Dataset Search Results

This dataset contains daily and hourly temperature measurements in twenty different bat box designs deployed in central Indiana, USA from May to September 2018. Daily and hourly environmental data (temperature, solar radiation, wind speed and direction) are also included for days and hours sampled. Bat box temperature data were reclassified to cool (</= 30°C), permissive (30.1–39.9°C), and stressful (>/= 40°C) categories according to known temperature tolerances of temperate-zone bats.

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 data set contains survey results from a 2021 survey of University of Illinois University Library patrons who identify as transgender or gender non-conforming conducted as part of the Becoming a Trans Inclusive Library Project to assess the experiences of transgender patrons seeking information and services in the University Library. Survey instruments are available in the IDEALS repository: http://hdl.handle.net/2142/110081.

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 all the data for the results section in the study presented in the paper entitled "Chemistry Across Multiple Phases (CAMP) version 1.0: An integrated multi-phase chemistry mode" submitted to Geoscientific Model Development (GMD). In this paper, two sets of simulations were run to test CAMP with this results included here. This consists of (1) box model inputs and outputs presented in Section 4.2 for modal, binned and particle-resolved simulations to compare the application of identical chemical mechanisms to different aerosol representations and (2) the 3D Eulerian output presented in Section 4.3.

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.

Agriculture has substantial socioeconomic and environmental impacts that vary between crops. However, information on how the spatial distribution of specific crops has changed over time across the globe is relatively sparse. We introduce the Probabilistic Cropland Allocation Model (PCAM), a novel algorithm to estimate where specific crops have likely been grown over time. Specifically, PCAM downscales annual and national-scale data on the crop-specific area harvested of 17 major crops to a global 0.5-degree grid from 1961-2014. The resulting database presented here provides annual global gridded likelihood estimates of crop-specific areas. Both mean and standard deviations of grid cell fractions are available for each of the 17 crops. Each netCDF file contains an individual year of data with an additional variable ("crs") that defines the coordinate reference system used. Our results provide new insights into the likely changes in the spatial distribution of major crops over the past half-century. For additional information, please see the related paper by Jackson et al. (2019) in Environmental Research Letters (https://doi.org/10.1088/1748-9326/ab3b93).

This dataset provides estimates of agricultural and food commodity flows [kg] between all county pairs within the United States for the years 2007, 2012, and 2017. The database provides 206.3 million data points, since pairwise information is provided between 3134 counties, for 7 commodity categories, and 3 time periods. The commodity categories correspond to the Standardized Classification of Transported Goods and are: - SCTG 1: Iive animals and fish - SCTG 2: cereal grains - SCTG 3: agricultural products (except for animal feed, cereal grains, and forage products) - SCTG 4: animal feed, eggs, honey, and other products of animal origin - SCTG 5: meat, poultry, fish, seafood, and their preparations - SCTG 6: milled grain products and preparations, and bakery products - SCTG 7: other prepared foodstuffs, fats and oils For additional information, please see the related paper by Karakoc et al. (2022) in Environmental Research Letters.

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"

These data and code enable replication of the findings and robustness checks in "No buzz for bees: Media coverage of pollinator decline," published in Proceedings of the National Academy of Sciences of the United States of America (2020)". In this paper, we find that although widespread declines in insect biomass and diversity are increasing concern within the scientific community, it remains unclear whether attention to pollinator declines has also increased within information sources serving the general public. Examining patterns of journalistic attention to the pollinator population crisis can also inform efforts to raise awareness about the importance of declines of insect species providing ecosystem services beyond pollination. We used the Global News Index developed by the Cline Center for Advanced Social Research at the University of Illinois at Urbana-Champaign to track news attention to pollinator topics in nearly 25 million news items published by two American national newspapers and four international wire services over the past four decades. We provide a link to documentation of the Global News Index in the "relationships with articles, code, o. We found vanishingly low levels of attention to pollinator population topics relative to coverage of climate change, which we use as a comparison topic. In the most recent subset of ~10 million stories published from 2007 to 2019, 1.39% (137,086 stories) refer to climate change/global warming, while only 0.02% (1,780) refer to pollinator populations in all contexts and just 0.007% (679) refer to pollinator declines. Substantial increases in news attention were detectable only in U.S. national newspapers. We also find that while climate change stories appear primarily in newspaper “front sections”, pollinator population stories remain largely marginalized in “science” and “back section” reports. At the same time, news reports about pollinator populations increasingly link the issue to climate change, which might ultimately help raise public awareness to effect needed policy changes.

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.

Simulation trajectory data and scripts for Nature Nanotechnology manuscript "A DNA turbine powered by a transmembrane potential across a nanopore" that demonstrates a rationally designed nanoscale DNA-origami turbine with three chiral blades that uses a transmembrane electrochemical potential across a nanopore to drive a DNA bundle into sustained unidirectional rotations of up to 10 revolutions/s. Driven by the asymmetric mobility of a DNA duplex, the rotation direction of the turbine is set by its designed chirality and the salinity of the solvent.

This dataset contains the PartMC-MOSAIC simulations used in the article "Quantifying Errors in the Aerosol Mixing-State Index Based on Limited Particle Sample Size". The 1000 simulations of output data is organized into a series of archived folders, each containing 100 scenarios. Within each scenario directory are 25 NetCDF files, which are the hourly output of a PartMC-MOSAIC simulation containing all information regarding the environment, particle and gas state. This dataset was used to investigate the impact of sample size on determining aerosol mixing state. This data may be useful as a data set for applying different types of estimators.

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 is the experimental data of isolated nanomagnet islands with or without the presence of large nanomagnet islands. The small islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the small islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the data can be found in the note.txt and Spe_2016.xlsx file. Note: The raw data folders are stored in five volumes during the compression. All five volumes are needed in order to recover the original folder.

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 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 consists of raw ADC readings from a 3 transmitter 4 receiver 77GHz FMCW radar, together with synchronized RGB camera and depth (active stereo) measurements. The data is grouped into 4 distinct radar configurations: - "indoor" configuration with range <14m - "30m" with range <38m - "50m" with range <63m - "high_res" with doppler resolution of 0.043m/s # Related code https://github.com/moodoki/radical_sdk # Hardware Project Page https://publish.illinois.edu/radicaldata