Datasets

These data were collected for an experiment examining effects of neonicotinoid (clothianidin) presence on hover fly (Diptera: Syrphidae) behavior. Hover flies of two species (Eristalis arbustorum and Toxomerus marginatus) were offered a choice to feed on artificial flowers laced with sucrose solution that was either contaminated (CLO) or not contaminated (CON) with clothianidin. Two different concentrations of clothianidin in 0.5 M sucrose solution were tested: 2.5 ppb and 150 ppb. We conducted four sets of 10 trials, each trial set examining a different combination of species and clothianidin dose. Across 6 hours of video for each trial we recorded 1) number of visits to each flower that resulted in feeding, and 2) amount of time spent feeding during each visit. We found that while neither species fed significantly longer on either of the solutions, E. arbustorum appeared to avoid flowers with clothianidin particularly at high rates. In the paper, we attribute this avoidance response, partially, to hover fly-visible spectral differences between the two flower choices and discuss potential implications for field and lab-based studies. In the enclosed zip file we have included all data for this project and code scripts from R. * Note: Data folder contains 4 files (instead of 6 as mentioned in Readme): e.tenax_photoreceptors.csv; hoverfly_data_UPDATE.csv; number_visits_UPDATE.csv; and Original 2018 hover fly choice test data_Clem2020.xlsx

Citation context annotation for papers citing retracted paper Matsuyama 2005 (RETRACTED: Matsuyama W, Mitsuyama H, Watanabe M, Oonakahara KI, Higashimoto I, Osame M, Arimura K. Effects of omega-3 polyunsaturated fatty acids on inflammatory markers in COPD. Chest. 2005 Dec 1;128(6):3817-27.), retracted in 2008 (Retraction in: Chest (2008) 134:4 (893) <a href="https://doi.org/10.1016/S0012-3692(08)60339-6">https://doi.org/10.1016/S0012-3692(08)60339-6<a/> ). This is part of the supplemental data for Jodi Schneider, Di Ye, Alison Hill, and Ashley Whitehorn. "Continued Citation of a Fraudulent Clinical Trial Report, Eleven Years after it was retracted for Falsifying Data" [R&R under review with Scientometrics]. Overall we found 148 citations to the retracted paper from 2006 to 2019, However, this dataset does not include the annotations described in the 2015. in Ashley Fulton, Alison Coates, Marie Williams, Peter Howe, and Alison Hill. "Persistent citation of the only published randomized controlled trial of omega-3 supplementation in chronic obstructive pulmonary disease six years after its retraction." Publications 3, no. 1 (2015): 17-26. In this dataset 70 new and newly found citations are listed: 66 annotated citations and 4 pending citations (non-annotated since we don't have full-text). "New citations" refer to articles published from March 25, 2014 to 2019, found in Google Scholar and Web of Science. "Newly found citations" refer articles published 2006-2013, found in Google Scholar and Web of Science, but not previously covered in Ashley Fulton, Alison Coates, Marie Williams, Peter Howe, and Alison Hill. "Persistent citation of the only published randomised controlled trial of omega-3 supplementation in chronic obstructive pulmonary disease six years after its retraction." Publications 3, no. 1 (2015): 17-26. NOTES: This is Unicode data. Some publication titles & quotes are in non-Latin characters and they may contain commas, quotation marks, etc. FILES/FILE FORMATS Same data in two formats: 2006-2019-new-citation-contexts-to-Matsuyama.csv - Unicode CSV (preservation format only) 2006-2019-new-citation-contexts-to-Matsuyama.xlsx - Excel workbook (preferred format) ROW EXPLANATIONS 70 rows of data - one citing publication per row COLUMN HEADER EXPLANATIONS Note - processing notes Annotation pending - Y or blank Year Published - publication year ID - ID corresponding to the network analysis. See Ye, Di; Schneider, Jodi (2019): Network of First and Second-generation citations to Matsuyama 2005 from Google Scholar and Web of Science. University of Illinois at Urbana-Champaign. <a href="https://doi.org/10.13012/B2IDB-1403534_V2">https://doi.org/10.13012/B2IDB-1403534_V2</a> Title - item title (some have non-Latin characters, commas, etc.) Official Translated Title - item title in English, as listed in the publication Machine Translated Title - item title in English, translated by Google Scholar Language - publication language Type - publication type (e.g., bachelor's thesis, blog post, book chapter, clinical guidelines, Cochrane Review, consumer-oriented evidence summary, continuing education journal article, journal article, letter to the editor, magazine article, Master's thesis, patent, Ph.D. thesis, textbook chapter, training module) Book title for book chapters - Only for a book chapter - the book title University for theses - for bachelor's thesis, Master's thesis, Ph.D. thesis - the associated university Pre/Post Retraction - "Pre" for 2006-2008 (means published before the October 2008 retraction notice or in the 2 months afterwards); "Post" for 2009-2019 (considered post-retraction for our analysis) Identifier where relevant - ISBN, Patent ID, PMID (only for items we considered hard to find/identify, e.g. those without a DOI-based URL) URL where available - URL, ideally a DOI-based URL Reference number/style - reference Only in bibliography - Y or blank Acknowledged - If annotated, Y, Not relevant as retraction not published yet, or N (blank otherwise) Positive / "Poor Research" (Negative) - P for positive, N for negative if annotated; blank otherwise Human translated quotations - Y or blank; blank means Google scholar was used to translate quotations for Translated Quotation X Specific/in passing (overall) - Specific if any of the 5 quotations are specific [aggregates Specific / In Passing (Quotation X)] Quotation 1 - First quotation (or blank) (includes non-Latin characters in some cases) Translated Quotation 1 - English translation of "Quotation 1" (or blank) Specific / In Passing (Quotation 1) - Specific if "Quotation 1" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 1) - Methods; Results; or Methods and Results - blank if "Quotation 1" not specific, no associated quotation, or not yet annotated Quotation 2 - Second quotation (includes non-Latin characters in some cases) Translated Quotation 2 - English translation of "Quotation 2" Specific / In Passing (Quotation 2) - Specific if "Quotation 2" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 2) - Methods; Results; or Methods and Results - blank if "Quotation 2" not specific, no associated quotation, or not yet annotated Quotation 3 - Third quotation (includes non-Latin characters in some cases) Translated Quotation 3 - English translation of "Quotation 3" Specific / In Passing (Quotation 3) - Specific if "Quotation 3" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 3) - Methods; Results; or Methods and Results - blank if "Quotation 3" not specific, no associated quotation, or not yet annotated Quotation 4 - Fourth quotation (includes non-Latin characters in some cases) Translated Quotation 4 - English translation of "Quotation 4" Specific / In Passing (Quotation 4) - Specific if "Quotation 4" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 4) - Methods; Results; or Methods and Results - blank if "Quotation 4" not specific, no associated quotation, or not yet annotated Quotation 5 - Fifth quotation (includes non-Latin characters in some cases) Translated Quotation 5 - English translation of "Quotation 5" Specific / In Passing (Quotation 5) - Specific if "Quotation 5" refers to methods or results of the Matsuyama paper (or blank) What is referenced from Matsuyama (Quotation 5) - Methods; Results; or Methods and Results - blank if "Quotation 5" not specific, no associated quotation, or not yet annotated Further Notes - additional notes

This data describes habitat use, availability, landscape level influences, and daily movement of dabbling ducks in the Wabash River Valley of southeastern Illinois and southwestern Indiana. It contains triangulated locations of individual ducks, associated habitat assignments of those locations, flood survey data to determine water availability, and randomly generated points to assess landscape level questions.

This dataset includes two data files that provide the time series (Jul. - Sep. 2017) data of sun-induced chlorophyll fluorescence (SIF_760) collected under sunny conditions at two maize sites (one rainfed and the other irrigated) in Nebraska in 2017. Data contain 392 SIF_760 records at the rainfed site and 707 records at the irrigated site. The timestamp uses local standard time. Data are available for the sunny conditions from 8 am to 5 pm (corresponding to 9 am to 6 pm local time) throughout the study period.

Morphologic data of dunes in the World's big rivers. Morphologic descriptors for large dunes include: dune height, dune mean leeside angle, dune maximum leeside angle, dune wavelength, dune flow depth (at the crest), and the fractional height of the maximum slope on the leeside for each dune. Morphologic descriptors for small dunes include: dune height, dune mean leeside angle, dune maximum leeside angle, dune wavelength, and dune flow depth (at the crest).

Dataset providing calculation of a Competition Index (CI) for Late Pleistocene carnivore guilds in Laos and Vietnam and their relationship to humans. Prey mass spectra, Prey focus masses, and prey class raw data can be used to calculate the CI following Hemmer (2004). Mass estimates were calculated for each species following Van Valkenburgh (1990). Full citations to methodological papers are included as relationships with other resources

This dataset provides the raw data, code and related figures for the paper, "Channel Activation of CHSH Nonlocality"

Human annotations of randomly selected judged documents from the AP 88-89, Robust 2004, WT10g, and GOV2 TREC collections. Seven annotators were asked to read documents in their entirety and then select up to ten terms they felt best represented the main topic(s) of the document. Terms were chosen from among a set sampled from the document in question and from related documents.

We are sharing the tweet IDs of four social movements: #BlackLivesMatter, #WhiteLivesMatter, #AllLivesMatter, and #BlueLivesMatter movements. The tweets are collected between May 1st, 2015 and May 30, 2017. We eliminated the location to the United States and focused on extracting the original tweets, excluding the retweets. Recommended citations for the data: Rezapour, R. (2019). Data for: How do Moral Values Differ in Tweets on Social Movements?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9614170_V1 and Rezapour, R., Ferronato, P., and Diesner, J. (2019). How do moral values differ in tweets on social movements?. In 2019 Computer Supported Cooperative Work and Social Computing Companion Publication (CSCW’19 Companion), Austin, TX.

Supporting secondary data used in a manuscript currently in submission regarding the invasion dynamics of the asian tiger mosquito, Aedes albopictus, in the state of Illinois

Software (Matlab .m files) for the article: Lying in Wait: Modeling the Control of Bacterial Infections via Antibiotic-Induced Proviruses. The files can be used to reproduce the analysis and figures in the article.

The data set here include data from NMR, LC-MS/MS, MALDI-MS, H/D exchange MS experiments used in paper "A novel rotifer derived alkaloid paralyzes schistosome larvae and prevents infection".

This is a dataset of 1101 comments from The New York Times (May 1, 2015-August 31, 2015) that contains a mention of the stemmed words vaccine or vaxx.

Simulation data related to the paper "Mastitis risk effect on the economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study"

Genotype calls are provided for a collection of 583 Miscanthus sinensis clones across 1,108,836 loci mapped to version 7 of the Miscanthus sinensis reference genome. Sequence and alignment information for all unique RAD tags is also provided to facilitate cross-referencing to other genomes.

Data used in paper published in the Journal of Applied Ecology titled " Bee diversity in tallgrass prairies affected by management and its effects on above- and below-ground resources" Bee Community file contains info on bees sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the bee species name in the first row and all individuals recorded. Plant Community file contains info on plants sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the plant species name in the first row and all individuals recorded. Soil PC1 file contains the soil PC1 values used in the analyses. The first column contain the Tallgrass Prairie Sites sampled, the second column contains the calculated soil PC1 values.

These files contain the data presented in the manuscript entitles "Iron redox reactions can drive microtopographic variation in upland soil carbon dioxide and nitrous oxide emissions".

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 %.

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.

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.

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.

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.

This dataset contains the raw nuclear background radiation data collected in the engineering campus of University of Illinois at Urbana-Champaign. It contains three columns, x, y, and counts, which corresponds to longitude, latitude, and radiation count rate (counts per second). In addition to the original background radiation data, there are several separate files that contain the simulated radioactive sources. For more detailed README file, please refer to this documentation: <a href= "https://www.dropbox.com/s/xjhmeog7fvijml7/README.pdf?dl=0">https://www.dropbox.com/s/xjhmeog7fvijml7/README.pdf?dl=0</a>

Chronic contact exposure to realistic soil concentrations (0, 7.5, 15, and 100 ppb) of the neonicotinoid pesticide imidacloprid had species- and sex-specific effects on bee adult longevity, immature development speed, and mass. This dataset contains a life table tracking the development, mass, and deaths of a single cohort of Osmia lignaria and Megachile rotundata over the course of two summers. Other data files include files created for multi-event survival analysis to analyze the effect on development speed. Detected effects included: decreased adult longevity for female O. lignaria at the highest concentration, a trend for a hormetic effect on female M. rotundata development speed and mass (longest development time and greatest mass in the 15 ppb treatment), and decreased adult longevity and increased development speed at high imidacloprid concentrations as well as a hormetic effect on mass (lowest in the 15 ppb treatment treatment) on male M. rotundata.

The bee visitation data includes the percentage of each bee pollinator group in bee bowls and observed. The data are referenced in the article with the following citation: Bennett, A.B., Lovell, S.T. 2019. Landscape and local site variables differentially influence pollinators and pollination services in urban agricultural sites. Accepted for publication in: PLOS ONE.