was deeper than 2 m and by grab sample when water was shallower. Zooplankton samples were concentrated and subsampled with a Hensen-Stempel pipette following protocols described in Detmer et al. (2019). Zooplankton were identified to the lowest feasible taxonomic unit according to Pennak (1989) and Thorp and Covich (2001) and were enumerated in a 1 mL Sedgewick-Rafter cell. Subsamples were analyzed until at least 200 individuals were enumerated from each site.were counted across for each of the three main taxonomic groups (cladocerans, copepods, and rotifers). Given the variation in zooplankton concentrations at each site, this process often lead to far more than 200 individuals being counted (x̄ = 269, min = 200, max = 487). A summary of the sample size from each site can be found in Supplementary Table S2. Abundances were corrected for volume of water filtered. For rare taxa (< 20 individuals per sample), all individuals were measured for length. For abundant taxa, length measurements were collected on the first 20 organisms of each abundant taxon encountered in a subsample. Dry mass was calculated from equations for microcrustaceans, rotifers, and Chaoborus sp. (Rosen ,1981; Botrell et al., 1976; Dumont and Balvay, 1979).

This dataset contains model code (including input data) to replicate the outcomes for "Assessing the Efficiency Implications of Renewable Fuel Policy Design in the United States". The model consists of: (1) The replication codes and data for the model. To run the model, using GAMS to run the "Models.gms" file.

Datasets that accompany Beilke and O'Keefe 2022 publication (Title: Bats reduce insect density and defoliation in temperate forests: an exclusion experiment; Journal: Ecology).

Data associated with the manuscript "Overlooked invaders? Ecological impacts of non-game, native transplant fishes in the United States" by Jordan H. Hartman and Eric R. Larson

We developed a new application of isotopic gas exchange which couples a tunable diode laser absorption spectroscope (TDL) with a leaf gas exchange system, analyzing leakiness through induction of C4 photosynthesis on dark to high-light transitions. The youngest fully expanded leaf was measured on 40-45 day-old maize(B73) and sorghum (Tx430). Detail definition of each variable in raw Li-6400XT and Li-6800 (in "Original_data_AND_Data_processing_code.zip") is summarized in: <a href="https://www.licor.com/env/support/LI-6800/topics/symbols.html#const">https://www.licor.com/env/support/LI-6800/topics/symbols.html#const</a>

The availability of economically marginal land for energy crops is identified using the Cropland Data Layer and other soil, wind, climate data resources. All data are recognized on a 30m spatial resolution across the continental United States.

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.

These datasets are for the four-dimensional scanning transmission electron microscopy (4D-STEM) and electron energy loss spectroscopy (EELS) experiments for cathode nanoparticles at different cutoff voltages and in different electrolytes. The raw 4D-STEM experiment datasets were collected by TEM image & analysis software (FEI) and were saved as SER files. The raw 4D-STEM datasets of SER files can be opened and viewed in MATLAB using our analysis software package of imToolBox available at <a href="https://github.com/flysteven/imToolBox">https://github.com/flysteven/imToolBox</a>. The raw EELS datasets were collected by DigitalMicrograph software and were saved as DM4 files. The raw EELS datasets can be opened and viewed in DigitalMicrograph software or using our analysis codes available at <a href="https://github.com/chenlabUIUC/OrientedPhaseDomain">https://github.com/chenlabUIUC/OrientedPhaseDomain</a>. All the datasets are from the work "Formation and impact of nanoscopic oriented phase domains in electrochemical crystalline electrodes" (2022). The 4D-STEM experiment data include four example datasets for cathode nanoparticles collected at different cutoff voltages and in different electrolytes as described below. Each dataset contains a stack of diffraction patterns collected at different probe positions scanned across the cathode nanoparticle. 1. Pristine cathode particle: "Pristine particle 4D-STEM.ser" 2. Cathode particle at the cutoff voltage of 0.09V during discharge at C/10 in the aqueous electrolyte: "Intermediate cutoff0_09V discharge (aqueous) 4D-STEM.ser" 3. Fully discharged cathode particle at C/10 in the aqueous electrolyte: "Fully discharged particle 4D-STEM.ser" 4. Fully discharged cathode particle at C/10 in the dry organic electrolyte: "Fully discharge particle (dry organic electrolyte).ser" The EELS experiment data includes three example datasets for cathode nanoparticles collected at different cutoff voltages during discharge in the aqueous electrolyte (in "EELS datasets.zip") as described below. Each EELS dataset contains the zero-loss and core-loss EELS spectra collected at different probe positions scanned across the cathode nanoparticle. 1. Pristine cathode particle: "Pristine particle EELS.zip" 2. Cathode particle at the cutoff voltage of 0.09V during discharge at C/10 in the aqueous electrolyte: "intermediate discharge (aqueous) EELS.zip" 3. Fully discharged cathode particle at C/10 in the aqueous electrolyte: "fully discharge (aqueous) EELS.zip" The details of the software package and codes that can be used to analyze the 4D-STEM datasets and EELS datasets are available at: https://github.com/chenlabUIUC/OrientedPhaseDomain. Once our paper is formally published, we will update the relationship of these datasets with our paper.

This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes". Please refer to that publication for details about methodologies used to generate these data and for the experimental design. For this verison 2, we added specific gross nitrogen mineralization rates (ugN/gOM/d), microbial biomass carbon (ugC/gdw), microbial biomass nitrogen (ugN/gdw) and microbial biomass C:N ratios to the newest version of the data set. Additionally, we updated values for gross nitrogen mineralization, microbial NO3 assimilation and microbial NH4 assimilation to reflect slight changes in data processing. Those changes are reflected in "220829_All data_repository.csv". "220829_nitrogen_mineralization_readme.txt " is updated readme for the new file. The other 2 files begin with “220426_” are older version and same as in V1.

Example scripts and configuration files needed to perform select simulations described in the manuscript "Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex."