Dataset Search

DNDC scripts and outputs that were generated as a part of the research publication 'Evaluation of DeNitrification DeComposition Model for Estimating Ammonia Fluxes from Chemical Fertilizer Application'.

This is the dataset for the manuscript titled, "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States"

This page contains the data for the manuscript "Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis" currently available in preprint on bioRxiv

The included files are the alignments of DNA or amino acid sequences used for phylogenetic analyses of Auchenorrhyncha (Insecta: Hemiptera) in the manuscript by Bin et al. submitted to the journal “Systematic Entomology.” The files are plain text in either FASTA (.fa or .fas suffix) or PHYLIP (.phy suffix) format. Matrix0 is the set of all loci after multiple sequence alignment and trimming (hereafter called). Matrix1 consists of loci having 75% average bootstrap support and 80% taxon completeness (hereafter called Matrix1). Matrix2 consists of loci having 75% average bootstrap support and 95% completeness. Matrix2_nt12 is the same as Matrix2 but with third codon positions excluded. More details on how the datasets were compiled is provided in the Methods section of the manuscript file, also included as a PDF. Supplemental figures for the submitted manuscript are also provided as a PDF for additional information.

This dataset was developed to create a census of sufficiently documented molecular biology databases to answer several preliminary research questions. Articles published in the annual Nucleic Acids Research (NAR) “Database Issues” were used to identify a population of databases for study. Namely, the questions addressed herein include: 1) what is the historical rate of database proliferation versus rate of database attrition?, 2) to what extent do citations indicate persistence?, and 3) are databases under active maintenance and does evidence of maintenance likewise correlate to citation? An overarching goal of this study is to provide the ability to identify subsets of databases for further analysis, both as presented within this study and through subsequent use of this openly released dataset.

This repository contains data and model weights associated with the publication "ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences". It includes the datasets used for training and evaluating a dynamic contact prediction model, ESMDynamic, as well as a script for conversion and usage.

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.

These datasets represent first-time collaborations between first and last authors (with mutually exclusive publication histories) on papers with 2 to 5 authors in years [1988,2009] in PubMed. Each record of each dataset captures aspects of the similarity, nearness, and complementarity between two authors about the paper marking the formation of their collaboration.

BAM files for founding strain (MG1655-motile) as well as evolved strains from replicate motility selection experiments in low-viscosity agar plates containing either rich medium (LB) or minimal medium (M63+0.18mM galactose)

This is the experimental data of isolated nanomagnet islands with or without the presence of large nanomagnet islands. The small islands are made of Permalloy materials with size of 170 nm by 470 nm by 2.5 nm. The systems are measured at a temperature where the small islands are fluctuating around room temperature. The data is recorded as photoemission electron microscopy intensity. More details about the data can be found in the note.txt and Spe_2016.xlsx file. Note: The raw data folders are stored in five volumes during the compression. All five volumes are needed in order to recover the original folder.

Three datasets: species_abundance_data, species_traits, and environmental_data. The three datasets were collected in the Fortuna Forest Reserve (8°45′ N, 82°15′ W) and Palo Seco Protected Forest (8°45′ N, 82°13′ W) located in western Panama. The two reserves support humid to super-humid rainforests, according to Holdridge (1947). The species_abundance_data and species_traits datasets were collected across 15 subplots of 25 m2 in 12 one-hectare permanent plots distributed across the two reserves. The subplots were spaced 20 m apart along three 5 m wide transects, each 30 m apart. Please read Prada et al. (2017) for details on the environmental characteristics of the study area. Prada CM, Morris A, Andersen KM, et al (2017) Soils and rainfall drive landscape-scale changes in the diversity and functional composition of tree communities in a premontane tropical forest. J Veg Sci 28:859–870. https://doi.org/10.1111/jvs.12540

All of the files in this dataset pertain to the evaluation of a novel statistic, Hind/He, for distinguishing Mendelian loci from paralogs. They are derived from a RAD-seq genotyping dataset of diploid and tetraploid Miscanthus sacchariflorus.

In 2020, early-season extreme precipitation events occurred following the planting of Sorghum bicolor (L.) Moench and Zea mays L. in central Illinois that caused ponding. Following the first rainfall event 50m transects were established to assess the waterlogging effects on seedling emergence and crop yields. Soil moisture, emergence, stem and tiller count, LAI, and yield were measured at various points in the season along these transects.

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 cited original paper.

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 <b>prior to March 10, 2023</b> (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.

This dataset contains sequencing data obtained from Illumina MiSeq device to prove the concept of the proposed 2DDNA framework. Please refer to README.txt for detailed description of each file.

Title: Airyscan confocal superresolution images of extant Malvaceae pollen with a focus on Bombacoideae Authors: Surangi W. Punyasena, Ingrid Romero, Michael A. Urban Subject: Biological sciences Keywords: Malvaceae; superresolution microscopy; Zeiss; Bombacacidites; Neotropics; CZI Funder: NSF-DBI Advances in Bioinformatics (NSF-DBI-1262561) Corresponding Creator: Surangi W. Punyasena This dataset includes a total of 430 images of extant specimens of the Malvaceae, with a focus on species that are or have been included within the subfamily Bombacoideae. There are 27 genera included within 26 folders. Each folder is named by genus and contains all the images that correspond to that genus. Note that the genus _Matisia_ is included with _Quararibea_ as detailed in the metadata READ ME file. The specimens imaged are from the palynological collections of the Swedish Museum of Natural History and Smithsonian Tropical Research Institute, and herbarium specimens from the Smithsonian Herbarium National Museum. The optical superresolution microscopy images were taken using a Zeiss LSM 880 with Airyscan at 630X magnification (63x/NA 1.4 oil DIC). The images are in the original CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or in ImageJ/FIJI. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/en/products/software/zeiss-zen/czi-image-file-format.html] Image metadata and file organization are described in the CSV file "METADATA_Malvaceae_Bombacoideae_modern-species.csv". The column headings are: Folder The folder in which the image file is found Subfamily The current subfamily determination based on the literature. Note that _Pentaplaris_ and _Septotheca_ have not been assigned a subfamily. Genus Genus name Species Species name Accepted name Accepted species name, updated from the literature Slide name Species name as denoted on the herbarium slide Collection Source of the herbarium slide: Sweden National Museum of Natural History or the Smithsonian Tropical Research Institute File name File name using the species name denoted on the herbarium slide Slide ID/Herbarium ID Specimen collection number Please cite this dataset as: Punyasena, Surangi W.; Romero, Ingrid; Urban, Michael A. (2025): Airyscan confocal superresolution images of extant Malvaceae pollen with a focus on Bombacoideae. University of Illinois Urbana-Champaign. https://doi.org/10.13012/B2IDB-2968712_V1

This dataset contains the data for PASTA and UPP. PASTA data was used in the following articles: Mirarab, Siavash, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.” Journal of Computational Biology 22, no. 5 (2015): 377–86. doi:10.1089/cmb.2014.0156. Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “PASTA: Ultra-Large Multiple Sequence Alignment.” Edited by Roded Sharan. Research in Computational Molecular Biology, 2014, 177–91. UPP data was used in: Nguyen, Nam-phuong D., Siavash Mirarab, Keerthana Kumar, and Tandy Warnow. “Ultra-Large Alignments Using Phylogeny-Aware Profiles.” Genome Biology 16, no. 1 (December 16, 2015): 124. doi:10.1186/s13059-015-0688-z.

A small and efficient DNA mutation-inducing machine was constructed with an array of microplasma jet devices (7 × 1) that can be operated at atmospheric pressure for microbial mutagenesis. Using this machine, we report disruption of a plasmid DNA and generation of mutants of an oleaginous yeast Rhodosporidium toruloides. Specifically, a compact-sized microplasma channel (25 × 20 × 2 mm3) capable of generating an electron density of greater than 1013 cm–3 was constructed to produce reactive species (N2*, N2+, O, OH, and Hα) under helium atmospheric conditions to induce DNA mutagenesis. The length of microplasma channels in the device played a critical role in augmenting both the volume of plasma and the concentration of reactive species. First, we confirmed that microplasma treatment can linearize a plasmid by creating nicks in vitro. Second, we treated R. toruloides cells with a jet device containing 7 microchannels for 5 min; 94.8% of the treated cells were killed, and 0.44% of surviving cells showed different colony colors as compared to their parental colony. Microplasma-based DNA mutation is energy-efficient and can be a safe alternative for inducing mutations compared to conventional methods using toxic mutagens. This compact and scalable device is amenable for industrial strain improvement involving large-scale mutagenesis.

This dataset contains the results of a three month audit of housing advertisements. It accompanies the 2020 ICWSM paper "Auditing Race and Gender Discrimination in Online Housing Markets". It covers data collected between Dec 7, 2018 and March 19, 2019. There are two json files in the dataset: The first contains a list of json objects representing advertisements separated by newlines. Each object includes the date and time it was collected, the image and title (if collected) of the ad, the page on which it was displayed, and the training treatment it received. The second file is a list of json objects representing a visit to a housing lister separated by newlines. Each object contains the url, training treatment applied, the location searched, and the metadata of the top sites scraped. This metadata includes location, price, and number of rooms. The dataset also includes the raw images of ads collected in order to code them by interest and targeting. These were captured by selenium and named using a perceptive hash to de-duplicate images.

This repository includes a simulated dataset and related scripts used for the paper "Moss: Accurate Single-Nucleotide Variant Calling from Multiple Bulk DNA Tumor Samples".

This dataset contains simulation results from numerical model PartMC-MOSAIC used in the article "Quantifying the effects of mixing state on aerosol optical properties". This article is submitted to the journal Atmospheric Physics and Chemistry. There are total 100 scenario directories in this dataset, denoted from 00-99. Each scenario contains 25 NetCDF files hourly output from PartMC-MOSAIC simulations containing the simulated gas and particle information. The data was produced using version 2.5.0 of PartMC-MOSAIC. Instructions to compile and run PartMC-MOSAIC are available at https://github.com/compdyn/partmc. The chemistry code MOSAIC is available by request from Rahul.Zaveri@pnl.gov. For more details of reproducing the cases, please contact nriemer@illinois.edu and yuyao3@illinois.edu.

Development of sustainable and scalable technologies to convert lignocellulosic biomass to biofuels is critical to achieving carbon neutrality. The potential of transgenic bioenergy crops as a renewable source of sugars and lipids has been demonstrated at bench-scale. However, scaling up these processes is important for holistic analysis. Here proof-of-concept for chemical-free hydrothermal pretreatment of transgenic energycane-oilcane line L13 at an industrially relevant scale to recover vegetative lipids along with cellulosic sugars is presented. Pilot-scale processing of 97 kg of transgenic energycane-oilcane L13 stems and high solids pretreatment of bagasse enhanced the recovery of cellulosic glucose and xylose by 5-fold as compared to untreated bagasse and helped in the enrichment of vegetative lipids in the biomass residues which allowed its recovery at the end of the bioprocess. Palmitic and oleic acids were the predominant fatty acids (FAs) extracted from stems and leaves. The processing did not affect lipid composition. The efficiency of lipid recovery from untreated biomass was 75.9% which improved to 88.7% upon pretreatment. The vegetative tissues of transgenic energycane-oilcane L13 contained 0.42 metric tons/hectare of lipids. Processing vegetative tissues yielded 0.38 metric tons/hectare of lipids. This approaches an oil yield similar to soybean (global average 0.44 metric tons/hectare) and is almost twice as high as the oil yield from sugarcane engineered to hyperaccumulate lipids (0.20 metric tons/hectare). The study suggests that further optimization by state-of-the-art metabolic engineering and biomass processing can establish transgenic bioenergy crops for commercial drop-in fuel production.

These data are from an observational study and small experiment investigating reproductive biology and hybridization between two plants, Celastrus scandens L. and Celastrus orbiculatus Thunb. (Celastraceae). These data were collected during the 2008 growing season from the Indiana Dunes National Park (formerly Indiana Dunes National Lakeshore), just east of the municipality of Ogden Dunes, Indiana, USA. The five data files provide information on floral output of the two species, fertilization rate, fruit set rate, hybridization rate at two scales (individual flowers in both species, individual maternal plants in C. scandens), and the results of a hand-pollination experiment that exchanged pollen between the two species. There are six data files associated with this submission, five data files in comma-separated values format and one text file (‘readme.txt’) that includes detailed explanations of the data files.