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Illinois Data Bank Dataset Search Results
Dataset Search Results
published: 2020-12-07
Tian, Yuan; Smith-Bolton, Rachel (2020): Data for Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1681718_V1
This page contains the data for the publication "Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila" published in Genetics, 2020
published: 2023-08-24
Kim, Hyunchul; Zhao, Helin; van der Zande, Arend (2023): Data for Strain-resilient field-effect transistors based on wrinkled graphene/MoS2 heterostructures. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6434046_V1
This data set includes all of data related to strain-resilient FETs based on 2D heterostructures including optical images of FETs, Raman characteristics data, Transport measurement data, and AFM topography data.
keywords:
2D materials; Stretchable electronics
published: 2019-07-08
Mishra, Shubhanshu (2019): Wikipedia category embeddings - Node2Vec, Poincare, Elmo. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4551278_V1
Wikipedia category tree embeddings based on wikipedia SQL dump dated 2017-09-20 (<a href="https://archive.org/download/enwiki-20170920">https://archive.org/download/enwiki-20170920</a>) created using the following algorithms: * Node2vec * Poincare embedding * Elmo model on the category title The following files are present: * wiki_cat_elmo.txt.gz (15G) - Elmo embeddings. Format: category_name (space replaced with "_") <tab> 300 dim space separated embedding. * wiki_cat_elmo.txt.w2v.gz (15G) - Elmo embeddings. Format: word2vec format can be loaded using Gensin Word2VecKeyedVector.load_word2vec_format. * elmo_keyedvectors.tar.gz - Gensim Word2VecKeyedVector format of Elmo embeddings. Nodes are indexed using * node2vec.tar.gz (3.4G) - Gensim word2vec model which has node2vec embedding for each category identified using the position (starting from 0) in category.txt * poincare.tar.gz (1.8G) - Gensim poincare embedding model which has poincare embedding for each category identified using the position (starting from 0) in category.txt * wiki_category_random_walks.txt.gz (1.5G) - Random walks generated by node2vec algorithm (https://github.com/aditya-grover/node2vec/tree/master/node2vec_spark), each category identified using the position (starting from 0) in category.txt * categories.txt - One category name per line (with spaces). The line number (starting from 0) is used as category ID in many other files. * category_edges.txt - Category edges based on category names (with spaces). Format from_category <tab> to_category * category_edges_ids.txt - Category edges based on category ids, each category identified using the position (starting from 1) in category.txt * wiki_cats-G.json - NetworkX format of category graph, each category identified using the position (starting from 1) in category.txt Software used: * <a href="https://github.com/napsternxg/WikiUtils">https://github.com/napsternxg/WikiUtils</a> - Processing sql dumps * <a href="https://github.com/napsternxg/node2vec">https://github.com/napsternxg/node2vec</a> - Generate random walks for node2vec * <a href="https://github.com/RaRe-Technologies/gensim">https://github.com/RaRe-Technologies/gensim</a> (version 3.4.0) - generating node2vec embeddings from random walks generated usinde node2vec algorithm * <a href="https://github.com/allenai/allennlp">https://github.com/allenai/allennlp</a> (version 0.8.2) - Generate elmo embeddings for each category title Code used: * wiki_cat_node2vec_commands.sh - Commands used to * wiki_cat_generate_elmo_embeddings.py - generate elmo embeddings * wiki_cat_poincare_embedding.py - generate poincare embeddings
keywords:
Wikipedia; Wikipedia Category Tree; Embeddings; Elmo; Node2Vec; Poincare;
published: 2017-03-08
Thapa, Sita; Schroeder, Nathan; Patel, Jayna; Reuter-Carlson, Ursula (2017): Data from: Embryogenesis in the plant parasitic nematode Heterodera glycines is independent of host-derived stimulation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6946735_V2
This dataset includes early embryogenesis and post-embryonic development of Soybean cyst nematode.
keywords:
Soybean cyst nematode; Embryogenesis; Post-embryonic development
published: 2023-12-01
Hohoff, Tara; Deppe, Jill (2023): Data for little brown occupancy and associated landcover data from McHenry County, Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0365076_V1
Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.
keywords:
little brown bats; mist netting; acoustics
published: 2017-03-07
Mickalide, Harry; Fraebel, David T.; Kuehn, Seppe (2017): Sample video and supplementary code for cell tracking. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4912922_V2
This is a sample 5 minute video of an E coli bacterium swimming in a microfluidic chamber as well as some supplementary code files to be used with the Matlab code available at https://github.com/dfraebel/CellTracking
published: 2016-12-14
Brown, Patrick (2016): 14IL008,16IL003,16IL007. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6648634_V1
published: 2017-09-19
Nute, Michael; Jed, Chou; Molloy, Erin K.; Warnow, Tandy (2017): Data from: The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7735354_V1
published: 2023-07-27
Feng, Ling; Takiya, Daniela; Krishnankutty, Sindhu; Dietrich, Christopher; Zhang, Yalin (2023): NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0855589_V1
The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). 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 257 taxa (species) and 2995 characters (nucleotide positions), 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 remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. 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 data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.
keywords:
Insect; leafhopper; dispersal; vicariance; evolution
published: 2022-03-09
Rapti, Zoi; Rivera Quinones, Vanessa; Stewart Merrill, Tara (2022): Codes for the analysis of an eco-immunological disease-transmission mathematical model. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1686840_V1
MATLAB files for the analysis of an ODE model for disease transmission. The codes may be used to find equilibrium points, study transient dynamics, evaluate the basic reproductive number (R0), and simulate the model when parameters depend on the independent variables. In addition, the codes may be used to perform local sensitivity analysis of R0 on the model parameters.
published: 2020-02-12
Price, Edward; Spyreas, Greg; Matthews, Jeffrey (2020): Biotic homogenization of wetland vegetation in the conterminous United States driven by Phalaris arundinacea and anthropogenic disturbance. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7128075_V1
This is the dataset used in the Landscape Ecology publication of the same name. This dataset consists of the following files: NWCA_Int_Veg.txt NWCA_Reg_Veg.txt NWCA_Site_Attributes.txt NWCA_Int_Veg.txt is a site and plot by species matrix. Column labeled SITES consists of site IDs. Column labeled Plots consist of Plot ID numbers. All other columns represent species abundances (estimates of percent cover, summed across five plots). NWCA_Reg_Veg.txt is a site by species matrix of species abundances. Column labeled SITES consist of site IDs. All other columns represent species abundances (estimates of percent cover within individual plots). NWCA_Site_Attributes.txt is a matrix of site attributes. Column labeled SITES consist of site IDs. Column labeled AA_CENTER_LAT consist of latitudinal coordinates for the Assessment Area center point in decimal degrees. Column labeled AA_CENTER_LONG consist of longitudinal coordinates for the Assessment Area center point in decimal degrees. Column REFPLUS_NWCA represents disturbance gradient classes including MIN (minimally disturbed), L (least disturbed), I (intermediate), M (most disturbed). Column REFPLUS_NWCA2 represents revised disturbance gradient classes based on protocols described in the article. These revised classes were used for analysis. Column labeled STRESS_HEAVYMETAL represents heavy metal stressor classes, used to ascertain which wetlands were missing soil data. Classes in the STRESS_HEAVYMETAL column include Low, Moderate, High, and Missing. Sites with Missing STRESS_HEAVYMETAL classes were removed from analysis. More information about this dataset: All of the data used in this analysis was gathered from the National Wetlands Condition Assessment. Wetland surveys were conducted from 4/4/2011 to 11/2/2011. The entire National Wetlands Condition Assessment Dataset, which includes 3640 unique taxonomic identities of plants, can be found at: https://www.epa.gov/national-aquatic-resource-surveys/data-national-aquatic-resource-surveys
keywords:
Anthropogenic disturbance; β-Diversity; Biotic homogenization; Phalaris arundinacea; reed canary grass; Wetlands
published: 2022-02-11
Hoang, Khanh Linh; Schneider, Jodi; Kansara, Yogeshwar (2022): Error Analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3407079_V3
The data 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 "Evaluation of publication type tagging as a strategy to screen randomized controlled trial articles in preparing systematic reviews". Change made in this V3 is that the data is divided into two parts: - Error Analysis of 44 Low Scoring Articles with MEDLINE RCT Publication Type. - Error Analysis of 244 Low Scoring Articles without MEDLINE RCT Publication Type.
keywords:
Cochrane reviews; automation; randomized controlled trial; RCT; systematic reviews
published: 2024-03-27
Zheng, Heng; Schneider, Jodi (2024): Dataset for "Arguing about Controversial Science in the News: Does Epistemic Uncertainty Contribute to Information Disorder?". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4781172_V1
To gather news articles from the web that discuss the Cochrane Review, we used Altmetric Explorer from Altmetric.com and retrieved articles on August 1, 2023. We selected all articles that were written in English, published in the United States, and had a publication date prior to March 10, 2023 (according to the “Mention Date” on Altmetric.com). This date is significant as it is when Cochrane issued a statement about the "misleading interpretation" of the Cochrane Review. The collection of news articles is presented in the Altmetric_data.csv file. The dataset contains the following data that we exported from Altmetric Explorer: - Publication date of the news article - Title of the news article - Source/publication venue of the news article - URL - Country We manually checked and added the following information: - Whether the article still exists - Whether the article is accessible - Whether the article is from the original source We assigned MAXQDA IDs to the news articles. News articles were assigned the same ID when they were (a) identical or (b) in the case of Article 207, closely paraphrased, paragraph by paragraph. Inaccessible items were assigned a MAXQDA ID based on their "Mention Title". For each article from Altmetric.com, we first tried to use the Web Collector for MAXQDA to download the article from the website and imported it into MAXQDA (version 22.7.0). If an article could not be retrieved using the Web Collector, we either downloaded the .html file or in the case of Article 128, retrieved it from the NewsBank database through the University of Illinois Library. We then manually extracted direct quotations from the articles using MAXQDA. We included surrounding words and sentences, and in one case, a news agency’s commentary, around direct quotations for context where needed. The quotations (with context) are the positions in our analysis. We also identified who was quoted. We excluded quotations when we could not identify who or what was being quoted. We annotated quotations with codes representing groups (government agencies, other organizations, and research publications) and individuals (authors of the Cochrane Review, government agency representatives, journalists, and other experts such as epidemiologists). The MAXQDA_data.csv file contains excerpts from the news articles that contain the direct quotations we identified. For each excerpt, we included the following information: - MAXQDA ID of the document from which the excerpt originates; - The collection date and source of the document; - The code with which the excerpt is annotated; - The code category; - The excerpt itself.
keywords:
altmetrics; MAXQDA; polylogue analysis; masks for COVID-19; scientific controversies; news articles
published: 2018-03-01
Chiavacci, Scott J.; Benson, Thomas J.; Ward, Michael P. (2018): Linking landscape composition to predator-specific nest predation requires examining multiple landscape scales. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5437353_V1
Data were used to analyze patterns in predator-specific nest predation on shrubland birds in Illinois as related to landscape composition at multiple landscape scales. Data were used in a Journal of Applied Ecology research paper of the same name. Data were collected between 2011 and 2014 at sites in east-central and northeastern Illinois, USA as part of a Ph.D. research project on the relationship between avian nest predation and landscape characteristics, and how nest predation affects adult and nestling bird behavior.
keywords:
nest predation; avian ecology; land cover; landscape composition; landscape scale; nest camera; nest survival; predator-specific mortality; scale-dependence; scrubland; shrub-nesting bird
published: 2021-10-15
Swenson, Gary (2021): SABER Intra-annual Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6186460_V1
Atomic oxygen densities in the MLT, averaged for 2002-2018 for 26, 14 day periods, beginning January 1.
keywords:
SABER data
published: 2018-12-20
Dong, Xiaoru; Xie, Jingyi; Hoang, Linh (2018): Words_Selected_by_Manual_Analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8659314_V1
File Name: WordsSelectedByManualAnalysis.csv Data Preparation: Xiaoru Dong, Linh Hoang Date of Preparation: 2018-12-14 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: this file contains the list of 407 informative words reselected from the 1655 words by manual analysis. In particular, from the 1655 words that we got from information gain feature selection, we then manually read and eliminated the domain specific words. The remaining words then were selected into the "Manual Analysis Words" as the results. Notes: Even though the list of words in this file was selected manually. However, 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.
keywords:
Inclusion criteria; Randomized controlled trials; Machine learning; Systematic reviews
published: 2021-12-31
Lyons, Lee Ann; Mateus-Pinilla, Nohra; Smith, Rebecca (2021): Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6268941_V1
We developed and delivered in-person training at local health department offices in six of the seven Illinois Department of Public Health “health regions” between April-May of 2019. Pre-, post-, and six-month follow-up questionnaires on knowledge, attitudes, and practices with regards to tick surveillance were administered to training participants.
keywords:
ticks; survey; tick-borne disease; public health
published: 2021-10-15
Swenson, Gary (2021): SCIAMACHY IAV Oxygen data, 2002-2012. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9526770_V1
Atomic oxygen data from SCIAMACHY, for the MLT, 2002-2012, averaged for 26, 14 day periods, beginning January 1.
keywords:
SCIAMACHY data
published: 2023-09-20
Chase, Marissa H. ; Charles, Brian; Harmon-Threatt, Alexandra; Fraterrigo, Jennifer (2023): Diverse forest management strategies support functionally and temporally distinct bee communities. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8891496_V1
Dataset includes bee trait information and species abundance information for bees collected at 29 forests plots in southern Illinois, USA. Plots are located within three public land sites. Environmental data were also collected for each of the 29 plots.
keywords:
wild bees; forest management; functional traits
published: 2023-09-19
Salami, Malik; Lee, Jou; Schneider, Jodi (2023): Stopwords and keywords for manual field assignment for the STI 2023 paper Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8847584_V2
We used the following keywords files to identify categories for journals and conferences not in Scopus, for our STI 2023 paper "Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science". The first four text files each contains keywords/content words in the form: 'keyword1', 'keyword2', 'keyword3', .... The file title indicates the name of the category: file1: healthscience_words.txt file2: lifescience_words.txt file3: physicalscience_words.txt file4: socialscience_words.txt The first four files were generated from a combination of software and manual review in an iterative process in which we: - Manually reviewed venue titles were not able to automatically categorize using the Scopus categorization or extending it as a resource. - Iteratively reviewed uncategorized venue titles to manually curate additional keywords as content words indicating a venue title could be classified in the category healthscience, lifescience, physicalscience, or socialscience. We used English content words and added words we could automatically translate to identify content words. NOTE: Terminology with multiple potential meanings or contain non-English words that did not yield useful automatic translations e.g., (e.g., Al-Masāq) were not selected as content words. The fifth text file is a list of stopwords in the form: 'stopword1', 'stopword2, 'stopword3', ... file5: stopwords.txt This file contains manually curated stopwords from venue titles to handle non-content words like 'conference' and 'journal,' etc. This dataset is a revision of the following dataset: Version 1: Lee, Jou; Schneider, Jodi: Keywords for manual field assignment for Assessing the agreement in retraction indexing across 4 multidisciplinary sources: Crossref, Retraction Watch, Scopus, and Web of Science. University of Illinois at Urbana-Champaign Data Bank. Changes from Version 1 to Version 2: - Added one author - Added a stopwords file that was used in our data preprocessing. - Thoroughly reviewed each of the 4 keywords lists. In particular, we added UTF-8 terminology, removed some non-content words and misclassified content words, and extensively reviewed non-English keywords.
keywords:
health science keywords; scientometrics; stopwords; field; keywords; life science keywords; physical science keywords; science of science; social science keywords; meta-science; RISRS
published: 2018-09-26
Cure, Anne; Calla, Bernarda; Berenbaum, May; Schuler, Mary (2018): Pastinaca sativa P450s - CYP71AJ4 variants in New Zealand and North America. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2087040_V1
Nucleotide sequences from wild parsnip CYP71AJ4 (angelic in synthase. <a href ="https://www.ncbi.nlm.nih.gov/nuccore/EF191021">Genbank EF191021</a>) were obtained by Sanger sequencing. Seeds from individual plants from different populations were harvested to obtain corresponding cDNA. The cDNA was cloned and directly sequenced. Aminoacid translations were obtained using standard codon usage. Alignments of CYP71AJ4 sequences (involved in angular furanocoumarin biosynthesis) with as the reference sequence. Consistent amino acid variabilities were found between some populations. The relationship between sequencing variability and selective pressure is not yet known.
keywords:
Pastinaca sativa; parsnip; furanocoumarins; psoralen
published: 2021-12-09
Burnham, Mark; Simon, Sandra; Lee, DK; Kent, Angela; DeLucia, Evan; Yang, Wendy (2021): Data for Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3696813_V1
These data were collected in 2018 and 2019 at the University of Illinois Energy Farm (N 40.063607, W 88.206926). During each growing season, bulk and rhizosphere soil were collected from replicate Sorghum bicolor nitrogen use efficiency trial plots at three separate time points (approximately July 1, August 1, and September 1). We measured soil moisture, pH, soil nitrate and ammonium, potential nitrification, potential denitrification, and extracted and sequenced the V4 region of the 16S rRNA gene for microbial community analysis. All microbial sequence data is archived in the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (accession number SRP326979, project number PRJNA741261).
keywords:
soil nitrogen; nitrification; nitrogen cycle; sorghum; bioenergy; Center for Advanced Bioenergy and Bioproducts Innovation
published: 2018-10-24
Ugarte, Carmen M.; Wander, Michelle M. (2018): Soil organic carbon (SOC) response to soil management practices in the continental United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3074701_V1
This dataset was compiled between 2010 and 2011 from data published in the scientific literature from articles evaluating the influence of cropping systems and soil management practices on soil organic Carbon. We used the Thomas Reuter Web of Science database and by reviewed the reference sections of key peer-reviewed articles. Articles included in the database presented results from field sites within the continental United States.
keywords:
Cropping systems; soil management; soil organic carbon; soil quality.
published: 2019-01-07
Carlstone, Jamie; Kenfield, Ayla Stein; Norman, Michael; Wilkin, John (2019): US books 1931 to 1933 All Parts Transcription from Vendor. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0873454_V1
Vendor transcription of the Catalogue of Copyright Entries, Part 1, Group 1, Books: New Series, Volume 29 for the Year 1932. This file contains all of the entries from the indicated volume.
keywords:
copyright; Catalogue of Copyright Entries; Copyright Office
published: 2023-12-13
Tiemann, Jeremy (2023): Distribution of nonindigenous Basket Clams (Corbicula spp.) in Mexico. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9221608_V1
Corbicula spp. are one of the most prolific aquatic invasive species in the world and can have negative effects on aquatic ecosystems. We performed qualitative field surveys, examined literature accounts and natural history museum holdings, and accessed citizen science data sources to document the distribution of Corbicula in Mexico and shared drainages. Through 26 publications (N = 127 records), 312 museum holdings, and 446 iNaturalist records, we documented 885 records pertaining to Corbicula in Mexico and shared drainages. The first record of the species in Mexico was in 1969, and it has since been reported from 26 of the 32 Mexican states and most of the major river basins throughout the country. However, we suggest Corbicula is more prevalent in Mexico than we report in this work as it is often under sampled / under reported.
keywords:
Corbicula; exotic species; invasive species; Asian Clams; Bivalvia; freshwater systems