104 Works

Datasets for SALMA: Scalable ALignment using MAFFT-add

Chengze Shen, Baqiao Liu, Kelly Williams & Tandy Warnow
This upload contains all datasets used in Experiments 2 and 3 of the SALMA paper (pending submission): Shen, Chengze, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. "SALMA: Scalable ALignment using MAFFT-Add". The zip file has the following structure (presented as an example): salma_paper_datasets/ |_README.md |_10aa/ |_crw/ |_homfam/ |_aat/ | |_... |_... |_het/ |_5000M2-het/ | |_... |_5000M3-het/ ... |_rec_res/ Generally, the structure can be viewed as: [category]/[dataset]/[replicate]/[alignment files] # Categories: 1. 10aa: There are 10...

Data from: Seed fate in ant-mediated dispersal: Seed dispersal effectiveness in the Ectatomma ruidum (Formicidae) - Zanthoyxlum ekmanii (Rutaceae) system

Selina A. Ruzi & Andrew V. Suarez.
Plants are often dispersal limited relying on passive or active agents to find suitable microhabitats for germination. Seeds of pioneer tree species, for example, require light gaps for growth but have short median dispersal distances and often do not provide a food reward to encourage animal dispersal. Zanthoxylum ekmanii seeds are frequently moved by ants but evaluating the effectiveness of ant-mediated seed removal requires knowledge of the species moving the seeds, how far they are...

Experimental realization of the 1D random field Ising model

Nicholas Bingham, Spencer Rooke, Jungsik Park, Alejandro Simon, William Zhu, Xiaoyu Zhang, Joseph Batley, Justin Watts, Chris Leighton, Karin Dahmen & Peter Schiffer
We have measured magnetic-field-induced avalanches in a square artificial spin ice array of interacting nanomagnets. Starting from the ground state ordered configuration, we imaged the individual nanomagnet moments after each successive application of an incrementally increasing field. The statistics of the evolution of the moment configuration show good agreement with the canonical one-dimensional random field Ising model. We extract information about the microscopic structure of the arrays from our macroscopic measurements of their collective behavior,...

Data for Responsiveness of Miscanthus and Switchgrass Yields to Stand Age and Nitrogen Fertilization: A Meta-regression Analysis

Bijay P. Sharma, Na Zhang, Lee DoKyoung, Emily Heaton, Evan H. Delucia, Erik J. Sacks, Ilsa B. Kantola, Nicholas N. Boersma, Stephen P. Long, Thomas B. Voigt & Madhu Khanna
The compiled datasets include plot level observations of energy crops (miscanthus and switchgrass) from recent experimental field trials in the US including dry biomass yield, location, state, region, harvest year, growing season degree days (GDD), winter season heating degree days (HDD), growing season cumulative precipitation, annual nitrogen application rate, age of the pant when harvested, National Commodity Crop Productivity Index (NCCPI) values, and cultivar type (switchgrass) from various published and unpublished sources. The stata codes...

Error Analysis

Khanh Linh Hoang, Jodi Schneider & Yogeshwar Kansara
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....

Data from Testing a filtering strategy for systematic reviews: Evaluating work savings and recall

Randi Proescholdt, Tzu-Kun Hsiao, Jodi Schneider, Aaron Cohen, Marian McDonagh & Neil Smalheiser
This dataset contains the files used to perform the work savings and recall evaluation in the study titled "Data from Testing a filtering strategy for systematic reviews: Evaluating work savings and recall."


Joshua Wurman & Karen Kosiba

Data for: The 30 Doradus Molecular Cloud at 0.4 pc Resolution with ALMA: Physical Properties and the Boundedness of CO-emitting Structures

Tony Wong, Luuk Oudshoorn, Eliyahu Sofovich, Alex Green, Charmi Shah, Remy Indebetouw, Margaret Meixner, Alvaro Hacar, Omnarayani Nayak, Kazuki Tokuda, Alberto D. Bolatto, Melanie Chevance, Guido De Marchi, Yasuo Fukui, Alec S. Hirschauer, K. E. Jameson, Venu Kalari, Vianney Lebouteiller, Leslie W. Looney, Suzanne C. Madden, Toshikazu Onishi, Julia Roman-Duval, Monica Rubio & A. G. G. M. Tielens
12CO and 13CO emission maps of the 30 Doradus molecular cloud in the Large Magellanic Cloud, obtained with the Atacama Large Millimeter/submillimeter Array (ALMA) during Cycle 7. See the associated article in the Astrophysical Journal, and README file, for details. Please cite the article if you use these data.

Data for \"Generic character of charge and spin density waves in superconducting cuprates\"

Sangjun Lee, Edwin W. Huang, Thomas A. Johnson, Xuefei Guo, Ali A. Husain, Matteo Mitrano, Kannan Lu, Alexander V. Zakrzewski, Gilberto A. de la Pena, Yingying Peng, Hai Huang, Sang-Jun Lee, Hoyoung Jang, Jun-Sik Lee, Young Il Joe, William B. Doriese, Paul Szypryt, Daniel S. Swetz, Songxue Chi, Adam A. Aczel, Gregory J. MacDougall, Steven A. Kivelson, Eduardo Fradkin & Peter Abbamonte
Data for "Generic character of charge and spin density waves in superconducting cuprates". - Neutron scattering data for SDW - RSXS scans of CDW of LESCO x=0.10, 0.125, 0.15, 0.17, 0.20 at various temperatures. - Temperature dependence of CDW peak intensity, correlation length, Qcdw (Lorentzian fit, S(q,T) fit, Landau-Ginzburg fit) - XAS data of LESCO x=0.10, 0.125, 0.15, 0.17, 0.20

Codes for the analysis of an eco-immunological disease-transmission mathematical model

Zoi Rapti, Vanessa Rivera Quinones & Tara Stewart Merrill
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.

Thermal tolerance of fish to heatwaves in agricultural streams: What does not kill you makes you stronger?

Qihong Dai
Heatwaves are increasing in frequency and intensity under climate change. Freshwater ecosystems are among the most thermally impacted systems, within which agricultural streams are experiencing the most extreme heatwaves and deserve prioritized focus. Heatwaves are approaching the upper thermal limits of many fishes but have received little attention to date. To study whether and how fish tolerate heatwaves from a physiological perspective, we simulated single, multiple, and extended heatwaves at 32 and 34 °C in...

SBKS - Chemical Raw Entity Mentions

Jacob Jett
A set of chemical entity mentions derived from an NERC dataset analyzing 900 synthetic biology articles published by the ACS. This data is associated with the Synthetic Biology Knowledge System repository (https://web.synbioks.org/). The data in this dataset are raw mentions from the NERC data.

SBKS - Species - Cleaned & Grounded Entity Mentions

Jacob Jett
This dataset represents the results of manual cleaning and annotation of the entity mentions contained in the raw dataset (https://doi.org/10.13012/B2IDB-4950847_V1). Each mention has been consolidated and linked to an identifier for a matching concept from the NCBI's taxonomy database.

SBKS - Species Raw Entity Mentions

Jacob Jett
A set of species entity mentions derived from an NERC dataset analyzing 900 synthetic biology articles published by the ACS. This data is associated with the Synthetic Biology Knowledge System repository (https://web.synbioks.org/). The data in this dataset are raw mentions from the NERC data.

Data for The Orinoco Low-level Jet and the Cross-Equatorial Moisture Transport over tropical South America: Lessons from seasonal WRF simulations

Francina Dominguez
This dataset contains results from WRF simulations over northern South America. The Orinoco Low-Level Jet (OLLJ) and the Cross-Equatorial Moisture Transport are important circulation structures of the climate of tropical South America. We explore the sensitivity of the OLLJ and cross-equatorial transport to the representation of surface fluxes and turbulence by using two different Land Surface Model (LSM) schemes (Noah and CLM) and three Planetary Boundary Layer (PBL) schemes (YSU, QNSE and MYNN).

Testing unified theories for ozone response in C4 species

Shuai Li, Christopher A. Moller, Noah G. Mitchell, DoKyoung Lee, Erik J. Sacks & Elizabeth A. Ainsworth
Twenty-two genotypes of C4 species grown under ambient and elevated O3 concentration were studied at the SoyFACE (40°02’N, 88°14’W) in 2019. This dataset contains leaf morphology, photosynthesis and nutrient contents measured at three time points. The results of CO2 response curves are also included.

Datasets for Phylogenomics of microleafhoppers (Hemiptera: Cicadellidae: Typhlocybinae): morphological evolution, divergence times and biogeography

Yanghui Cao, Christopher H. Dietrich, Joel Kits, Dmitry A. Dmitriev, Ye Xu & Min Huang
The following files were used to reconstruct the phylogeny of the leafhopper subfamily Typhlocybinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. 1) Taxon_sampling.csv: contains the sample IDs (1st column) and the taxonomic information (2nd column). Sample IDs were used in the alignment files and partition files. 2) concatenated_nt_complete.phy: a complete concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 154,992 nucleotide positions (intron...

Data for: Functional traits and responses to nutrient and mycorrhizal addition are inconsistently related to wetland plant species’ coefficients of conservatism

Jack Zinnen
This is the core data for Zinnen et al., "Functional traits and responses to nutrient and mycorrhizal addition are inconsistently related to wetland plant species’ coefficients of conservatism." This is submitted to Wetlands Ecology and Management. Two datasets are submitted here. The first is greenhouse-collected data of 9 plant traits and concurrent treatment responses of Illinois wetland plant species. The second are field-collected leaf trait data of Illinois wetland plant species. These data are analyzed...

Multi-modal dataset of a polycrystalline metallic material: 3D microstructure and deformation fields

J.C. Stinville, J.M. Hestroffer, M.A. Charpagne, A.T. Polonsky, M.P. Echlin, C.J. Torbet, V. Valle, A. Loghin, O. Klaas, M.P. Miller, K.E. Nygren, I.J Beyerlein & T.M. Pollock
The development of high-fidelity mechanical property prediction models for the design of polycrystalline materials relies on large volumes of microstructural feature data. Concurrently, at these same scales, the deformation fields that develop during mechanical loading can be highly heterogeneous. Spatially correlated measurements of 3D microstructure and the ensuing deformation fields at the micro-scale would provide highly valuable insight into the relationship between microstructure and macroscopic mechanical response. They would also provide direct validation for numerical...

5000-het: Dataset of Nucleotide Sequences with a Form of Evolutionary Sequence Length Heterogeneity

Baqiao Liu, Chengze Shen & Tandy Warnow
Simulated sequences provide a way to evaluate multiple sequence alignment (MSA) methods where the ground truth is exactly known. However, the realism of such simulated conditions often comes under question compared to empirical datasets. In particular, simulated data often does not display heterogeneity in the sequence lengths, a common feature in biological datasets. In order to imitate sequence length heterogeneity, we here present a set of data that are evolved under a mixture model of...

The 16S.B.ALL dataset in 100-HF condition

Chengze Shen, Minhyuk Park & Tandy Warnow
This upload includes the 16S.B.ALL in 100-HF condition (referred to as 16S.B.ALL-100-HF) used in Experiment 3 of the WITCH paper (currently accepted in principle by the Journal of Computational Biology). 100-HF condition refers to making sequences fragmentary with an average length of 100 bp and a standard deviation of 60 bp. Additionally, we enforced that all fragmentary sequences to have lengths > 50 bp. Thus, the final average length of the fragments is slightly higher...

Trivellone, Valeria; Cao, Yanghui; Blackshear, Millon ; Kim, Chang-Hyun ; Stone, Christopher (2022): FASTA file of the final sequence alignment used in the haplotype analyses of Culex pipiens complex populations collected in south-eastern Illinois (2016-2017). University of Illinois at Urbana-Champaign.

Valeria Trivellone, Yanghui Cao, Millon Blackshear, Chang-Hyun Kim & Christopher Stone
The Culex_Trivellone_etal.fas fasta file contains the original final sequence alignment used in the haplotype analyses of Trivellone et al. (Frontiers in Public Health, under review). The 492 sequences (from specimens of Culex pipiens complex collected in different habitat types using a BG-sentinel traps) were aligned using PASTA v1.8.5 under default settings. The final dataset contains 686 positions of the cytochrome c oxidase subunit I (COI) mitochondrial gene. The data analyses are further described in the...

Multi-State Survey of State Opportunity Zones Laws (Last Updated Jan. 14, 2022)

Michelle Layser
This dataset provides a 50-state (and DC) survey of state-level Opportunity Zones laws, including summaries of states' Opportunity Zone tax preferences, supplemental tax preferences, and approach to Opportunity Zones conformity. Data was last updated on January 14, 2022.

Standardizing protocols for determining the cause of mortality in wildlife studies

Bogdan Cristescu, Mark Elbroch, Tavis Forrester, Maximilian Allen, Derek Spitz, Christopher Wilmers & Heiko Wittmer
Mortality site investigations of telemetered wildlife are important for cause-specific survival analyses and understanding underlying causes of observed population dynamics. Yet eroding ecoliteracy and a lack of quality control in data collection can lead researchers to make incorrect conclusions, which may negatively impact management decisions for wildlife populations. We reviewed a random sample of 50 peer-reviewed studies published between 2000 and 2019 on survival and cause-specific mortality of ungulates monitored with telemetry devices. This concise...

Demonstration of local adaptation in maize landraces by reciprocal transplantation

Garrett Janzen, Maria Rocio Aguilar-Rangel, Carolina Cintora-Martinez, Karla Azucena Blocher-Juarez, Eric Gonzalez-Segovia, Anthony Studer, Daniel Runcie, Sherry Flint-Garcia, Ruben Rellan-Alvarez, Ruairidh Sawers & Matthew Hufford
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican...

Registration Year

  • 2022

Resource Types

  • Dataset


  • University of Illinois
  • University of Illinois Urbana-Champaign
  • University of Illinois at Urbana Champaign
  • University of Minnesota
  • Arkansas State University
  • Yale University
  • University of Illinois at Urbana-Champaign
  • Victoria University of Wellington
  • University of Jos
  • University of Eastern Finland