Dataset Search Results

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.

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.

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

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.

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.

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

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.

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.

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).

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.

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.

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.

This dataset includes images and extracted centerlines from experiments looking at the formation and evolution of meltwater meandering channels on ice. The laboratory data includes centimeter- and millimeter-scale rivulets. Dataset also includes an image and corresponding centerlines from the Peterman Ice Island. All centerlines were manually digitized in Matlab but no distributable code was developed for the process. Once digitized, centerlines were smoothed and standardized following methods and routines developed by other authors (Zolezzi and Guneralp, 2016; Guneralp and Rhoads, 2008). Details about the preparation of the centerlines and processing with these methods is included in the dissertation by Fernández (2018) linked to this dataset. "Millimeter scale and Peterman Ice Island centerlines.pdf": This file includes the images of two mm-scale experimetns and the Peterman Ice Island image. Seventeen centerlines were digitized from the former and seven were digitized from the latter. Those centerlines are shown above the images themselves. "Centimeter scale rivulet images.pdf": This file includes images corresponding to all cm-scale centerlines used for the analysis presented in the dissertation by Fernandez (2018). Each image has a short caption indicating the run ID and the time at which it was captured. The images were used to extract centerlines to look at the planform evolution of cm-scale meltwater meandering rivulets on ice. Images include 26 centerlines from four different runs. "Meltwater meandering channel centerlines.xlsx": This spreadsheet contains the centerline data for all fifty centerlines. The workbook includes 51 sheets. The first 50 are related to each one of the channels. The mm scale and Peterman Ice Island ones are identified using the same IDs shown in "Millimeter scale and Peterman Ice Island centerlines.pdf". The cm-scale centerlines are identified by run ID and a number indicating the time in minutes (with t = 0 min being the time at which water started flowing over the ice block). The naming convention is also associated to the images in "Centimeter scale rivulet images.pdf". The last sheet in the workbook includes a summary of the channel widths measured from every image for each centerline. The 50 sheets with the centerline information have four columns each. The titles of the columns are X, Y, S, and C. X,Y are dimensionless coordinates of the centerline. S is dimensionless streamwise coordinate (location along the centerline). C is dimensionless curvature value. All these values were non-dimensionalized with the channel width. See Fernandez (2018), Zolezzi and Guneralp (2016), and Guneralp and Rhoads (2008) for more details regarding the process of smoothing, standardizing and non-dimensionalization of the centerline coordinates.

We conducted long-term capture-mark-recapture surveys on two isolated ornate box turtle (Terrapene ornata) populations in northern Illinois, USA. This dataset provides the capture history strings and additional demographic information used for estimating population vital rates with robust design capture-mark-recapture models. The vital rates were then used in a stage-based population projection matrix model for each population.

Data from an a field survey at Nikko National Park in central Japan. Data contain information about deer carcass, environment of sites, and vertebrate scavenging.

This dataset contains 1 CSV file: RozanskyLarsonTaylorMsat.csv which contains microsatellite fragment lengths for Virile and Spothanded Crayfish from the Current River watershed of Missouri, U.S., and complimentary data, including assignments to species by phenotype and COI sequence data, GenBank accession numbers for COI sequence data, study sites with dates of collection and geographic coordinates, and Illinois Natural History Survey (INHS) Crustacean Collection lots where specimens are stored.

This data set includes survey responses collected during 2015 from academic libraries with library publishing services. Each institution responded to questions related to its use of user studies or information about readers in order to shape digital publication design, formats, and interfaces. Survey data was supplemented with institutional categories to facilitate comparison across institutional types.

# 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.

Prepared by Vetle Torvik 2018-04-15 The dataset comes as a single tab-delimited ASCII encoded file, and should be about 717MB uncompressed. &bull; How was the dataset created? First and last names of authors in the Author-ity 2009 dataset was processed through several tools to predict ethnicities and gender, including Ethnea+Genni as described in: <i>Torvik VI, Agarwal S. Ethnea -- an instance-based ethnicity classifier based on geocoded author names in a large-scale bibliographic database. International Symposium on Science of Science March 22-23, 2016 - Library of Congress, Washington, DC, USA. http://hdl.handle.net/2142/88927</i> <i>Smith, B., Singh, M., & Torvik, V. (2013). A search engine approach to estimating temporal changes in gender orientation of first names. Proceedings Of The ACM/IEEE Joint Conference On Digital Libraries, (JCDL 2013 - Proceedings of the 13th ACM/IEEE-CS Joint Conference on Digital Libraries), 199-208. doi:10.1145/2467696.2467720</i> EthnicSeer: http://singularity.ist.psu.edu/ethnicity <i>Treeratpituk P, Giles CL (2012). Name-Ethnicity Classification and Ethnicity-Sensitive Name Matching. Proceedings of the Twenty-Sixth Conference on Artificial Intelligence (pp. 1141-1147). AAAI-12. Toronto, ON, Canada</i> SexMachine 0.1.1: <a href="https://pypi.python.org/pypi/SexMachine/">https://pypi.org/project/SexMachine</a> First names, for some Author-ity records lacking them, were harvested from outside bibliographic databases. &bull; The code and back-end data is periodically updated and made available for query at <a href ="http://abel.ischool.illinois.edu">Torvik Research Group</a> &bull; What is the format of the dataset? The dataset contains 9,300,182 rows and 10 columns 1. auid: unique ID for Authors in Author-ity 2009 (PMID_authorposition) 2. name: full name used as input to EthnicSeer) 3. EthnicSeer: predicted ethnicity; ARA, CHI, ENG, FRN, GER, IND, ITA, JAP, KOR, RUS, SPA, VIE, XXX 4. prop: decimal between 0 and 1 reflecting the confidence of the EthnicSeer prediction 5. lastname: used as input for Ethnea+Genni 6. firstname: used as input for Ethnea+Genni 7. Ethnea: predicted ethnicity; either one of 26 (AFRICAN, ARAB, BALTIC, CARIBBEAN, CHINESE, DUTCH, ENGLISH, FRENCH, GERMAN, GREEK, HISPANIC, HUNGARIAN, INDIAN, INDONESIAN, ISRAELI, ITALIAN, JAPANESE, KOREAN, MONGOLIAN, NORDIC, POLYNESIAN, ROMANIAN, SLAV, THAI, TURKISH, VIETNAMESE) or two ethnicities (e.g., SLAV-ENGLISH), or UNKNOWN (if no one or two dominant predictons), or TOOSHORT (if both first and last name are too short) 8. Genni: predicted gender; 'F', 'M', or '-' 9. SexMac: predicted gender based on third-party Python program (default settings except case_sensitive=False); female, mostly_female, andy, mostly_male, male) 10. SSNgender: predicted gender based on US SSN data; 'F', 'M', or '-'

This annotation study compared RobotReviewer's data extraction to that of three novice data extractors, using six included articles synthesized in one Cochrane review: Bailey E, Worthington HV, van Wijk A, Yates JM, Coulthard P, Afzal Z. Ibuprofen and/or paracetamol (acetaminophen) for pain relief after surgical removal of lower wisdom teeth. Cochrane Database Syst Rev. 2013; CD004624; doi:10.1002/14651858.CD004624.pub2 The goal was to assess the relative advantage of RobotReviewer's data extraction with respect to quality.

We have recently created an approach for high throughput single cell measurements using matrix assisted laser desorption / ionization mass spectrometry (MALDI MS) (J Am Soc Mass Spectrom. 2017, 28, 1919-1928. doi: 10.1007/s13361-017-1704-1. Chemphyschem. 2018, 19, 1180-1191. doi: 10.1002/cphc.201701364). While chemical detail is obtained on individual cells, it has not been possible to correlate the chemical information with canonical cell types. Now we combine high-throughput single cell mass spectrometry with immunocytochemistry to determine lipid profiles of two known cell types, astrocytes and neurons from the rodent brain, with the work appearing as “Lipid heterogeneity between astrocytes and neurons revealed with single cell MALDI MS supervised by immunocytochemical classification” (DOI: 10.1002/anie.201812892). Here we provide the data collected for this study. The dataset provides the raw data and script files for the rodent cerebral cells described in the manuscript.

This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).