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2018 (61)
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published: 2019-06-13
 
This lexicon is the expanded/enhanced version of the Moral Foundation Dictionary created by Graham and colleagues (Graham et al., 2013). Our Enhanced Morality Lexicon (EML) contains a list of 4,636 morality related words. This lexicon was used in the following paper - please cite this paper if you use this resource in your work. Rezapour, R., Shah, S., & Diesner, J. (2019). Enhancing the measurement of social effects by capturing morality. Proceedings of the 10th Workshop on Computational Approaches to Subjectivity, Sentiment and Social Media Analysis (WASSA). Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), Minneapolis, MN. In addition, please consider citing the original MFD paper: <a href="https://doi.org/10.1016/B978-0-12-407236-7.00002-4">Graham, J., Haidt, J., Koleva, S., Motyl, M., Iyer, R., Wojcik, S. P., & Ditto, P. H. (2013). Moral foundations theory: The pragmatic validity of moral pluralism. In Advances in experimental social psychology (Vol. 47, pp. 55-130)</a>.
keywords: lexicon; morality
published: 2019-06-12
 
The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatcher hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3). ITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3). Supplemental files 1 through 5 contain the raw data files. Supplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. Supplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files. Supplemental 5 is the map file needed to process the forward reads and index files in QIIME. Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following: 1 Brachythecium sp. 2 Usnea cornuta 3 Dicranum sp. 4 Leucodon julaceus 5 Lobaria quercizans 6 Rhizomnium sp. 7 Dicranum sp. 8 Thuidium delicatulum 9 Myelochroa aurulenta 10 Atrichum angustatum 11 Dicranum sp. 12 Hypnum sp. 13 Atrichum angustatum 14 Hypnum sp. 15 Thuidium delicatulum 16 Leucobryum sp. 17 Polytrichum commune 18 Atrichum angustatum 19 Atrichum angustatum 20 Atrichum crispulum 21 Bryaceae 22 Leucobryum sp. 23 Conocephalum conicum 24 Climacium americanum 25 Atrichum angustatum 26 Huperzia serrata 27 Polytrichum commune 28 Diphasiastrum sp. 29 Anomodon attenuatus 30 Bryoandersonia sp. 31 Polytrichum commune 32 Thuidium delicatulum 33 Brachythecium sp. 34 Leucobryum glaucum 35 Bryoandersonia sp. 36 Anomodon attenuatus 37 Pohlia sp. 38 Cinclidium sp. 39 Hylocomium splendens 40 Polytrichum commune 41 negative control 42 Soil 43 Soil 44 Soil 45 Soil 46 Soil 47 Soil If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.
published: 2018-06-05
 
A complete building coverage area dataset (i.e. area occupied by building structures, excluding other built surfaces such as roads, parking lots, and public parks) at the level of census block groups for the contiguous United States (CONUS). The dataset was assembled based on an ensemble prediction of nonlinear hierarchical models to account for spatial heterogeneities in the distribution of built surfaces across different urban communities. Percentage of impervious land and housing density were used as predictors of the estimated area of buildings and cross-validation results showed that the product estimated area represented by buildings with a mean error of 0.049 %.
keywords: Building Coverage Area; Urban Geography; Regional; Sustainability; US Census Block Groups; CONUS Data
published: 2018-12-31
 
Sixty undergraduate STEM lecture classes were observed across 14 departments at the University of Illinois Urbana-Champaign in 2015 and 2016. We selected the classes to observe using purposive sampling techniques with the objectives of (1) collecting classroom observations that were representative of the STEM courses offered; (2) conducting observations on non-test, typical class days; and (3) comparing these classroom observations using the Class Observation Protocol for Undergraduate STEM (COPUS) to record the presence and frequency of active learning practices utilized by Community of Practice (CoP) and non-CoP instructors. Decimal values are the result of combined observations. All COPUS codes listed are from Smith (2013) "The Classroom Observation Protocol for Undergraduate STEM (COPUS): A New Instrument to Characterize STEM Classroom Practices" paper. For more information on the data collection process, see "Evidence that communities of practice are associated with active learning in large STEM lectures" by Tomkin et. al. (2019) in the International Journal of STEM Education.
keywords: COPUS, Community of Practice
published: 2019-06-03
 
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords: Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-06-06
 
This lexicon is the expanded/enhanced version of the Moral Foundation Dictionary created by Graham and colleagues (Graham et al., 2013). Our Enhanced Morality Lexicon (EML) contains a list of 4,636 morality related words. This lexicon was used in the following paper - please cite this paper if you use this resource in your work. Rezapour, R., Shah, S., & Diesner, J. (2019). Enhancing the measurement of social effects by capturing morality. Proceedings of the 10th Workshop on Computational Approaches to Subjectivity, Sentiment and Social Media Analysis (WASSA). Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL), Minneapolis, MN. In addition, please consider citing the original MFD paper: Graham, J., Haidt, J., Koleva, S., Motyl, M., Iyer, R., Wojcik, S. P., & Ditto, P. H. (2013). Moral foundations theory: The pragmatic validity of moral pluralism. In Advances in experimental social psychology (Vol. 47, pp. 55-130).
keywords: lexicon; morality
published: 2019-06-05
 
This dataset contains the data files for the PhD thesis entitled: Species Distribution, Phylogenetic Structure and Functional Roles of Detritus Inhabiting Fungi Across Contrasting Aquatic Environments by Daniel Bruce Raudabaugh. More specifically, it contains the forward Illumina reads for ITS1, ITS2, Beta-tubulin and LSU in addition to the index files and map files needed to process the reads in QIIME 1.9.1. The sequences represent environmental sequencing from detrital samples from Black Moshannon State park (Pennsylvania), Pepper run (Pennsylvania), Nescopeck State park (Pennsylvania), Tannersville Cranberry bog (Pennsylvania), Beulah bog (Wisconsin) and Honey Creek Nature preserve (Wisconsin). The term Peatland includes both bogs and fens habitats. Peatland sites consisted of Black Moshannon State park, Tannersville Cranberry bog and Beulah bog. Stream sites consisted of Pepper Run, Nescopeck State park and Honey Creek Nature preserve. The data set also includes each OTU table with taxonomic determination and the OTU representative sequence, ITS1 alignment files for each fungal class and final RAxML phylogenetic tree MiSeq v2 platform run number 1 QIIME Map file.txt: map file is needed to parse information in QIIME 1.9.1. This file is used in conjunction with ITS1, ITS2, beta-tubulin, and LSU R1 forward read and Index files. ITS1 Index file.fastq: file is associated with ITS1 R1 forward Illumina reads.fastq. ITS1 R1 forward Illumina reads.fastq: ITS1 forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3) primers. ITS2 Index file.fastq: file is associated with ITS2 R1 forward Illumina reads.fastq. ITS2 R1 forward Illumina reads.fastq: ITS2 forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3) primers. Beta tubulin Index file.fastq: file is associated with Beta tubulin forward Illumina reads.fastq. Beta tubulin forward Illumina reads.fastq: : Beta tubulin forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using BT2AF (5'-GGTAACCAAATCGGTGCTGCTTTC-'3) and BT2BR (5'-ACCCTCAGTGTAGTGACCCTTGGC-'3) primers. MiSeq v2 platform run number 2 QIIME Map file is needed to parse information in QIIME 1.9.1. This file is used in conjunction with LSU R1forward read and Index files. LSU Index file.fastq: file is associated with LSU R1 forward Illumina reads.fastq. LSU R1 forward Illumina reads.fastq: : LSU forward reads from the Illumina MiSeq v2 250 bp run. Reads were generated using PCR product amplified using LROR (5'-CCGCTGAACTTAAGCATATCA-'3) and LR3 (5'-CCGTGTTTCAAGACGGG-'3) primers. OTU tables ITS1 OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from Unite, NCBI, and CONSTAX. The representative sequence for each OTU is included. ITS2 OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from Unite, NCBI, and CONSTAX. The representative sequence for each OTU is included. Beta tubulin OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from NCBI. In addition, the representative. The representative sequence for each OTU is included. LSU OTU table with taxonomy and sequence data.csv: Standard OTU table with assigned taxonomy from SILVA and NCBI. The representative sequence for each OTU is included. Alignment files and resulting RAxML tree for Class level community phylogenetic analyses Alignments were completed in PASTA using the MAFFT alignment option. All alignment files contain backbone sequences obtained from TBAS or NCBI in addition to OTU sequences. All phylogenetic trees were completed in PASTA using the RAxML post-processing option. Alignment_file_Agarcomycetes_trimmed_Phylip RAxML_Agaricomycetes_ITS1_Tree.tre Alignment_file_Dothidiomycetes_trimmed_Phylip RAxML_Dothideomycetes_ITS1_Tree.tre Alignment_file_Eurotiomycetes_trimmed_Phylip: RAxML_Eurotiomycetes_ITS1_Tree.tre Alignment_file_Leotiomycetes_Trimmed_Phylip RAxML_Leotiomycetes_ITS1_Tree.tre Alignment_file_Microbotryomycetes_trimmed_phylip RAxML_Microbotryomycetes_ITS1_Tree.tre Alignment_file_Mortierellomycetes_Trimmed_phylip RAxML_Mortierella_ITS1_Tree.tre Alignment_file_Saccharomycetes_Trimmed_Phylip RAxML_Saccharomycetes_ITS1_Tree.tre Alignment_file_Sordariomycetes_trimmed_Phylip RAxML_Sordriomycetes_ITS1_Tree.tre Alignment_file_Tremellomycetes_trimmed_phylip RAxML_Tremellomycetes_ITS1_Tree.tre Alignment file and resulting RAxML tree for Community level phylogenetic analyses Alignment was completed in PASTA using the MAFFT alignment option and resulting tree was completed using the RAxML post-processing option. Alignment_file_ LSU_RDP_fungal_community.aln LSU_RDP_fungal_community_Tree.tre
keywords: ITS1 forward reads; Illumina; peatlands; streams; bogs; fens
published: 2019-05-31
 
The data are provided to illustrate methods in evaluating systematic transactional data reuse in machine learning. A library account-based recommender system was developed using machine learning processing over transactional data of 383,828 transactions (or check-outs) sourced from a large multi-unit research library. The machine learning process utilized the FP-growth algorithm over the subject metadata associated with physical items that were checked-out together in the library. The purpose of this research is to evaluate the results of systematic transactional data reuse in machine learning. The analysis herein contains a large-scale network visualization of 180,441 subject association rules and corresponding node metrics.
keywords: evaluating machine learning; network science; FP-growth; WEKA; Gephi; personalization; recommender systems
published: 2019-05-31
 
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords: denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-05-07
 
Data set of trophic cascade in mesocosms experiments for zooplankton (biomass and body size) and phytoplankton (chlorophyll a concentration) caused by Bluegill as well as zooplankton production in those same treatment groups. Zooplankton were collected by tube sampler and phytoplankton were collected through grab samples.
keywords: Trophic cascades; size-selective predation; compensatory mechanisms; biomanipulation; invasive fish; Daphnia; Moina
published: 2019-05-08
 
The data file contains a list of articles that have PubMed identifiers, which were used in a project associated with the manuscript "An in-situ evaluation of the RCT Tagger using 7413 articles included in 570 Cochrane reviews with RCT-only inclusion criteria".
keywords: Cochrane reviews; Randomized controlled trials; RCT; Automation; Systematic reviews
published: 2019-05-08
 
The data file contains a list of articles and their RCT Tagger prediction scores, which were used in a project associated with the manuscript "An in-situ evaluation of the RCT Tagger using 7413 articles included in 570 Cochrane reviews with RCT-only inclusion criteria".
keywords: Cochrane reviews; automation; randomized controlled trial; RCT; systematic reviews
published: 2019-05-10
 
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords: Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-16
 
The associated data sets include information on stable isotopes from organic matter sources in high elevation lakes, the percentage of production assimilated from the different sources of organic matter, and the relationship between different metrics for trophic position and environmental variables.
keywords: Stable isotopes; macroinvertebrate production; trophic position
published: 2018-11-20
 
A dataset of acoustic impulse responses for microphones worn on the body. Microphones were placed at 80 positions on the body of a human subject and a plastic mannequin. The impulse responses can be used to study the acoustic effects of the body and can be convolved with sound sources to simulate wearable audio devices and microphone arrays. The dataset also includes measurements with different articles of clothing covering some of the microphones and with microphones placed on different hats and accessories. The measurements were performed from 24 angles of arrival in an acoustically treated laboratory. Related Paper: Ryan M. Corey, Naoki Tsuda, and Andrew C. Singer. "Acoustic Impulse Responses for Wearable Audio Devices," IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Brighton, UK, May 2019. All impulse responses are sampled at 48 kHz and truncated to 500 ms. The impulse response data is provided in WAVE audio and MATLAB data file formats. The microphone locations are provided in tab-separated-value files for each experiment and are also depicted graphically in the documentation. The file wearable_mic_dataset_full.zip contains both WAVE- and MATLAB-format impulse responses. The file wearable_mic_dataset_matlab.zip contains only MATLAB-format impulse responses. The file wearable_mic_dataset_wave.zip contains only WAVE-format impulse responses.
keywords: Acoustic impulse responses; microphone arrays; wearables; hearing aids; audio source separation
published: 2019-05-22
 
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.
keywords: artificial spin ice; magnetism
published: 2019-05-20
 
This is the experimental data of tetris artificial spin ice. The 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 islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the dataset can be found in the file Note.txt and Tetris_data_list.xlsx Note: 2 files name bl11_teris600_033 and bl11_tetris600_2_135 are not recorded in the excel sheet because they are corrupted during the measurement. Any data that is not recorded in the excel sheet is either corrupted or of low quality. From files *_028 to *_049, tetris is spelled with “t” while in the raw data folder without “t”. This is a typo. Throughout the dataset, tetris and teris are supposed to have the same meaning.
keywords: artificial spin ice
published: 2019-05-16
 
This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> &bull; Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> &bull; Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> &bull; Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>
keywords: divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-08
 
The data file contains a list of articles given low score by the RCT Tagger and an error analysis of them, which were used in a project associated with the manuscript "An in-situ evaluation of the RCT Tagger using 7413 articles included in 570 Cochrane reviews with RCT-only inclusion criteria".
keywords: Cochrane reviews; automation; randomized controlled trial; RCT; systematic reviews
published: 2019-05-08
 
The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "An in-situ evaluation of the RCT Tagger using 7413 articles included in 570 Cochrane reviews with RCT-only inclusion criteria".
keywords: Cochrane reviews; automation; randomized controlled trial; RCT; systematic review
published: 2019-05-08
 
The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "An in-situ evaluation of the RCT Tagger using 7413 articles included in 570 Cochrane reviews with RCT-only inclusion criteria".
keywords: Cochrane reviews; systematic reviews; randomized control trial; RCT; automation
published: 2019-05-01
 
This dataset contains scripts and data developed as a part of the research manuscript titled “Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt”. This includes (1) Spatial and temporal factors for ammonia emissions from agricultural fertilizer usage developed using the hybrid ISS-DNDC method for the Midwest U.S., (2) CAMx job scripts and outputs of predictions of ambient ammonia and total and speciated PM2.5, (3) Observation data used to statistically evaluate CAMx predictions, and (4) MATLAB programs developed to pair CAMx predictions with ground-based observation data in space and time.
keywords: Air quality; Ammonia; Emissions; PM2.5; CAMx; DNDC; spatial resolution; Midwest U.S.
planned publication date: 2020-04-22
 
Nest survival and Fledgling production data for Bell's Vireo and Willow Flycatcher nests.
keywords: Bell's Vireo;Willow Flycatcher;habitat selection;fitness;
published: 2019-04-05
 
File Name: Inclusion_Criteria_Annotation.csv Data Preparation: Xiaoru Dong Date of Preparation: 2019-04-04 Data Contributions: Jingyi Xie, Xiaoru Dong, Linh Hoang Data Source: Cochrane systematic reviews published up to January 3, 2018 by 52 different Cochrane groups in 8 Cochrane group networks. Associated Manuscript authors: Xiaoru Dong, Jingyi Xie, Linh Hoang, and Jodi Schneider. Associated Manuscript, Working title: Machine classification of inclusion criteria from Cochrane systematic reviews. Description: The file contains lists of inclusion criteria of Cochrane Systematic Reviews and the manual annotation results. 5420 inclusion criteria were annotated, out of 7158 inclusion criteria available. Annotations are either "Only RCTs" or "Others". There are 2 columns in the file: - "Inclusion Criteria": Content of inclusion criteria of Cochrane Systematic Reviews. - "Only RCTs": Manual Annotation results. In which, "x" means the inclusion criteria is classified as "Only RCTs". Blank means that the inclusion criteria is classified as "Others". Notes: 1. "RCT" stands for Randomized Controlled Trial, which, in definition, is "a work that reports on a clinical trial that involves at least one test treatment and one control treatment, concurrent enrollment and follow-up of the test- and control-treated groups, and in which the treatments to be administered are selected by a random process, such as the use of a random-numbers table." [Randomized Controlled Trial publication type definition from https://www.nlm.nih.gov/mesh/pubtypes.html]. 2. In order to reproduce the relevant data to this, please get the code of the project published on GitHub at: https://github.com/XiaoruDong/InclusionCriteria and run the code following the instruction provided. 3. This datafile (V2) is a updated version of the datafile published at https://doi.org/10.13012/B2IDB-5958960_V1 with some minor spelling mistakes in the data fixed.
keywords: Inclusion criteri; Randomized controlled trials; Machine learning; Systematic reviews