72 Works

Data from: FastMulRFS: Statistically consistent polynomial time species tree estimation under gene duplication

Erin K. Molloy & Tandy Warnow
This repository includes scripts and datasets for the paper, "FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models." Note: The results from estimating species trees with ASTRID-multi (included in this repository) are *not* included in the FastMulRFS paper. We estimated species trees with ASTRID-multi in the fall of 2019, but ASTRID-multi had an important bug fix in January 2020. Therefore, the ASTRID-multi species trees in this repository should be ignored.

Honeybee F2F event data for The origin of heavy tails in honeybee and human interaction times

Sang Hyun Choi, Vikyath D. Rao, Tim Gernat, Adam R. Hamilton, Gene E. Robinson & Nigel Goldenfeld
Dataset for F2F events of honeybees. F2F events are defined as face-to-face encounters of two honeybees that are close in distance and facing each other but not connected by the proboscis, thus not engaging in trophallaxis. The first and the second columns show the unique id's of honeybees participating in F2F events. The third column shows the time at which the F2F event started while the fourth column shows the time at which it ended....

Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments

Andrew Miller & Daniel Raudabaugh
This dataset contains the data files for the PhD thesis entitled: Species Distribution, Phylogenetic Structure and Functional Roles of Detritus Inhabiting Fungi Across Contrasting Aquatic Environments by Daniel Bruce Raudabaugh. More specifically, it contains the forward Illumina reads for ITS1, ITS2, Beta-tubulin and LSU in addition to the index files and map files needed to process the reads in QIIME 1.9.1. The sequences represent environmental sequencing from detrital samples from Black Moshannon State park (Pennsylvania),...

Honeybee trophallaxis event data for The origin of heavy tails in honeybee and human interaction times

Sang Hyun Choi, Vikyath Rao, Tim Gernat, Adam Hamilton, Gene Robinson & Nigel Goldenfeld
Filtered trophallaxis interactions for two honeybee colonies, each containing 800 worker bees and one queen. Each colony consists of bees that were administered a juvenile hormone analogy, a vehicle treatment, or a sham treatment to determine the effect of colony perturbation on the duration of trophallaxis interactions. Columns one and two display the unique identifiers for each bee involved in a particular trophallaxis exchange, and columns three and four display the Unix timestamp of the...

Monet - Blue Waters Network Dataset

Jha Saurabh, Patke Archit, Showerman Mike, Enos Jeremy, Bauer Greg, Kalbarczyk Zbigniew, Iyer Ravishankar & Kramer William
This dataset contains collected and aggregated network information from NCSA’s Blue Waters system, which is comprised of 27,648 nodes connected via Cray Gemini* 3D torus (dimension 24x24x24) interconnect, from Jan/01/2017 to May/31/2017. Network performance counters for links are exposed via Cray's gpcdr (https://github.com/ovis-hpc/ovis/wiki/gpcdr-kernel-module) kernel module. Lightweight Distributed Metric Service ([LDMS](https://github.com/ovis-hpc/ovis)) is used to sampled the performance counters at 60 second intervals. Please read "README.md" file. Acknowledgement: This dataset is collected as a part of the...

Data for: A molecular phylogenetic analysis of the genera of fruit doves and their allies using dense taxonomic sampling

Jennifer E. Nowak, Andrew D. Sweet, Jason D. Weckstein & Kevin P. Johnson
Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and...

Data for STREETS: A Novel Camera Network Dataset for Traffic Flow

Corey Snyder & Minh Do
This dataset accompanies the paper "STREETS: A Novel Camera Network Dataset for Traffic Flow" at Neural Information Processing Systems (NeurIPS) 2019. Included are: *Over four million still images form publicly accessible cameras in Lake County, IL. The images were collected across 2.5 months in 2018 and 2019. *Directed graphs describing the camera network structure in two communities in Lake County. *Documented non-recurring traffic incidents in Lake County coinciding with the 2018 data. *Traffic counts for...

Dataset of 3D fluid phase distribution from drainage simulations (in micromodel and real rock geometry) examining inertial effects

Yu Chen, Qinjun Kang, Albert Valocchi & Hari Viswanathan
The dataset contains fluid phase distribution obtained from high-resolution drainage simulations in both a heterogenous micromodel and Bentheimer sandstone. The purpose is to investigate the influence of inertial effects on scCO2-brine displacement in complex geometries, where scCO2 is much less viscous than brine or oil meaning that the inertial effects may not be negligible. The direct numerical simulations in this work employ the continuum-surface-force based color-gradient multiple-relaxation-time lattice Boltzmann model combined with a geometrical wetting...

Correlation Between Soil Quality Indictors including β-glucosidase, Fluorescein Diacetate Hydrolysis and Permanganate Oxidizable Carbon, and Ecosystem Functions represented by Crop Productivity and Greenhouse Gas Emissions

Yushu Xia & Michelle Wander
We summarize peer reviewed literature reporting associations between for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) and crop yield and greenhouse gas emissions. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, or...

Data from: Consequences of climatic thresholds for projecting fire activity and ecological change

Adam M. Young, Philip E. Higuera, John T. Abatzoglou, Paul A. Duffy & Feng Sheng Hu
Aim: Ecological properties governed by threshold relationships can exhibit heightened sensitivity to climate, creating an inherent source of uncertainty when anticipating future change. We investigated the impact of threshold relationships on our ability to project ecological change outside the observational record (e.g., the 21st century), using the challenge of predicting late‐Holocene fire regimes in boreal forest and tundra ecosystems. Location: Boreal forest and tundra ecosystems of Alaska. Time period: 850–2100 CE. Major taxa studied: Not...

Data from: Weighting effective number of species measures by abundance weakens detection of diversity responses

Yong Cao & Charles Patrick Hawkins
1. The effective number of species (ENS) has been proposed as a robust measure of species diversity that overcomes several shortcomings of both diversity indices and species richness measures. However, it is not yet clear if ENS improves interpretation and comparison of biodiversity monitoring data, and ultimately resource management decisions. 2. We used simulations of five stream macroinvertebrate assemblages and spatially extensive field data of stream fishes and mussels to show (1) how different ENS...

Data from: Looking back to look ahead: a vision for soil denitrification research

Maya Almaraz, Michelle Wong & Wendy Yang
Denitrification plays a critical role in regulating ecosystem nutrient availability and anthropogenic reactive nitrogen (N) production. Its importance has inspired an increasing number of studies, yet it remains the most poorly constrained term in terrestrial ecosystem N budgets. We censused the peer-reviewed soil denitrification literature (1975 to 2015) to identify opportunities for future studies to advance our understanding despite the inherent challenges in studying the process. We found that only one-third of studies reported estimates...

Data for: How do moral values differ in tweets on social movements?

Rezvaneh Rezapour
We are sharing the tweet IDs of four social movements: #BlackLivesMatter, #WhiteLivesMatter, #AllLivesMatter, and #BlueLivesMatter movements. The tweets are collected between May 1st, 2015 and May 30, 2017. We eliminated the location to the United States and focused on extracting the original tweets, excluding the retweets. Recommended citations for the data: Rezapour, R. (2019). Data for: How do Moral Values Differ in Tweets on Social Movements?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9614170_V1 and Rezapour, R.,...

UIUC Campus Gamma-Ray Radiation Data

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

Control of bacterial infections via antibiotic-induced proviruses

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

Datasets from \"Predicting Controlled Vocabulary Based on Text and Citations: Case Studies in Medical Subject Headings in MEDLINE and Patents\"

Adam K. Kehoe & Vetle I. Torvik
# Overview These datasets were created in conjunction with the dissertation "Predicting Controlled Vocabulary Based on Text and Citations: Case Studies in Medical Subject Headings in MEDLINE and Patents," by Adam Kehoe. The datasets consist of the following: * twin_not_abstract_matched_complete.tsv: a tab-delimited file consisting of pairs of MEDLINE articles with identical titles, authors and years of publication. This file contains the PMIDs of the duplicate publications, as well as their medical subject headings (MeSH) and...

Response of Soil Quality Indictors including β-glucosidase, Fluorescein Diacetate Hydrolysis and Permanganate Oxidizable Carbon

Yushu Xia & Michelle Wander
Dataset compiled by Yushu Xia and Michelle Wander for the Soil Health Institute. Data were recovered from peer reviewed literature reporting results for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) in terms of their relative response to management where soils under grassland cover, no-tillage, cover crops, residue return and organic amendments were compared to conventionally managed controls. Peer-reviewed articles published between January of 1990 and May...

Social Political Economic Event Dataset (SPEED): Liberia, Philippines, and Sierra Leone (1979-2008). Cline Center for Advanced Social Research. V1.0.0. August 29

Peter Nardulli, Buddy Peyton, Joseph Bajjalieh, Ajay Singh, Michael Martin, Dan Shalmon & Scott Althaus
This is part of the Cline Center’s ongoing Social, Political and Economic Event Database Project (SPEED) project. Each observation represents an event involving civil unrest, repression, or political violence in Sierra Leone, Liberia, and the Philippines (1979-2009). These data were produced in an effort to describe the relationship between exploitation of natural resources and civil conflict, and to identify policy interventions that might address resource-related grievances and mitigate civil strife. This work is the result...

Jones et al. FE-2019-01175

Todd M. Jones, Thomas J. Benson & Michael P. Ward
Dataset associated with Jones et al FE-2019-01175 submission: Does the size and developmental stage of traits at fledging reflect juvenile flight ability among songbirds? Excel CSV files with all of the 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):...

Data from: Rapid experimental evolution of reproductive isolation from a single natural population

Scott M. Villa, Juan C. Altuna, James S. Ruff, Andrew B. Beach, Lane I. Mulvey, Erik J. Poole, Heidi E. Campbell, Kevin P. Johnson, Michael D. Shapiro, Sarah E. Bush & Dale H. Clayton
Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations. Here, we show that experimental evolution of parasite body size over 4 y (approximately 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of...

Data from: Habitat explains patterns of population decline for an invasive crayfish

Eric R. Larson, Timothy A. Kreps, Brett Peters, Jody A. Peters & David M. Lodge
Invasive non-indigenous species are defined by their impacts: they substantially change native communities or ecosystems. Accordingly, invasive species might transform their habitats in ways that eventually become unfavorable to them, causing population declines or even extirpations. Here we use over 40 years of systematically collected data on the abundance of the invasive rusty crayfish Faxonius rusticus from 17 lakes in northern Wisconsin, USA to explore if population declines of this invader are related to the...

Data from: Host defense triggers rapid adaptive radiation in experimentally evolving parasites

Sarah E. Bush, Scott M. Villa, Juan C. Altuna, Kevin P. Johnson, Michael D. Shapiro & Dale H. Clayton
Adaptive radiation occurs when the members of a single lineage evolve different adaptive forms in response to selection imposed by competitors or predators. Iconic examples include Darwin’s finches, Caribbean anoles, and Hawaiian silverswords, all of which live on islands. Although adaptive radiation is thought to be an important generator of biodiversity, most studies concern groups that have already diversified. Here we take the opposite approach. We experimentally triggered diversification in the descendants of a single...

Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis

Katy Heath, Justin Podowski, Stephanie Heniff, Christie Klinger, Jennifer Lau, Wendy Yang, Dylan Weese & Patricia Burke
Premise of the study: Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here...

Data from: Multiple maize reference genomes impact the identification of variants by GWAS in a diverse inbred panel

Joseph L. Gage, Brieanne Vaillancourt, John P. Hamilton, Norma C. Manrique-Carpintero, Timothy J. Gustafson, Kerrie Barry, Anna Lipzen, William F. Tracy, Mark A. Mikel, Shawn M. Kaeppler, C. Robin Buell & Natalia De Leon
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence/absence variations (PAVs). In this study, we present the draft de novo genome assembly of PHJ89, an Oh43-type inbred line. Using three separate reference genome assemblies (B73, PH207, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate...

Cline Center Historical Phoenix Event Data. Cline Center for Advanced Social Research. v1.1.0. August 30

Scott Althaus, Joseph Bajjalieh, John Carter, Buddy Peyton & Dan Shalmon
The Cline Center Historical Phoenix Event Data covers the period 1945-2018 and includes several million events extracted from 17.5 million news stories. This data was produced using the state-of-the-art PETRARCH-2 software to analyze content from the New York Times (1945-2019), the BBC Monitoring's Summary of World Broadcasts (1979-2015) 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...

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of Illinois
  • University of Illinois at Urbana Champaign
  • Indiana University
  • University of Wisconsin-Madison
  • Environment Canada
  • University of California, Santa Barbara
  • University of California, Riverside
  • University of Utah
  • Iowa State University
  • Michigan State University