Datasets

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.

Dataset associated with Jones et al. GCB-23-1273.R1 submission: Phenotypic signatures of urbanization? Resident, but not migratory, songbird eye size varies with urban-associated light pollution levels. Excel CSV file with all of the data used in analyses and file with descriptions of each column.

This dataset was developed as part of a study that examined the correlational relationships between local journal authorship, local and external citation counts, full-text downloads, link-resolver clicks, and four global journal impact factor indices within an all-disciplines journal collection of 12,200 titles and six subject subsets at the University of Illinois at Urbana-Champaign (UIUC) Library. While earlier investigations of the relationships between usage (downloads) and citation metrics have been inconclusive, this study shows strong correlations in the all-disciplines set and most subject subsets. The normalized Eigenfactor was the only global impact factor index that correlated highly with local journal metrics. Some of the identified disciplinary variances among the six subject subsets may be explained by the journal publication aspirations of UIUC researchers. The correlations between authorship and local citations in the six specific subject subsets closely match national department or program rankings. All the raw data used in this analysis, in the form of relational database tables with multiple columns. Can be opned using MS Access. Description for variables can be viewed through "Design View" (by right clik on the selected table, choose "Design View"). The 2 PDF files provide an overview of tables are included in each MDB file. In addition, the processing scripts and Pearson correlation code is available at <a href="https://doi.org/10.13012/B2IDB-0931140_V1">https://doi.org/10.13012/B2IDB-0931140_V1</a>.

The Delt_Comb.NEX text file contains the original data used in the phylogenetic analyses of Zahniser & Dietrich, 2013 (European Journal of Taxonomy, 45: 1-211). 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 nine lines of the file indicate the file type (Nexus), that 152 taxa were analyzed, that a total of 3971 characters were analyzed, the format of the data, and specification for two symbols used in the dataset. There are four datasets separated into blocks, one each for: 28S rDNA gene, Histone H3 gene, morphology, and insertion/deletion characters scored based on the alignment of the 28S rDNA dataset. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the publication using this dataset. A text file, Delt_morph_char.txt, is available here that states the morphological characters and characters states that were scored in the Delt_Comb.NEX dataset. The original DNA sequence data are available from NCBI GenBank under the accession numbers indicated in publication. Chromatogram files for each sequencing read are available from the first author upon request.

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.

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.

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

Trained models for multi-task multi-dataset learning for text classification as well as sequence tagging in tweets. Classification tasks include sentiment prediction, abusive content, sarcasm, and veridictality. Sequence tagging tasks include POS, NER, Chunking, and SuperSenseTagging. Models were trained using: <a href="https://github.com/socialmediaie/SocialMediaIE/blob/master/SocialMediaIE/scripts/multitask_multidataset_classification_tagging.py">https://github.com/socialmediaie/SocialMediaIE/blob/master/SocialMediaIE/scripts/multitask_multidataset_classification_tagging.py</a> See <a href="https://github.com/socialmediaie/SocialMediaIE">https://github.com/socialmediaie/SocialMediaIE</a> and <a href="https://socialmediaie.github.io">https://socialmediaie.github.io</a> for details. If you are using this data, please also cite the related article: Shubhanshu Mishra. 2019. Multi-dataset-multi-task Neural Sequence Tagging for Information Extraction from Tweets. In Proceedings of the 30th ACM Conference on Hypertext and Social Media (HT '19). ACM, New York, NY, USA, 283-284. DOI: https://doi.org/10.1145/3342220.3344929

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.

Data: Variation in pesticide toxicity in the western honey bee (Apis mellifera) associated with consuming phytochemically different monofloral honeys Includes: Identification and quantification of phenolic components of honeys: Raw_data_JOCE.xlsx – sheet: “HoneyPhytochemicals” Effects of honey phytochemicals on acute pesticide toxicity: Raw_data_JOCE.xlsx – sheet: “raw_LD50 Raw_data_JOCE.xlsx – sheet: “raw_LD50_hive_based”

A defining feature of the Anthropocene is the distortion of the biosphere phosphorus (P) cycle. A relatively sudden acceleration of input fluxes without a concomitant increase in output fluxes has led to net accumulation of P in the terrestrial-aquatic continuum. Over the past century, P has been mined from geological deposits to produce crop fertilizers. When P inputs are not fully removed with harvest of crop biomass, the remaining P accumulates in soils. This residual P is a uniquely anthropogenic pool of P, and its management is critical for agronomic and environmental sustainability. This dataset includes data for us to quantify residual P from different long-term managed systems. The following is the desccription of the dataset. There are 7 sheets in total. 1. P_balance: From Morrow Plots maize-maize rotaiton (1888-2021), L: Low estimation; M: medium estimation; H: high estimation; 2. M3P: From Morrow Plots selected plots (selected years), M3P_sur: Mehlich III P concentration in surface 17cm soils; M3P_sub: Mehlich III P concentration in 17-34cm subsoils; P_balance: the difference between P inputs and P outputs; TP_sur: total P stocks in surface 17cm soils; TP_sub: total P stocks in 17-34cm subsoils; 3. Morrow_Plot_P_pool_all: Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; Fertilized: P stocks in the fertilized plot; Unfertilized: P stocks in the unfertilized plot; F-U: difference between P stocks in ther fertilized and unfertilized plots; dif%: percent difference in total P; 4. Rothamsted_P_pool_all: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 5. L'Acadie_P_pool_all: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 6. Rothamsted_P_pool_duration: Treatment: Unfertilized: no fertilization; FYM: farmyard manure; PK: synthetic P and K fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P; 7. L'Acadie_P_pool_duration: Treatment: MP_LowP: moldboard plow with low rate of P fertilizer; MP_HighP: moldboard plow with high rate of P fertilizer; NT_LowP: no till with low rate of P fertilizer; NT_HighP: no till with high rate of P fertilizer; Duration: from a year to another year; Group: a - labile P; b - Fe/Al-P; c - Ca-P; d - total organic P; e - non-extractable P; P_change: differnce in P stocks over time; dif%: percent difference in total P;

Atomic oxygen densities in the MLT, averaged for 2002-2018 for 26, 14 day periods, beginning January 1.

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.

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.

Atomic oxygen data from SCIAMACHY, for the MLT, 2002-2012, averaged for 26, 14 day periods, beginning January 1.

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.

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.

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.

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).

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.

The organizations that contribute to the longevity of 67 long-lived molecular biology databases published in Nucleic Acids Research (NAR) between 1991-2016 were identified to address two research questions 1) which organizations fund these databases? and 2) which organizations maintain these databases? Funders were determined by examining funding acknowledgements in each database's most recent NAR Database Issue update article published (prior to 2017) and organizations operating the databases were determine through review of database websites.

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.

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.

The text file contains the original DNA nucleotide sequence data used in the phylogenetic analyses of Xue et al. (in review), comprising the 13 protein-coding genes and 2 ribosomal gene subunits of the mitochondrial genome. 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 30 taxa (species) and 13078 characters, 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 positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes (version 3.2.6) beginning near the end of the file. The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the Methods section of the submitted manuscript. 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 individual mitochondrial genes and for different codon positions of the protein-coding genes used for analyses in the programs MrBayes and IQ-Tree (version 1.6.8) (Table S2). Full citations for references listed in Table S1 can be found by searching GenBank using the corresponding accession number. The supplemental tables will also be linked to the article upon publication at the journal website.

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.