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Schneider, Jodi; Ye, Di; Hill, Alison (2020): Second-generation citation context analysis (2010-2019) to retracted paper Matsuyama 2005. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3331845_V2
Citation context annotation. This dataset is a second version (V2) and part of the supplemental data for Jodi Schneider, Di Ye, Alison Hill, and Ashley Whitehorn. (2020) "Continued post-retraction citation of a fraudulent clinical trial report, eleven years after it was retracted for falsifying data". Scientometrics. In press, DOI: 10.1007/s11192-020-03631-1 Publications were selected by examining all citations to the retracted paper Matsuyama 2005, and selecting the 35 citing papers, published 2010 to 2019, which do not mention the retraction, but which mention the methods or results of the retracted paper (called "specific" in Ye, Di; Hill, Alison; Whitehorn (Fulton), Ashley; Schneider, Jodi (2020): Citation context annotation for new and newly found citations (2006-2019) to retracted paper Matsuyama 2005. University of Illinois at Urbana-Champaign. <a href="https://doi.org/10.13012/B2IDB-8150563_V1">https://doi.org/10.13012/B2IDB-8150563_V1</a> ). The annotated citations are second-generation citations to the 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/> ). <b>OVERALL DATA for VERSION 2 (V2)</b> FILES/FILE FORMATS Same data in two formats: 2010-2019 SG to specific not mentioned FG.csv - Unicode CSV (preservation format only) - same as in V1 2010-2019 SG to specific not mentioned FG.xlsx - Excel workbook (preferred format) - same as in V1 Additional files in V2: 2G-possible-misinformation-analyzed.csv - Unicode CSV (preservation format only) 2G-possible-misinformation-analyzed.xlsx - Excel workbook (preferred format) <b>ABBREVIATIONS: </b> 2G - Refers to the second-generation of Matsuyama FG - Refers to the direct citation of Matsuyama (the one the second-generation item cites) <b>COLUMN HEADER EXPLANATIONS </b> File name: 2G-possible-misinformation-analyzed. Other column headers in this file have same meaning as explained in V1. The following are additional header explanations: Quote Number - The order of the quote (citation context citing the first generation article given in "FG in bibliography") in the second generation article (given in "2G article") Quote - The text of the quote (citation context citing the first generation article given in "FG in bibliography") in the second generation article (given in "2G article") Translated Quote - English translation of "Quote", automatically translation from Google Scholar Seriousness/Risk - Our assessment of the risk of misinformation and its seriousness 2G topic - Our assessment of the topic of the cited article (the second generation article given in "2G article") 2G section - The section of the citing article (the second generation article given in "2G article") in which the cited article(the first generation article given in "FG in bibliography") was found FG in bib type - The type of article (e.g., review article), referring to the cited article (the first generation article given in "FG in bibliography") FG in bib topic - Our assessment of the topic of the cited article (the first generation article given in "FG in bibliography") FG in bib section - The section of the cited article (the first generation article given in "FG in bibliography") in which the Matsuyama retracted paper was cited
citation context annotation; retraction; diffusion of retraction; second-generation citation context analysis
Han, Kanyao; Yang, Pingjing; Mishra, Shubhanshu; Diesner, Jana (2020): WikiCSSH - Computer Science Subject Headings from Wikipedia. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0424970_V1
# WikiCSSH If you are using WikiCSSH please cite the following: > Han, Kanyao; Yang, Pingjing; Mishra, Shubhanshu; Diesner, Jana. 2020. “WikiCSSH: Extracting Computer Science Subject Headings from Wikipedia.” In Workshop on Scientific Knowledge Graphs (SKG 2020). https://skg.kmi.open.ac.uk/SKG2020/papers/HAN_et_al_SKG_2020.pdf > Han, Kanyao; Yang, Pingjing; Mishra, Shubhanshu; Diesner, Jana. 2020. "WikiCSSH - Computer Science Subject Headings from Wikipedia". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0424970_V1 Download the WikiCSSH files from: https://doi.org/10.13012/B2IDB-0424970_V1 More details about the WikiCSSH project can be found at: https://github.com/uiuc-ischool-scanr/WikiCSSH This folder contains the following files: WikiCSSH_categories.csv - Categories in WikiCSSH WikiCSSH_category_links.csv - Links between categories in WikiCSSH Wikicssh_core_categories.csv - Core categories as mentioned in the paper WikiCSSH_category_links_all.csv - Links between categories in WikiCSSH (includes a dummy category called <ROOT> which is parent of isolates and top level categories) WikiCSSH_category2page.csv - Links between Wikipedia pages and Wikipedia Categories in WikiCSSH WikiCSSH_page2redirect.csv - Links between Wikipedia pages and Wikipedia page redirects in WikiCSSH This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit <a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a> or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
wikipedia; computer science;
Jetti, Yaswanth Sai; Dunn, Alison C. (2020): The matrix of influence coefficients due to pyramidal distribution on an overlapping hexagonal grid. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0925335_V1
This data set is a matrix of values. The element in the row "i" and the column "j" denotes the influence of hexagonal pyramidal distribution at node "i" on the node "j". The size of the matrix is 16641x16641. This matrix corresponds to a 129x129 grid. Influence coefficient matrix on a smaller grid can be obtained by appropriately choosing the elements from the bigger matrix.
Althaus, Scott; Berenbaum, May; Jordan, Jenna; Shalmon, Dan (2020): Replication Data for "No buzz for bees: Media coverage of pollinator decline". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4237085_V1
These data and code enable replication of the findings and robustness checks in "No buzz for bees: Media coverage of pollinator decline," published in Proceedings of the National Academy of Sciences of the United States of America (2020)". In this paper, we find that although widespread declines in insect biomass and diversity are increasing concern within the scientific community, it remains unclear whether attention to pollinator declines has also increased within information sources serving the general public. Examining patterns of journalistic attention to the pollinator population crisis can also inform efforts to raise awareness about the importance of declines of insect species providing ecosystem services beyond pollination. We used the Global News Index developed by the Cline Center for Advanced Social Research at the University of Illinois at Urbana-Champaign to track news attention to pollinator topics in nearly 25 million news items published by two American national newspapers and four international wire services over the past four decades. We provide a link to documentation of the Global News Index in the "relationships with articles, code, o. We found vanishingly low levels of attention to pollinator population topics relative to coverage of climate change, which we use as a comparison topic. In the most recent subset of ~10 million stories published from 2007 to 2019, 1.39% (137,086 stories) refer to climate change/global warming, while only 0.02% (1,780) refer to pollinator populations in all contexts and just 0.007% (679) refer to pollinator declines. Substantial increases in news attention were detectable only in U.S. national newspapers. We also find that while climate change stories appear primarily in newspaper “front sections”, pollinator population stories remain largely marginalized in “science” and “back section” reports. At the same time, news reports about pollinator populations increasingly link the issue to climate change, which might ultimately help raise public awareness to effect needed policy changes.
News Coverage; Text Analytics; Insects; Pollinator; Cline Center; Cline Center for Advanced Social Research; political; social; political science; Global News Index; Archer; news; mass communication; journalism
Zinnen, Jack; Spyreas, Greg; Erdős, László; Berg, Christian; Matthews, Jeffrey (2020): Expert-based measures of human impact to vegetation- Bibliographic analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9374105_V1
These are text files downloaded from the Web of Science for the bibliographic analyses found in Zinnen et al. (2020) in Applied Vegetation Science. They represent the papers and reference lists from six expert-based indicator systems: Floristic Quality Assessment, hemeroby, naturalness indicator values (& social behaviors), Ellenberg indicator values, grassland utilization values, and urbanity indicator values. To examine data, download VOSviewer and see instructrions from van Eck & Waltman (2019) for how to upload data. Although we used bibliographic coupling, there are a number of other interesting bibliographic analyses you can use with these data (e.g., visualizing citations between journals from this set of documents). Note: There are two caveats to note about these data and Supplements 1 & 2 associated with our paper. First, there are some overlapping papers in these text files (i.e., raw data). When added individually, the papers sum to more than the numbers we give. However, when combined VOSviewer recognizes these as repeats, and matches the numbers we list in S1 and the manuscript. Second, we labelled the downloaded papers in S2 with their respective systems. In some cases, the labels do not completely match our counts listed in S1 and raw data. This is because some of these papers use another system, but were not captured in our systematic literature search (e.g., a paper may have used hemeroby, but was not picked up by WoS, so this paper is not listed as one of the 52 hemeroby papers).
Web of Science; bibliographic analyses; vegetation; VOSviewer
Rhoads, Bruce ; Lewis, Quinn; Sukhodolov, Alexander; Constantinescu, George (2020): Mixing Data for Three Small Confluences in East Central Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1255710_V1
This data set includes information used to determine patterns of mixing at three small confluences in East Central Illinois based on differences in the temperature or turbidity of the two confluent flows.
mixing; confluences; flow structure
Clem, Scott; Harmon-Threatt, Alexandra (2020): Raw data and code for the paper "Semi-natural wildflower-strip field borders provide winter refuge for pest natural enemies: a case study on organic farms". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8470827_V1
These are the data sets associated with our publication "Semi-natural wildflower-strip field borders provide winter refuge for pest natural enemies: a case study on organic farms." For this project, we compared the communities of overwintering arthropod natural enemies in organic cultivated fields and wildflower-strip field borders at five different sites in central Illinois. Abstract: Strips of wildflowers along field borders are frequently used in midwestern U.S. sustainable agriculture. These properties help diversify otherwise monocultural landscapes and provision them with ecosystem services, including biological control. Predatory and parasitic arthropods (i.e., natural enemies) often flourish in these habitats and will move into crops to help control pests. However, the capacity of wildflower strips for providing overwintering refuge for these arthropods is poorly understood. In this study, we used soil emergence tents to characterize natural enemy communities overwintering in cultivated organic crop fields and adjacent wildflower strip field borders. We found a greater abundance and species richness, and a unique community composition, of predatory and parasitic arthropods in wildflower strips compared to arable crop fields. These results demonstrate that semi-natural habitats such as wildflower strips can be important for maintaining natural enemies in agricultural landscapes.
Natural enemy; wildflower strips; conservation biological control; semi-natural habitat; field border; organic farming
Mishra, Shubhanshu (2020): SocialMediaIE Tutorial Material for IC2S2 2020. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0851257_V1
Dataset to be for SocialMediaIE tutorial
social media; deep learning; natural language processing
Smirnov, Vladimir (2020): Vlad's Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6955387_V1
Legried, Brandon; Molloy, Erin K.; Warnow, Tandy; Roch, Sebastien (2020): Data from: Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2626814_V3
This repository includes scripts and datasets for the paper, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss."
Species tree estimation; gene duplication and loss; identifiability; statistical consistency; quartets; ASTRAL
Rykhlevskii, Andrei; Huff, Kathryn D. (2020): SaltProc output for TAP MSR and MSBR online reprocessing depletion simulations. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7364919_V1
molten salt; fuel cycle; reprocessing; refueling
Chakraborty, Sulagna; Cristina Drumond Andrade , Flavia; Lee Smith, Rebecca (2020): Case Studies for 'An Interdisciplinary Approach to One Health: Course Design, Development and Delivery'. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0595759_V1
This file contains 13 unique case studies that were created for the One health: Infectious diseases course offered at the University of Illinois at Urbana-Champaign campus. The case studies are being made available as educational resources for other One health courses. Each case study is focused on a theme/topic which is associated with One health. These case studies were created using publicly available information and references have been provided for each case study.
One health education; infectious diseases; case studies
Gasparik, Jessica T.; Ye, Qing; Curtis, Jeffrey H.; Presto, Albert A.; Donahue, Neil M.; Sullivan, Ryan C.; West, Matthew; Riemer, Nicole (2020): Data from: Quantifying Errors in the Aerosol Mixing-State Index Based on Limited Particle Sample Size. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2774261_V1
This dataset contains the PartMC-MOSAIC simulations used in the article "Quantifying Errors in the Aerosol Mixing-State Index Based on Limited Particle Sample Size". The 1000 simulations of output data is organized into a series of archived folders, each containing 100 scenarios. Within each scenario directory are 25 NetCDF files, which are the hourly output of a PartMC-MOSAIC simulation containing all information regarding the environment, particle and gas state. This dataset was used to investigate the impact of sample size on determining aerosol mixing state. This data may be useful as a data set for applying different types of estimators.
Atmospheric aerosols; single-particle measurements; sampling uncertainty; NetCDF
Asplund, Joshua; Karahalios, Karrie (2020): Data for: Auditing Race and Gender Discrimination in Online Housing Markets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1408573_V1
This dataset contains the results of a three month audit of housing advertisements. It accompanies the 2020 ICWSM paper "Auditing Race and Gender Discrimination in Online Housing Markets". It covers data collected between Dec 7, 2018 and March 19, 2019. There are two json files in the dataset: The first contains a list of json objects representing advertisements separated by newlines. Each object includes the date and time it was collected, the image and title (if collected) of the ad, the page on which it was displayed, and the training treatment it received. The second file is a list of json objects representing a visit to a housing lister separated by newlines. Each object contains the url, training treatment applied, the location searched, and the metadata of the top sites scraped. This metadata includes location, price, and number of rooms. The dataset also includes the raw images of ads collected in order to code them by interest and targeting. These were captured by selenium and named using a perceptive hash to de-duplicate images.
algorithmic audit; advertisement audit;
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
Anthropogenic disturbance; β-Diversity; Biotic homogenization; Phalaris arundinacea; reed canary grass; Wetlands
Zaya, David N.; Leicht-Young, Stacey A.; Pavlovic, Noel B.; Ashley, Mary V. (2020): Reproduction and hybridization in Celastrus scandens and C. orbiculatus at the Indiana Dunes National Park. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6925722_V1
These data are from an observational study and small experiment investigating reproductive biology and hybridization between two plants, Celastrus scandens L. and Celastrus orbiculatus Thunb. (Celastraceae). These data were collected during the 2008 growing season from the Indiana Dunes National Park (formerly Indiana Dunes National Lakeshore), just east of the municipality of Ogden Dunes, Indiana, USA. The five data files provide information on floral output of the two species, fertilization rate, fruit set rate, hybridization rate at two scales (individual flowers in both species, individual maternal plants in C. scandens), and the results of a hand-pollination experiment that exchanged pollen between the two species. There are six data files associated with this submission, five data files in comma-separated values format and one text file (‘readme.txt’) that includes detailed explanations of the data files.
Celastrus; invasive species; hybridization; heterospecific pollen; hand pollination
Copas, Katherine (2020): World Values Survey and World Bank Data for measuring perceptions of expertise in developing nations . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2476863_V1
This dataset include data pulled from the World Bank 2009, the World Values Survey wave 6, Transparency International from 2009. The data were used to measure perceptions of expertise from individuals in nations that are recipients of development aid as measured by the World Bank.
World Values Survey; World Bank; expertise; development
Fu, Yuanxi; Hsiao, Tzu-Kun (2020): Dataset for "Visualizing evidence-based disagreement over time: the landscape of a public health controversy 2002-2014". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9222782_V1
This is a network of 14 systematic reviews on the salt controversy and their included studies. Each edge in the network represents an inclusion from one systematic review to an article. Systematic reviews were collected from Trinquart (Trinquart, L., Johns, D. M., & Galea, S. (2016). Why do we think we know what we know? A metaknowledge analysis of the salt controversy. International Journal of Epidemiology, 45(1), 251–260. https://doi.org/10.1093/ije/dyv184 ). <b>FILE FORMATS</b> 1) Article_list.csv - Unicode CSV 2) Article_attr.csv - Unicode CSV 3) inclusion_net_edges.csv - Unicode CSV 4) potential_inclusion_link.csv - Unicode CSV 5) systematic_review_inclusion_criteria.csv - Unicode CSV 6) Supplementary Reference List.pdf - PDF <b>ROW EXPLANATIONS</b> 1) Article_list.csv - Each row describes a systematic review or included article. 2) Article_attr.csv - Each row is the attributes of a systematic review/included article. 3) inclusion_net_edges.csv - Each row represents an inclusion from a systematic review to an article. 4) potential_inclusion_link.csv - Each row shows the available evidence base of a systematic review. 5) systematic_review_inclusion_criteria.csv - Each row is the inclusion criteria of a systematic review. 6) Supplementary Reference List.pdf - Each item is a bibliographic record of a systematic review/included paper. <b>COLUMN HEADER EXPLANATIONS</b> <b>1) Article_list.csv:</b> ID - Numeric ID of a paper paper assigned ID - ID of the paper from Trinquart et al. (2016) Type - Systematic review / primary study report Study Groupings - Groupings for related primary study reports from the same report, from Trinquart et al. (2016) (if applicable, otherwise blank) Title - Title of the paper year - Publication year of the paper Attitude - Scientific opinion about the salt controversy from Trinquart et al. (2016) Doi - DOIs of the paper. (if applicable, otherwise blank) Retracted (Y/N) - Whether the paper was retracted or withdrawn (Y). Blank if not retracted or withdrawn. <b>2) Article_attr.csv:</b> ID - Numeric ID of a paper year - Publication year Attitude - Scientific opinion about the salt controversy from Trinquart et al. (2016) Type - Systematic review/ primary study report <b>3) inclusion_net_edges.csv:</b> citing_ID - The numeric ID of a systematic review cited_ID - The numeric ID of the included articles <b>4) potential_inclusion_link.csv:</b> This data was translated from the Sankey diagram given in Trinquart et al. (2016) as Web Figure 4. Each row indicates a systematic review and each column indicates a primary study. In the matrix, "p" indicates that a given primary study had been published as of the search date of a given systematic review. <b>5)systematic_review_inclusion_criteria.csv:</b> ID - The numeric IDs of systematic reviews paper assigned ID - ID of the paper from Trinquart et al. (2016) attitude - Its scientific opinion about the salt controversy from Trinquart et al. (2016) No. of studies included - Number of articles included in the systematic review Study design - Study designs to include, per inclusion criteria population - Populations to include, per inclusion criteria Exposure/Intervention - Exposures/Interventions to include, per inclusion criteria outcome - Study outcomes required for inclusion, per inclusion criteria Language restriction - Report languages to include, per inclusion criteria follow-up period - Follow-up period required for inclusion, per inclusion criteria
systematic reviews; evidence synthesis; network visualization; tertiary studies
Kwang, Jeffrey; Parker, Gary (2018): Dataset: Ultra-sensitivity of Numerical Landscape Evolution Models to their Initial Conditions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4484338_V1
This dataset contains experimental measurements used in the paper, "Ultra-sensitivity of Numerical Landscape Evolution Models to their Initial Conditions." (to be submitted). The data is taken from experimental runs in a miniature landscape model named the eXperimental Landscape Evolution (XLE) facility. In this facility, we complete five >24hr runs at 5 minute temporal resolution. Every five minutes, an planform image was capture, and a digital elevation model (DEM) was generated. For each run, images and a corresponding animation of images are documented. In addition,ASCII formatted DEMs along with color hillshade maps were generated. The hillshade map images were also made into an animation. This dataset is associated with the following publication: https://doi.org/10.1029/2019GL083305
landscape evolution model; digital elevation model; geomorphology
planned publication date: 2021-06-08
Todd, Jones; Michael, Ward (2021): Jones and Ward JAE-2020-0031.R1. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6218430_V1
Dataset associated with Jones and Ward JAE-2020-0031.R1 submission: Pre-to post-fledging carryover effects and the adaptive significance of variation in wing development for juvenile songbirds. Excel CSV files with data used in analyses and file with descriptions of each column. The flight ability variable in this dataset was derived from fledgling drop tests, examples of which can be found in the related dataset: Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1.
fledgling; wing development; life history; adaptive significance; post-fledging; songbirds
Xue, Qingquan; Dietrich, Christopher; Zhang, Yalin (2020): NEXUS file for phylogenetic analysis of Eurymelinae (Hemiptera: Cicadellidae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3573054_V1
The text file contains the original data used in the phylogenetic analyses of Xue et al. (2020: Systematic Entomology, in press). 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 89 taxa (species) and 2676 characters, indicate that the first 2590 characters are DNA sequence and the last 86 are morphological, that gaps inserted into the DNA sequence alignment and inapplicable morphological characters are indicated by a dash, and that missing data are indicated by a question mark. The file contains aligned nucleotide sequence data for 5 gene regions and 86 morphological characters. The positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes at the end of the file (Subset1 = 16S gene; Subset2 = 28S gene; Subset3 = COI gene; Subset 4 = Histone H3 and H2A genes). The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the original publication. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the supplementary document included as a separate pdf, also available from the journal website. The original raw DNA sequence data are available from NCBI GenBank under the accession numbers indicated in the supplementary file.
phylogeny; DNA sequence; morphology; Insecta; Hemiptera; Cicadellidae; leafhopper; evolution; 28S rDNA; 16S rDNA; histone H3; histone H2A; cytochrome oxidase I; Bayesian analysis
Zhang, Jun; Wuebbles, Donald; Kinnison, Douglas; Baughcum, Steven (2020): Potential Impacts of Supersonic Aircraft on Stratospheric Ozone and Climate. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9081595_V1
This datasets provide basis of our analysis in the paper - Potential Impacts of Supersonic Aircraft on Stratospheric Ozone and Climate. All datasets here can be categorized into emission data and model output data (WACCM). All the model simulations (background and perturbation) were run to steady-state and only the datasets used in analysis are archived here.
NetCDF; Supersonic aircraft; Stratospheric ozone; Climate
Zachwieja, Alexandra (2020): Ecological niche models of Late Pleistocene human land preference: an Australasian test case. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0065911_V1
This dataset provides files for use in analysis of human land preference across Australasia, and in a localized analysis of land preference in Laos and Vietnam. All files can be imported into ArcGIS for visualization, and re-analyzed using the open source Maxent species distribution modeling program. CSV files contain known human presence sites for model validation. ASC files contain geographically coded environmental data for mean annual temperature and mean annual precipitation during the Last Glacial Maximum, as well as downward slope data. All ASC files are in the WGS 1984 Mercator map projection for visualization in ArcGIS and can be opened as text files in text editors supporting large file sizes.
human dispersal; ecological niche modeling; Australasia; Late Pleistocene; land preference
Zhang, Chuanyi; El-Kebir, Mohammed; Ochoa, Idoia (2020): Simulated multi-sample tumor bulk sequencing data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9059263_V1
This repository includes a simulated dataset and related scripts used for the paper "Moss: Accurate Single-Nucleotide Variant Calling from Multiple Bulk DNA Tumor Samples".
Somatic Mutations; Bulk DNA Sequencing; Cancer Genomics
Long, Stephen Patrick (2020): Original data for "Light, Not Age, Underlies the Q9 Maladaptation of Maize and Miscanthus Photosynthesis to Self-Shading". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4821336_V1
Original leaf gas exchange and absorptance data used in the Collison et al. (2020) Light, Not Age, Underlies the Q9 Maladaptation of Maize and Miscanthus Photosynthesis to Self-Shading - Frontiers in Plant Science doi: 10.3389/fpls.2020.00783
C4 photosynthesis; canopy; bioenergy; food security; quantum yield; shade acclimation; photosynthetic light-use efficiency; leaf aging