Dataset Search Results

Data collected at 71 study sites from 2023 to 2024 for Reves, Olivia P. (2025): Using Environmental DNA Metabarcoding to Inform Biodiversity Conservation in Agricultural Landscapes. Master's thesis, University of Illinois Urbana-Champaign. Files include study site information, taxa by site matrices for vertebrates from environmental DNA metabarcoding using multiple mitochondrial DNA primers (COI, 12S), and bird species audibly detected by a phone app at study sites.

Data was generated from a field and lab study to determine the influence of thermal variation in livewells on largemouth bass recovery from angling tournaments. The field study data includes temperature data from inside angler livewells during a tournament day. This was collected across four tournaments. The laboratory data was generated from a series of experiments simulating tournament practices and trends in thermal variation within livewells observed in the field proponent. Following simulation, blood was collected to determine levels of analytes consistent with primary, secondary, and tertiary stress response in largemouth bass. Reflex impairment was also included.

These data files were used for phylogenomic analyses of Darnini and related Membracidae (Hemiptera: Auchenorrhyncha) in the referenced article by Gonzalez-Mozo et al. - The "mem_50p_alignment.fas" file contains the aligned, concatenated nucleotide sequence data for 51 species and 492 genetic loci included in the phylogenetic analyses ("N" indicates missing data and "-" indicates an alignment gap). - The file "Table1.rtf" lists the included species, country of origin and genbank accession number. Species newly sequenced for this study have a Sample ID with prefix "DAR"; previously sequenced species for which data were downloaded from genbank have "NCBI" indicated in the same column of the table. - The file "partition_def.txt" lists the 492 genetic loci included in the alignment with their exact positions indicated by the range of numbers given at the end of each line (e.g., locus "uce-1" occupies positions 1-280 in the alignment). - The substitution model file "mem_50p.model" contains information on the substitution models used in the partitioned maximum likelihood analysis, including the models used for different data partitions and parameter values, as output by the phylogenetic software IQ-TREE. - Individual tree files in Newick format (plain text) are provided for the phylogeny from concatenated analysis with the best likelihood score ("mem_50p_bestLikelihoodScore"), concatenated likelihood analysis with gene concordance factors ("mem_50p_gcf") and site concordance factors ("mem_50p_scf"). - The tree file from the ASTRAL analysis is "mem_50p_astral". - The zip archive entitled “IQ-TREE analysis results.zip” includes output from the maximum likelihood analysis of the concatenated nucleotide sequence data, including the following: (1) main output file “mem_50p.iqtree” summarizing model selection, partitioning schemes, likelihood scores, and run parameters; (2) “mem_50p.mldist” including pairwise ML distances between taxa; (3) “mem_50p.best_scheme.nex” with the best partitioning scheme identified by ModelFinder in NEXUS format and (4) “mem_50p.best_scheme” the RAxM-compatible version of the same file. - The “Ultrafast bootstrap results.zip” zip archive contains: (1) “mem_50p.ufboot” with the bootstrap replicate trees; (2) “mem_50p.contree” with the majority-rule consensus tree with support values; (3) “mem_50p.splits.nex”, with split support values across the replicates; (4) “mem_50p.log” is the log file. - The “gene_trees.zip” zip archive contains the individual gene trees as input for subsequent coalescent gene tree analysis in the phylogenetic program ASTRAL. - The file "DarniniAHE_Character Matrix.csv" contains the data for 6 morphological characters for which the ancestral states were reconstructed using the phylogenetic results from analysis of anchored-hybrid data (see article text for details). - The file "scriptACRDarnini.txt" contains the commands used to reconstruct ancestral morphological characters states using the corHMM 2.8 R package. See the Methods section of the article for more details.

The data and code provided in this dataset can be used to generate plots that show the results of linear prediction algorithm and the amplified modes, supporting the key argument of the manuscript. It is divided into five subfolders, each corresponding to one combination of external condition (magnetic field B, temperature), scan parameter (temperature, magnetic field B), pump laser polarization (linear s, linear p, and circular), and sample orientation ( B parallel to c axis, B perpendicular to c axis): 1) B parallel to c axis, linear pump polarization in s, linear THz emission polarization in s, field dependence (B_parallel_c_linear_spump_sprobe_field). 2) B parallel to c axis, linear pump polarization in s, linear THz emission polarization in s, temperature dependence (B_parallel_c_linear_spump_sprobe_temperature). 3) B perpendicular to c axis, linear pump polarization in s, linear THz emission polarization in s, field dependence (B_perp_c_linear_spump_sprobe_field). 4) B perpendicular to c axis, linear pump polarization in s, linear THz emission polarization in s, temperature dependence (B_perp_c_linear_spump_sprobe_temperature). 5) B parallel to c axis, circular pump polarization (left circularly polarized LCP and right circularly polarized RCP), linear THz emission polarization in s, field dependence (B_parallel_c_LCPRCP_pump_sprobe_field). Each folder contains the raw data (.mat), the oscillator parameters obtained through linear prediction algorithm (.mat), and the plot-generating code (.m). The code plots the raw data, the fit to the processed data, and the amplified modes. Codes are written in MATLAB R2024a; the working directory of each code should be the corresponding subfolder that contains it.

The dataset includes responses from approximately 550 participants to survey questions about trust in images labeled with AI-related tags, compared to other images found online. The questions also explore how the type of label influences their trust.

This dataset contains the first-generation (1st-gen) and second-generation (2nd-gen) citation relationships to a set of focal papers. The 1st-gen citation relationships are the instances of one paper citing a focal paper. These citing papers are called "1st-gen citations." The 2nd-gen citation relationships are the instances that a paper cites a 1st-gen citation. The citing paper in the 2nd-gen citation relationship is a second-generation (2nd-gen) citation. When a 2nd-gen citation is also a 1st-gen citation, it creates a transitive closure with the focal paper. Each focal paper has an abbreviation, which can be found below. The 1st-gen and 2nd-gen citation relationships were extracted from the Curated Open Citation Dataset (Korobskiy & Chacko, 2023), which is derived from a copy of COCI, the OpenCitations Index of Crossref Open DOI-to-DOI Citations, downloaded on May 6, 2023. Scripts used to collect this dataset can be found at https://github.com/yuanxiesa/transitive_closure_study. Each focal paper currently has two files: {abbreviation}_1st.csv contains the 1st-gen citation relationships; {abbreviation}_2nd.csv contains the 2nd-gen citation relationships. Focal paper abbreviation == "louvain": Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment, 2008(10), P10008. https://doi.org/10.1088/1742-5468/2008/10/P10008 Focal paper abbreviation == "lp": Raghavan, U. N., Albert, R., & Kumara, S. (2007). Near linear time algorithm to detect community structures in large-scale networks. Physical Review E, 76(3), 036106. https://doi.org/10.1103/PhysRevE.76.036106 Focal paper abbreviation == "gn": Newman, M. E. J., & Girvan, M. (2004). Finding and evaluating community structure in networks. Physical Review E, 69(2), 026113. https://doi.org/10.1103/PhysRevE.69.026113

BEPAM, Biofuel and Environmental Policy Analysis Model, models the agricultural sector and determines economically optimal land-use and feedstock mix at the US scale by maximizing the sum of agricultural sector consumers’ and producers’ surplus subject to various resource balances, land availability, and technological constraints under a range of biomass prices, from zero to $140 Mg-1 over the 2016-2030 period. Here BEPAM is used to model SAF production using energy crops and crop residues. BEPAM uses the GAMS format and uses yield and GHG balance projections from the biogeochemical model, DayCent.

This dataset represents the results of targeted eDNA assays via quantitative PCR for two imperiled freshwater species.

Please cite as: Wuebbles, D., J. Angel, K. Petersen, and A.M. Lemke, (Eds.), 2021: An Assessment of the Impacts of Climate Change in Illinois. The Nature Conservancy, Illinois, USA. https://doi.org/10.13012/B2IDB-1260194_V1 Climate change is a major environmental challenge that is likely to affect many aspects of life in Illinois, ranging from human and environmental health to the economy. Illinois is already experiencing impacts from the changing climate and, as climate change progresses and temperatures continue to rise, these impacts are expected to increase over time. This assessment takes an in-depth look at how the climate is changing now in Illinois, and how it is projected to change in the future, to provide greater clarity on how climate change could affect urban and rural communities in the state. Beyond providing an overview of anticipated climate changes, the report explores predicted effects on hydrology, agriculture, human health, and native ecosystems.

This repository contains the data and computational analysis notebooks that were used in the following manuscript. For more information on the methods and contributing authors, please refer to the original manuscript. "Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function Omid Gholamalamdari et al. 2024"

The immunofluorescence and segmented images of three nuclear locales, (nuclear periphery, nuclear speckles, and nucleolus) in four human cells lines (H1-hESC, HCT116, HFFc6, and K562). For each of the cell lines, this dataset includes original, cropped, and binary 4D images (3D + antibody) in addition to max projected thumbnails of cell nuclei.

Coagulation testing (VCM Vet™) was performed on 57 horses with acute abdominal pain at admission to the University of Illinois Veterinary Teaching Hospital. Additional clinical data were recorded retrospectively. ROC analysis was performed to determine the optimal number of abnormal coagulation parameters for coagulopathy diagnosis based on survival. General linear regression (GLM) and random forest (RF) classification models were developed to predict short-term survival. A training cohort of 40 horses was used for model development, and model performance was determined using the remaining 17 horses.

This dataset contains records of four years of taxi operations in New York City and includes 697,622,444 trips. Each trip records the pickup and drop-off dates, times, and coordinates, as well as the metered distance reported by the taximeter. The trip data also includes fields such as the taxi medallion number, fare amount, and tip amount. The dataset was obtained through a Freedom of Information Law request from the New York City Taxi and Limousine Commission. The files in this dataset are optimized for use with the ‘decompress.py’ script included in this dataset. This file has additional documentation and contact information that may be of help if you run into trouble accessing the content of the zip files.

This page contains the data for the publication "The pioneer transcription factor Zelda controls the exit from regeneration and restoration of patterning in Drosophila" published in the journal Science Advances.

This dataset is derived from the COCI, the OpenCitations Index of Crossref open DOI-to-DOI references (opencitations.net). Silvio Peroni, David Shotton (2020). OpenCitations, an infrastructure organization for open scholarship. Quantitative Science Studies, 1(1): 428-444. https://doi.org/10.1162/qss_a_00023 We have curated it to remove duplicates, self-loops, and parallel edges. These data were copied from the Open Citations website on May 6, 2023 and subsequently processed to produce a node list and an edge-list. Integer_ids have been assigned to the DOIs to reduce memory and storage needs when working with these data. As noted on the Open Citation website, each record is a citing-cited pair that uses DOIs as persistent identifiers.

Dataset of the standing dead trees at Trelease Woods in 2022. Dataset contains volume, biomass, decay class, and GPS coordinates for each standing dead tree.

Soil data for ten soil cores collected at Trelease Woods in 2022. Soil samples were analyzed with an elemental analyzer via combustion to obtain total carbon (C) and nitrogen. A subset of these samples were analyzed using the Walkley-Black method to obtain organic C. A calibration curve relating organic C and total C was created using these data.

Downed woody debris census data for Trelease Woods collected in the summer of 2022. Dataset contains volume, biomass, decay class, and GPS coordinates for each downed woody debris piece.

This is an Excel file containing data about the physical environments of four Brazilian schools and the average daily minutes/day of physical activity and sedentary behavior exhibited by schoolchildren during school hours. The Following Key describes the basic variables: Subject IDs and Characteristics Subject_ID: ID of Subject total_days: Total number of days subject participated in experiment Gender : Gender of subject Age: Age of subject School IDs and Characteristics ID_School = ID of School school1 = 1 if ID_School = 1, else = 0 school2 = 1 if ID_School = 2, else = 0 school3 = 1 if ID_School = 3, else = 0 school4 = 1 if ID_School = 4, else = 0 TotalSiteArea: Total Site Area on School Campus PatioArea: Area of Patio(s) CourtyardArea: Area of Courtyard(s) TotalOpenArea: Total Area of Open Spaces on Campus Class: Number of Sections in the School Population: Total Number of Students Enrolled in the School

Historical census data collected at Trelease Woods from 1986 to 2004 with information on tree species, diameter at breast height (DBH), and plot location.

Census data collected at Trelease Woods in 1936 with information on tree species, stem count, diameter at breast height (DBH), and basal area. The plot boundaries from the 1936 census were georeferenced to subset 2018 census data for a direct comparison between the two census years.

Zika virus (ZIKV) infection has been linked to neurological disorders such as microcephaly in children. Cases of Guillain-Barré Syndrome (GBS), a peripheral nervous system (PNS) disorder, have been reported in adults with ZIKV infection. These ZIKV-related GBS cases often exhibit atypical clinical features compared to classic GBS, including central nervous system (CNS) involvement. This dataset comprises two patient groups and a healthy control group. The first patient group includes adults with confirmed ZIKV infection, presenting both PNS-related GBS symptoms and CNS manifestations. The second group consists of adults with GBS but without ZIKV infection. The final group includes healthy, unaffected individuals.

The Cline Center Historical Phoenix Event Data covers the period 1945-2019 and includes 8.2 million events extracted from 21.2 million news stories. This data was produced using the state-of-the-art PETRARCH-2 software to analyze content from the New York Times (1945-2018), the BBC Monitoring's Summary of World Broadcasts (1979-2019), the Wall Street Journal (1945-2005), and the Central Intelligence Agency’s Foreign Broadcast Information Service (1995-2004). It documents the agents, locations, and issues at stake in a wide variety of conflict, cooperation and communicative events in the Conflict and Mediation Event Observations (CAMEO) ontology. The Cline Center produced these data with the generous support of Linowes Fellow and Faculty Affiliate Prof. Dov Cohen and help from our academic and private sector collaborators in the Open Event Data Alliance (OEDA). For details on the CAMEO framework, see: Schrodt, Philip A., Omür Yilmaz, Deborah J. Gerner, and Dennis Hermreck. "The CAMEO (conflict and mediation event observations) actor coding framework." In 2008 Annual Meeting of the International Studies Association. 2008. http://eventdata.parusanalytics.com/papers.dir/APSA.2005.pdf Gerner, D.J., Schrodt, P.A. and Yilmaz, O., 2012. Conflict and mediation event observations (CAMEO) Codebook. http://eventdata.parusanalytics.com/cameo.dir/CAMEO.Ethnic.Groups.zip For more information about PETRARCH and OEDA, see: http://openeventdata.org/

Includes two files (.csv) behind all analyses and results in the paper published with the same title. <b>1) 'sites.species.counts'</b> is the raw 2018-2022 data from Angella Moorehouse (Illinois Nature Preserves Commission) including her 456 identified pollinator species and her raw counts per site (there may be a few errors of identification or naming, and there will always be name changes over time). Headers in columns F through Q correspond to the remnant-site labels in Figure 1 and Table 1 of the paper. Columns R to AB are the “nonremnant” sites, which have not been uniquely labelled since the specific sites aren't referenced anywhere in the manuscript. <b>2) 'C.scores'</b> has the 265 species assigned empirical C values (empirical.C) along with the four sets of expert C values and their confidence ranks (low, medium, high), and the Illinois/Indiana conservation ranks (S-ranks). Other headers in these files: - taxa.code: four-letter abbreviation for genus and specific name - genus: genus name - species: specific epithet - common.name: English name - group: general pollinator taxa group - empirical.C: empirically estimated conservatism score - expert#.C: conservatism score assigned by each of four experts - expert#.conf: expert's confidence in their conservatism score Blank cells in the site-species abundance matrix indicates species absence (or non-detection) Blank cells in C.scores.csv indicates missing S-ranks and unassigned C-scores (with associated missing confidence ranks) where experts lacked knowledge or confidence