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Illinois Data Bank Dataset Search Results
Dataset Search Results
published: 2023-09-21
Clarke, Caitlin; Lischwe Mueller, Natalie; Joshi, Manasi Ballal; Fu, Yuanxi; Schneider, Jodi (2023): The Inclusion Network of 27 Review Articles Published between 2013-2018 Investigating the Relationship Between Physical Activity and Depressive Symptoms. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-4614455_V4
The relationship between physical activity and mental health, especially depression, is one of the most studied topics in the field of exercise science and kinesiology. Although there is strong consensus that regular physical activity improves mental health and reduces depressive symptoms, some debate the mechanisms involved in this relationship as well as the limitations and definitions used in such studies. Meta-analyses and systematic reviews continue to examine the strength of the association between physical activity and depressive symptoms for the purpose of improving exercise prescription as treatment or combined treatment for depression. This dataset covers 27 review articles (either systematic review, meta-analysis, or both) and 365 primary study articles addressing the relationship between physical activity and depressive symptoms. Primary study articles are manually extracted from the review articles. We used a custom-made workflow (Fu, Yuanxi. (2022). Scopus author info tool (1.0.1) [Python]. <a href="https://github.com/infoqualitylab/Scopus_author_info_collection">https://github.com/infoqualitylab/Scopus_author_info_collection</a> that uses the Scopus API and manual work to extract and disambiguate authorship information for the 392 reports. The author information file (author_list.csv) is the product of this workflow and can be used to compute the co-author network of the 392 articles. This dataset can be used to construct the inclusion network and the co-author network of the 27 review articles and 365 primary study articles. A primary study article is "included" in a review article if it is considered in the review article's evidence synthesis. Each included primary study article is cited in the review article, but not all references cited in a review article are included in the evidence synthesis or primary study articles. The inclusion network is a bipartite network with two types of nodes: one type represents review articles, and the other represents primary study articles. In an inclusion network, if a review article includes a primary study article, there is a directed edge from the review article node to the primary study article node. The attribute file (article_list.csv) includes attributes of the 392 articles, and the edge list file (inclusion_net_edges.csv) contains the edge list of the inclusion network. Collectively, this dataset reflects the evidence production and use patterns within the exercise science and kinesiology scientific community, investigating the relationship between physical activity and depressive symptoms. FILE FORMATS 1. article_list.csv - Unicode CSV 2. author_list.csv - Unicode CSV 3. Chinese_author_name_reference.csv - Unicode CSV 4. inclusion_net_edges.csv - Unicode CSV 5. review_article_details.csv - Unicode CSV 6. supplementary_reference_list.pdf - PDF 7. README.txt - text file 8. systematic_review_inclusion_criteria.csv - Unicode CSV <b>UPDATES IN THIS VERSION COMPARED TO V3</b> (Clarke, Caitlin; Lischwe Mueller, Natalie; Joshi, Manasi Ballal; Fu, Yuanxi; Schneider, Jodi (2023): The Inclusion Network of 27 Review Articles Published between 2013-2018 Investigating the Relationship Between Physical Activity and Depressive Symptoms. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4614455_V3) - We added a new file systematic_review_inclusion_criteria.csv.
keywords:
systematic reviews; meta-analyses; evidence synthesis; network visualization; tertiary studies; physical activity; depressive symptoms; exercise; review articles
published: 2024-11-01
Zhang, Ziliang; Eddy, William C.; Stuchiner, Emily R.; DeLucia, Evan H.; Yang, Wendy (2024): Data for A conceptual model explaining spatial variation in soil nitrous oxide emissions in agricultural fields. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-3526278_V1
This dataset includes data on soil nitrous oxide fluxes, soil properties, and climate presented in the manuscript, "A conceptual model explaining spatial variation in soil nitrous oxide emissions in agricultural fields," published in Commucations Earth & Environment. Please refer to that publication for details about methodologies used to generate these data and for the experimental design.
keywords:
soil nitrous oxide emissions; gross nitrous oxide production; gross nitrous oxide consumption; N2O; denitrification; maize; cannon model
published: 2024-11-07
Zheng, Heng; Fu, Yuanxi; Vandel, Ellie; Schneider, Jodi (2024): Dataset of 286 publications citing the 2014 Willoughby-Jansma-Hoye protocol. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-4610831_V3
This dataset consists of the 286 publications retrieved from Web of Science and Scopus on July 6, 2023 as citations for Willoughby et al., 2014: Patrick H. Willoughby, Matthew J. Jansma, and Thomas R. Hoye (2014). A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts. Nature Protocols, 9(3), Article 3. https://doi.org/10.1038/nprot.2014.042 We added the DOIs of the citing publications into a Zotero collection. Then we exported all 286 DOIs in two formats: a .csv file (data export) and an .rtf file (bibliography). <b>Willoughby2014_286citing_publications.csv</b> is a Zotero data export of the citing publications. <b>Willoughby2014_286citing_publications.rtf</b> is a bibliography of the citing publications, using a variation of the American Psychological Association style (7th edition) with full names instead of initials. To create <b>Willoughby2014_citation_contexts.csv</b>, HZ manually extracted the paragraphs that contain a citation marker of Willoughby et al., 2014. We refer to these paragraphs as the citation contexts of Willoughby et al., 2014. Manual extraction started with 286 citing publications but excluded 2 publications that are not in English, those with DOIs 10.13220/j.cnki.jipr.2015.06.004 and 10.19540/j.cnki.cjcmm.20200604.201 The silver standard aimed to triage the citing publications of Willoughby et al., 2014 that are at risk of propagating unreliability due to a code glitch in a computational chemistry protocol introduced in Willoughby et al., 2014. The silver standard was created stepwise: First one chemistry expert (YF) manually annotated the corpus of 284 citing publications in English, using their full text and citation contexts. She manually categorized publications as either at risk of propagating unreliability or not at risk of propagating unreliability, with a rationale justifying each category. Then we selected a representative sample of citation contexts to be double annotated. To do this, MJS turned the full dataset of citation contexts (Willoughby2014_citation_contexts.csv) into word embeddings, clustered them using similarity measures using BERTopic's HDBS, and selected representative citation contexts based on the centroids of the clusters. Next the second chemistry expert (EV) annotated the 77 publications associated with the citation contexts, considering the full text as well as the citation contexts. <b>double_annotated_subset_77_before_reconciliation.csv</b> provides EV and YF's annotation before reconciliation. To create the silver standard YF, EV, and JS discussed differences and reconciled most differences. YF and EV had principled reasons for disagreeing on 9 publications; to handle these, YF updated the annotations, to create the silver standard we use for evaluation in the remainder of our JCDL 2024 paper (<b>silver_standard.csv</b>) <b>Inter_Annotator_Agreement.xlsx</b> indicates publications where the two annotators made opposite decisions and calculates the inter-annotator agreement before and after reconciliation together. <b>double_annotated_subset_77_before_reconciliation.csv</b> provides EV and YF's annotation after reconciliation, including applying the reconciliation policy.
keywords:
unreliable cited sources; knowledge maintenance; citations; scientific digital libraries; scholarly publications; reproducibility; unreliability propagation; citation contexts
published: 2018-04-19
Torvik, Vetle I. (2018): MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-4354331_V1
MapAffil 2016 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide. Prepared by Vetle Torvik 2018-04-05 The dataset comes as a single tab-delimited Latin-1 encoded file (only the City column uses non-ASCII characters), and should be about 3.5GB uncompressed. • How was the dataset created? The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in the first week of October, 2016. Check here for information to get PubMed/MEDLINE, and NLMs data <a href ="https://www.nlm.nih.gov/databases/download/pubmed_medline.html">Terms and Conditions</a> • Affiliations are linked to a particular author on a particular article. Prior to 2014, NLM recorded the affiliation of the first author only. However, MapAffil 2016 covers some PubMed records lacking affiliations that were harvested elsewhere, from PMC (e.g., PMID 22427989), NIH grants (e.g., 1838378), and Microsoft Academic Graph and ADS (e.g. 5833220). • Affiliations are pre-processed (e.g., transliterated into ASCII from UTF-8 and html) so they may differ (sometimes a lot; see PMID 27487542) from PubMed records. • All affiliation strings where processed using the MapAffil procedure, to identify and disambiguate the most specific place-name, as described in: <i>Torvik VI. MapAffil: A bibliographic tool for mapping author affiliation strings to cities and their geocodes worldwide. D-Lib Magazine 2015; 21 (11/12). 10p</i> • Look for <a href="https://doi.org/10.1186/s41182-017-0073-6">Fig. 4</a> in the following article for coverage statistics over time: <i>Palmblad M, Torvik VI. Spatiotemporal analysis of tropical disease research combining Europe PMC and affiliation mapping web services. Tropical medicine and health. 2017 Dec;45(1):33.</i> Expect to see big upticks in coverage of PMIDs around 1988 and for non-first authors in 2014. • The code and back-end data is periodically updated and made available for query by PMID at <a href="http://abel.ischool.illinois.edu/">Torvik Research Group</a> • What is the format of the dataset? The dataset contains 37,406,692 rows. Each row (line) in the file has a unique PMID and author postition (e.g., 10786286_3 is the third author name on PMID 10786286), and the following thirteen columns, tab-delimited. All columns are ASCII, except city which contains Latin-1. 1. PMID: positive non-zero integer; int(10) unsigned 2. au_order: positive non-zero integer; smallint(4) 3. lastname: varchar(80) 4. firstname: varchar(80); NLM started including these in 2002 but many have been harvested from outside PubMed 5. year of publication: 6. type: EDU, HOS, EDU-HOS, ORG, COM, GOV, MIL, UNK 7. city: varchar(200); typically 'city, state, country' but could inlude further subvisions; unresolved ambiguities are concatenated by '|' 8. state: Australia, Canada and USA (which includes territories like PR, GU, AS, and post-codes like AE and AA) 9. country 10. journal 11. lat: at most 3 decimals (only available when city is not a country or state) 12. lon: at most 3 decimals (only available when city is not a country or state) 13. fips: varchar(5); for USA only retrieved by lat-lon query to https://geo.fcc.gov/api/census/block/find
keywords:
PubMed, MEDLINE, Digital Libraries, Bibliographic Databases; Author Affiliations; Geographic Indexing; Place Name Ambiguity; Geoparsing; Geocoding; Toponym Extraction; Toponym Resolution
published: 2024-07-08
Chong, Jer Pin; Minnaert-Grote, Jamie; Zaya, David N.; Ashley, Mary V.; Coons, Janice; Ramp Neal, Jennifer M.; Molano-Flores, Brenda (2024): Microsatellite genotypes and locations for three Physaria taxa on and near the Kaibab Plateau, Arizona, USA. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-2540221_V1
A population genetics study was conducted on three plant taxa in the genus Physaria that are found on the Kaibab Plateau (Arizona, USA). Physaria kingii subsp. kaibabensis is endemic to the Kaibab Plateau, and is of conservation concern because of its rarity, limited range, and potential threats to its long-term persistence. Additionally, the taxon is a candidate for federal protection under the Endangered Species Act. It was not clear how genetically isolated P. k. subsp. kaibabensis was from Physaria kingii subsp. latifolia, which is a widespread subspecies found throughout the southwestern USA, including on the Kaibab Plateau. Additionally, other authors have suggested that P. k. subsp. kaibabensis may hybridize with Physaria arizonica, a different species that is also widespread and found on and off the Kaibab Plateau. We conducted a population genetics study of all three groups to better determine the conservation status of P. k. subsp. kaibabensis. Genetic data are in the form of nuclear DNA microsatellites for 13 loci (all apparently diploid). Additionally, we have included location information for the collection sites. We collected tissue samples from on and off the Kaibab Plateau. The overall findings are shared in a manuscript being submitted for peer-review.
keywords:
Physaria kingii; Kaibab Plateau; endemism; conservation genetics; rare species biology
published: 2024-11-15
Blanke, Steven; Ringling, Megan; Tan, Ivilyn; Oh, Seung (2024): Vacuolating cytotoxin A interactions with the host cell surface . University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-7490114_V1
This page contains the data for the manuscript "Vacuolating cytotoxin A interactions with the host cell surface". This manuscript is currently in prep.
keywords:
Steven R Blanke; Vacuolating cytotoxin A; VacA; Helicobacter pylori; protein binding; sphingomyelin; cell surface
published: 2024-11-15
Cheng, Ho Kei (2024): BL30K. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-1702934_V1
BL30K is a synthetic dataset rendered using Blender with ShapeNet's data. We break the dataset into six segments, each with approximately 5K videos. The videos are organized in a similar format as DAVIS and YouTubeVOS, so dataloaders for those datasets can be used directly. Each video is 160 frames long, and each frame has a resolution of 768*512. There are 3-5 objects per video, and each object has a random smooth trajectory -- we tried to optimize the trajectories in a greedy fashion to minimize object intersection (not guaranteed), with occlusions still possible (happen a lot in reality). See [Modular Interactive Video Object Segmentation: Interaction-to-Mask, Propagation and Difference-Aware Fusion (MiVOS), CVPR 2022] for details.
published: 2024-11-14
Matthews, Jeffrey W.; Huang, Annie H. (2024): Data for The invasion of Japanese hop (Humulus japonicus) in a restored floodplain forest. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6760644_V1
These data represent the raw data from the paper “The invasion of Japanese hop (Humulus japonicus) in a restored floodplain forest” published in Invasive Plant Science and Management by Annie H. Huang and Jeffrey W. Matthews.
keywords:
invasive plants; restored wetlands
published: 2024-11-13
Tang, Zhichu; Chen, Wenxiang; Yin, Kaijun; Busch, Robert; Hou, Hanyu; Lin, Oliver; Lyu, Zhiheng; Zhang, Cheng; Yang, Hong; Zuo, Jian-Min ; Chen, Qian (2024): Nanoscale Stacking Fault Engineering and Mapping in Spinel Oxides for Reversible Multivalent Ion Insertion. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-8188066_V1
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 states. 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 https://github.com/flysteven/imToolBox. 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 https://github.com/chenlabUIUC/OrientedPhaseDomain. All the datasets are from the work "Nanoscale Stacking Fault Engineering and Mapping in Spinel Oxides for Reversible Multivalent Ion Insertion" (2024). The 4D-STEM experiment data include four example datasets for cathode nanoparticles collected at pristine and discharged states. Each dataset contains a stack of diffraction patterns collected at different probe positions scanned across the cathode nanoparticle. 1. Pristine untreated nanoparticle: "Pristine U-NP.ser" 2. Pristine 200ºC heated nanoparticle: "Pristine H200-NP.ser" 3. Untreated nanoparticle after first discharge in Zn-ion batteries: "Discharged U-NP.ser" 4. 200ºC heated nanoparticle after first discharge in Zn-ion batteries: "Discharged H200-NP.ser" The EELS experiment data includes six example datasets for cathode nanoparticles collected at different states (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 untreated nanoparticle: "Pristine U-NP EELS.zip" 2. Pristine 200ºC heated nanoparticle: "Prisitne H200-NP EELS.zip" 3. Untreated nanoparticle after first discharge in Zn-ion batteries: "Discharged U-NP EELS.zip" 4. Untreated nanoparticle after first charge in Zn-ion batteries: "Charged U-NP EELS.zip" 5. 200ºC heated nanoparticle after first discharge in Zn-ion batteries: "Discharged H200-NP EELS.zip" 6. 200ºC heated nanoparticle after first charge in Zn-ion batteries: "Charged H200-NP 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.
keywords:
4D-STEM; EELS; defects; strain; cathode; nanoparticle; energy storage
published: 2024-06-04
Park, Minhyuk; Tabatabaee, Yasamin; Warnow, Tandy; Chacko, George (2024): Data for Well-Connectedness and Community Detection. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-6271968_V1
This dataset contains files and relevant metadata for real-world and synthetic LFR networks used in the manuscript "Well-Connectedness and Community Detection (2024) Park et al. presently under review at PLOS Complex Systems. The manuscript is an extended version of Park, M. et al. (2024). Identifying Well-Connected Communities in Real-World and Synthetic Networks. In Complex Networks & Their Applications XII. COMPLEX NETWORKS 2023. Studies in Computational Intelligence, vol 1142. Springer, Cham. https://doi.org/10.1007/978-3-031-53499-7_1. “The Overview of Real-World Networks image provides high-level information about the seven real-world networks. TSVs of the seven real-world networks are provided as [network-name]_cleaned to indicate that duplicated edges and self-loops were removed, where column 1 is source and column 2 is target. LFR datasets are contained within the zipped file. Real-world networks are labeled _cleaned_ to indicate that duplicate edges and self loops were removed. #LFR datasets for the Connectivity Modifier (CM) paper ### File organization Each directory `[network-name]_[resolution-value]_lfr` includes the following files: * `network.dat`: LFR network edge-list * `community.dat`: LFR ground-truth communities * `time_seed.dat`: time seed used in the LFR software * `statistics.dat`: statistics generated by the LFR software * `cmd.stat`: command used to run the LFR software as well as time and memory usage information
published: 2023-07-06
Schneider, Amy; Suski, Cory; Esbaugh, Andrew (2023): Dataset for Silver carp experience metabolic and behavioral changes when exposed to water from the Chicago Area Waterway; implications for upstream movement. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0037727_V1
published: 2024-11-07
Fernandez-Materan, Francelys; Olivos-Caicedo, Kelly; Daniel, Steven; Walden, Kimberly; Fields, Christopher; Hernandez, Alvaro; Alves, Joao; Ridlon, Jason (2024): Genome annotation of Nine Clostridium scindens Strains Isolated from Human Feces with Prokka v.1.14.6. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1661997_V1
This dataset is part of a genome annoucement. The main folder PROKKA_results contain nine Prokka v.1.14.6 annotation files from nine Clostridium scindens genome sequences. Each file provide 12 output files including predicted protein sequences (.faa), nucleotide sequences of the predicted coding regions (.ffn), nucleotide sequence of the genome (.fna and .fsa), annotated genome in GenBank format (.gbk), steps recording performed during the annotation process (.log), error messages or warnings (.err), annotations in Sequin format (.sqn), summary of the annotations in tabular (.tbl), tab-separated values (.tsv) and plain text (.txt) formats.
keywords:
Clostridium scindens; genome annotation; PROKKA;
published: 2024-10-28
Trinklein, Timothy; Lam, Fan; Sweedler, Jonathan (2024): Plaque-associated lipids dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4907703_V1
This dataset contains MALDI imaging and fluorescence imaging data of 5xFAD mice and control animals. 1+2) Animal_1_5xFAD_s1 and s2 : A MATLAB file of 50 micron spatial resolution imaging of whole brain slice from a 5xFAD animal. 3) Slide28_Animal1_stitch_channels__Thioflavin S : A PNG file of the corresponding Thioflavin S- stained fluorescence image obtained post-MSI from the same section. 4) Slide28_Animal1_stitch_merged : A PNG file of the corresponding merged imaged including brightfield, Thioflavin S (GFP channel) and Hoechst staining (DAPI channel) used for image registration 5) mz_bins_use_neg.mat : A MATLAB array of the m/z channels all MSI images (whole brain slice, 50 micron spatial resolution) were binned to in order to enable comparison 6) Animal3_S18_HR.mat : A MATLAB array of high-spatial-resolution (5 micron) imaging of a 5xFAD mouse hippocampus and cortex. Due to the large dataset, 22 m/z channels are included. 7) Animal5_S18_HR.mat : A MATLAB array of high-spatial-resolution (5 micron) imaging of a wildtype mouse hippocampus and cortex 8) mz_features_22.mat : A MATLAB array of the 22 m/z channels included in the high spatial resolution imaging data
keywords:
amyloid beta; 5xfad, lipids; maldi;
published: 2024-07-30
Mori, Jameson (2024): Deer land cover utility (LCU) score datasets (TRS, township, and county). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0160590_V1
This file contains the white-tailed deer (Odocoileus virginianus) land cover utility score (deer LCU score) datasets for every TRS (township, range, and section), township, and county in Illinois, USA. The file is an Excel spreadsheet with a metadata sheet, separate sheets for the deer LCU scores for each spatial level, and a sheet with the data required to replicate how the deer LCU score approach was validated. The deer LCU score is a unitless value, with larger scores corresponding to a spatial unit with more and/or better deer habitat.
keywords:
habitat; white-tailed deer; deer; Odocoileus virginianus; land cover; land classification; landscape; habitat suitability index; ecology; environment
published: 2017-10-11
McEntee, Kenneth B. (2017): International Registry of Reproductive Pathology Database. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3175716_V1
The International Registry of Reproductive Pathology Database is part of pioneering work done by Dr. Kenneth McEntee to comprehensively document thousands of disease cases studies. His large and comprehensive collection of case reports and physical samples was complimented by development of the International Registry of Reproductive Pathology Database in the 1980s. The original FoxPro Database files and a migrated access version were completed by the College of Veterinary Medicine in 2016. Access CSV files were completed by the University of Illinois Library in 2017.
keywords:
Animal Pathology; Databases; Veterinary Medicine
published: 2021-08-28
Southey, Bruce; Rodriguez-Zas, Sandra (2021): Metabolics of weaning and maternal immune activation in 22 day old pigs. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9043394_V1
Metabolite identifications and profiles of liver samples from 22 day old male and female pigs from gilt that exposed to porcine reproductive and respiratory syndrome virus (P) or not (C) that were weaned at 21 days of age (W) or not (N). Profiles were obtained by University of Illinois Carver Metabolomics Center. Spectrum for each sample was acquired using a gas chromatography mass spectrometry system consisting of an Agilent 7890 gas chromatograph, an Agilent 5975 MSD, and an HP 7683B auto sampler.
keywords:
gas chromatography; mass spectrometry; maternal immune activation; weaning; liver
published: 2024-08-02
Morrow Plots Data Curation Working Group (2024): Morrow Plots Treatment and Yield Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7865141_V2
The Morrow Plots at the University of Illinois at Urbana-Champaign are the longest-running continuous experimental plots in the Americas. In continuous operation since 1876, the plots were established to explore the impact of crop rotation and soil treatment on corn crop yields. In 2018, The Morrow Plots Data Curation Working Group began to identify, collect and curate the various data records created over the history of the experiment. The resulting data table published here includes planting, treatment and yield data for the Morrow Plots since 1888. Please see the included codebook for a detailed explanation of the data sources and their content. This dataset will be updated as new yield data becomes available. *NOTE: While digitized and accessed through IDEALS, the physical copy of the field notebook: <a href="https://archon.library.illinois.edu/archives/index.php?p=collections/controlcard&id=11846">Morrow Plots Notebook, 1876-1913, 1967</a> is also held at the University of Illinois Archives.
keywords:
Corn; Crop Science; Experimental Fields; Crop Yields; Agriculture; Illinois; Morrow Plots
published: 2024-10-11
Zinnen, Jack; Barak, Rebecca; Matthews, Jeffrey (2024): Data for Influence of ecological characteristics and phylogeny on native plant species’ commercial availability. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1143125_V1
This is the core data for Influence of ecological characteristics and phylogeny on native plant species’ commercial availability, a manuscript pending publication in Ecological Applications. The data regard ecological characteristics, phenology, and phylogeny of plant species native to the Midwestern United States and how those factors relate to commercial availability.
keywords:
biodiversity; native plant nursery; plant trade; plant vendors; restoration
published: 2024-10-10
Zeiri, Offer; Hatzis, Katherine Marie; Gomez, Maurea; Cook, Emily A; Kincanon, Maegen; Murphy, Catherine (2024): Data for Self-Assembly of Hard Anions Around Cationic Gold Nanorods: Potential Structures for SERS. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8630796_V1
keywords:
Gold nanorods, Surface enhanced Raman spectroscopy, SERS, Polyoxometalates
published: 2024-10-08
Mersich, Ina; Bishop, Rebecca; Diaz Yucupicio, Sandra; Nobrega, Ana D.; Austin, Scott; Barger, Anne; Fick , Megan E.; Wilkins, Pamela (2024): Data for Decreased Circulating Red Cell Mass (Packed Cell Volume) Alters Viscoelastic and Traditional Plasma Coagulation Testing Results in Healthy Horses. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9153919_V1
Acepromazine was administered to healthy adult horses to induce transient anemia secondary to splenic sequestration. Data was collected at baseline (T0), 1 hour (T1) and 12 hours (T2) post acepromazine administration. Data collection included PCV, TP, CBC, fibrinogen, PT, PTT and viscoelastic coagulation profiles (VCM Vet) as well as ultrasonographic measurements of the spleen at all 3 time points.
keywords:
horse; coagulation; viscoelastic testing; anemia; acepromazine
published: 2024-10-07
Kole Aspray, Elise; Ainsworth, Elizabeth; McGrath, Jesse; McGrath, Justin; Montes, Christopher; Whetten, Andrew; Ort, Donald; Long, Stephen; Puthuval, Kannan; Mies, Timothy; Bernacchi, Carl; DeLucia, Evan; Dalsing, Bradley; Leakey, Andrew; Li, Shuai; Herriott, Jelena; Miglietta, Franco (2024): SoyFACE Fumigation Data Files. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3496460_V4
This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. This V4 contains new experimental data files, hourly fumigation files, and weather/ambient files for 2022 and 2023, since the original dataset only included files for 2001-2021. The MATLAB code has also been updated for efficiency, and explanatory files have been updated accordingly. Below are new changes in V4: - The "SoyFACE Plot Information 2001 to 2021" file is renamed to “SoyFACE ring information 2001 to 2023.xlsx”. Data for 2022 and 2023 were added. File contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - The "SoyFACE 1-Minute Fumigation Data Files" were updated to contain sub-folders for each year of the experiments (2001-2023), each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments ("SoyFACE Hourly Fumigation Data Files" folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments ("Hourly Weather and Ambient Data Files" folder which has also been updated to include 2022 and 2023 data). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - “Rings.xlsx” is new in this version. This file lists the rings and treatments used in each year of the SoyFACE experiments between 2001 and 2023 and is used in several of the MATLAB codes. - “CMI Weather Data Explanation.docx” is newly added. This file contains specific information about the processing of raw weather data, which is used in the hourly weather and ambient data files. - Files that were in RAR format in V3 are now updated and saved as ZIP format, including: Hourly Weather and Ambient Data Files.zip , SoyFACE 1-Minute Fumigation Data Files.zip , SoyFACE Hourly Fumigation Data Files.zip, and Matlab Files.zip. - The "Fumigation Target Percentages" file was updated to add data for 2022 and 2023. This file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The "Matlab Files" folder contains custom code (Aspray, E.K.) that was used to clean the "SoyFACE 1-Minute Fumigation Data" files and to generate the "SoyFACE Hourly Fumigation Data" and "Fumigation Target Percentages" files. Code information can be found in the various "Explanation" files. The Matlab code changes are as follows: 1. “Data_Issues_Finder.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 2. “Data_Issues_Finder_all.m” code is new. This code is the same as the “Data_Issues_Finder.m” code except that it identifies all CO2 and O3 repeats. In contrast, the “Data_Issues_Finder.m” code only identifies CO2 and O3 repeats that occur when the fumigation system is turned on. 3. “Target_Yearly.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 4. “HourlyFumCode.m” code is new. This code uses the “Rings.xlsx” file to gather ring and treatment information based on the contents of the file instead of the user needing to define these values explicitly. This code also defines a list of all ring folders for the year selected and runs the hourly code for each ring, instead of the user having to run the hourly code for each ring individually. Finally, the code generates two dialog boxes for the user, one which allows user to specify whether they want the hourly code to be run for 1-minute fumigation files or 1-minute ambient files, and another which allows user to specify whether they would like the hourly fumigation averages to be replaced with hourly ambient averages when the fumigation system is turned off. 5. “HourlyDataFun.m” code was changed to run either “HourlyData.m” code or “HourlyDataAmb.m” code, depending on user input in the first dialog box. 6. “HourlyData.m” code was changed to replace hourly fumigation averages with hourly ambient averages when the fumigation system is turned off, depending on user input in the second dialog box. 7. “HourlyDataAmb.m” code is new. This code is similar to “HourlyData.m” code but is used to calculate hourly averages for 1-minute ambient files instead 1-minute fumigation files. 8. “batch.m” code was changed to account for new function input variables in “HourlyDataFun.m” code, along with adding header columns for “FumOutput.xlsx” and “AmbOutput.xlsx” output files generated by “HourlyData.m” and “HourlyDataAmb.m” code. - Finally, the " * Explanation" files contain information about the column names, units of measurement, steps needed to use Matlab code, and other pertinent information for each data file. Some of them have been updated to reflect the current change of data.
keywords:
SoyFACE; agriculture; agricultural; climate; climate change; atmosphere; atmospheric change; CO2; carbon dioxide; O3; ozone; soybean; fumigation; treatment
published: 2024-08-12
Hartman, Jordan H; Davis, Mark A; Iacaruso, Nicholas J; Tiemann, Jeremy S; Larson, Eric R (2024): Data for Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7837995_V2
Data associated with the manuscript "Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies." by Jordan H. Hartman, Mark A. Davis, Nicholas J. Iacaruso, Jeremy S. Tiemann, Eric R. Larson. For this project, we sampled six locations in Michigan and Illinois for Eastern and Western Banded Killifish and primary consumers. Using stable isotope analysis we found that Eastern Banded Killifish had higher variance in littoral dependence and trophic position than Western Banded Killifish, but both stable isotope and gut content metabarcoding analyses revealed an overlap in the diet composition and trophic position between the subspecies. This dataset provides the sampling locations, accession numbers for gut content metabarcoding data from the National Center for Biotechnology Information Sequence Read Archive, the assignment of each family used in the gut content metabarcoding analysis as littoral, pelagic, terrestrial, or parasite. and the raw stable isotope data from University of California Davis.
keywords:
non-game fish; invasive species; imperiled species; stable isotope analysis; gut content metabarcoding
published: 2024-07-01
Edmonds, Devin; Andriantsimanarilafy, Raphali; Crottini, Angelica; Dreslik, Michael; Newton-Youens, Jade; Andoniana, Ramahefason; Christian, Randrianantoandro; Andreone, Franco (2024): Data and code for estimating population sizes, annual survival, and inferring absence of the frog Mantella cowanii. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0681943_V1
This data and code accompany the manuscript "Small population size and possible extirpation of the threatened Malagasy poison frog Mantella cowanii". The data were collected using photograph capture-recapture at three sites in the central highlands of Madagascar. In Part 1, the script implements robust design capture-mark-recapture models in program MARK through the RMark interface to estimate population sizes and annual survival probabilities. In Part 2, it estimates the number of surveys needed to infer absence at sites where we did not detect the frog.
keywords:
abundance; amphibian; capture-recapture
published: 2024-10-01
Li, Shengyun; Wu, Wen-Yen; Liao, Ling-Hsiu; Berenbaum, May (2024): Data for Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1147122_V1
This dataset is associated with the manuscript "Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment" This dataset includes 2 Excel files: 1) raw_data_bioassay.xlsx: this file contains the raw data for waxworm bioassay. There are 2 worksheets within this file: - LC50: raw data for measuring LC50 in the laboratory and field strain of Galleria mellonella. - RGR: Relative Growth Rate, raw data for measuring body weight of field strain of Galleria mellonella . 2) raw-data_RT-qPCR.xlsx: this file contains raw data (Ct value) of RT-qPCR.
keywords:
Apis mellifera; cytochrome P450; honey bee; pesticide; waxworm
published: 2024-09-16
Wu, Steven; Smith, Hannah (2024): Data on Controversies in Electric Vehicle Batteries. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9365647_V1
This dataset describes an analysis of research documents about the debate between hydrogen fuel cells and lithium-ion batteries within the context of electric vehicles. To create this dataset, we first analyzed news articles on the topic of sustainable development. We searched for related science using keywords in Google Scholar. We then identified subtopics and selected one specific subtopic: electric vehicles. We started to identify positions and players about electric vehicles [1]. Within electric vehicles, we started searching in OpenAlex for a topic of reasonable size (about 300 documents) related to a scientific or technical debate. We narrowed to electric vehicles and batteries, then trained a cluster model [2] on OpenAlex’s keywords to develop some possible search queries, and chose one. Our final search query (May 7, 2024) returned 301 document in OpenAlex: Title & abstract includes: Electric Vehicle + Hydrogen + Battery filter is Lithium-ion Battery Management in Electric Vehicle We used a Python script and the Scopus API to find missing abstracts and DOIs [3]. To identify relevant documents, we used a combination of Abstractkr [4] and manual screening. As a starting point for Abstractkr [4], one person manually screened 200 documents by checking the abstracts for “hydrogen fuel cells” and “battery comparisons”. Then we used Abstractkr [4] to predict the relevance of the remaining documents based on the title, abstract, and keywords. The settings we used were single screening, ordered by most likely to be relevant, and 0 pilot size. We set a threshold of 0.6 for the predictions. After screening and predictions, 176 documents remained
keywords:
controversy mapping; sustainable development; evidence synthesis; OpenAlex; Abstrackr; Scopus; meta-analysis; electric vehicle; hydrogen fuel cells; battery