Datasets

This dataset contains weather data taken at the University of Illinois Urbana-Champaign Energy Farm using automatic sensors and averaged every 15 minutes. Measurements include average air temperature, average relative humidity, average wind speed, maximum wind speed, average wind direction, average photosynthetically active radiation, total precipitation, and average air pressure.

This data set includes all of data related to strain-resilient FETs based on 2D heterostructures including optical images of FETs, Raman characteristics data, Transport measurement data, and AFM topography data.

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 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 is a sample 5 minute video of an E coli bacterium swimming in a microfluidic chamber as well as some supplementary code files to be used with the Matlab code available at https://github.com/dfraebel/CellTracking

The files are plain text and contain the original data used in phylogenetic analyses of of Typhlocybinae (Bin, Dietrich, Yu, Meng, Dai and Yang 2022: Ecology & Evolution, in press). The three files with extension .phy are text files with aligned DNA sequences in the standard PHYLIP format and correspond to Matrix 1 (amino acid alignment), Matrix 2 (nucleotide alignment of first two codon positions of protein-coding genes) and Matrix 3 (nucleotide alignment of protein-coding genes plus 2 ribosomal genes) described in the Methods section. An additional text file in NEXUS format (.nex extension) contains the morphological character data used in the ancestral state reconstruction (ASCR) analysis described in the Methods. NEXUS is a standard format used by various phylogenetic analysis software. For more information on data file content, see the included "readme" files.

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.

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.

This deposit contains all raw data and analysis from the paper "In-cell titration of small solutes controls protein stability and aggregation". Data is collected into several types: 1) analysis*.tar.gz are the analysis scripts and the resulting data for each cell. The numbers correspond to the numbers shown in Fig.S1. (in publication) 2) scripts.tar.gz contains helper scripts to create the dataset in bash format. 3) input.tar.gz contains headers and other information that is fed into bash scripts to create the dataset. 4) All rawData*.tar.gz are tarballs of the data of cells in different solutes in .mat files readable by matlab, as follows: - Each experiment included in the publication is represented by two matlab files: (1) a calibration jump under amber illumination (_calib.mat suffix) (2) a full jump under blue illumination (FRET data) - Each file contains the following fields:        coordleft - coordinates of cropped and aligned acceptor channel on the original image        coordright - coordinates of cropped and aligned donor channel on the original image]        dataleft - a 3d 12-bit integer matrix containing acceptor channel flourescence for each pixel and time step. Not available in _calib files        dataright - a 3d 12-bit integer matrix containing donor channel flourescence for each pixel and time step. This will be mCherry in _calib files and AcGFP in data files.        frame1 - original image size        imgstd - cropped dimensions        numFrames - number of frames in dataleft and dataright        videos - a structure file containing camera data. Specifically, videos.TimeStamp includes the time from each frame.

Related to the raw entity mentions (https://doi.org/10.13012/B2IDB-4163883_V1), this dataset represents the effects of the data cleaning process and collates all of the entity mentions which were too ambiguous to successfully link to the ChEBI ontology.

This dataset contains five files. (i) open_citations_jan2024_pub_ids.csv.gz, open_citations_jan2024_iid_el.csv.gz, open_citations_jan2024_el.csv.gz, and open_citation_jan2024_pubs.csv.gz represent a conversion of Open Citations to an edge list using integer ids assigned by us. The integer ids can be mapped to omids, pmids, and dois using the open_citation_jan2024_pubs.csv and open_citations_jan2024_pub_ids.scv files. The network consists of 121,052,490 nodes and 1,962,840,983 edges. Code for generating these data can be found https://github.com/chackoge/ERNIE_Plus/tree/master/OpenCitations. (ii) The fifth file, baseline2024.csv.gz, provides information about the metadata of PubMed papers. A 2024 version of PubMed was downloaded using Entrez and parsed into a table restricted to records that contain a pmid, a doi, and has a title and an abstract. A value of 1 in columns indicates that the information exists in metadata and a zero indicates otherwise. Code for generating this data: https://github.com/illinois-or-research-analytics/pubmed_etl

The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper: 1. Taxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier. 2. Alignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis. 3. Concatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE. 4. Genes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder. 5. Partitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition. 6. (New in this version 2) Scripts & Description.zip includes 8 custom shell or perl scripts used to assemble the DNA sequence data by perform reciprocal blast searches between the reference sequences and assemblies for each sample, extract the best sequences based on the blast searches, screen the hits for each locus and keep only the best result, and generate the nucleotide sequence dataset for the predicted orthologues (see the file description.txt for details). 7. (New in this version 2) Full_genetic_distances_matrix.csv shows the genetic distances between pairs of samples in the datset (proportion of nucleotides that differ between samples).

This dataset contains all material required to produce the figures found within the manuscript submitted to Geoscientific Model Development entitled “Explicit stochastic advection algorithms for the regional scale particle-resolved atmospheric aerosol model WRF-PartMC (v1.0)”. The dataset consists of Python Jupyter notebooks and any applicable WRF-PartMC output. This dataset covers the three numerical examples of the manuscript, 1D advection by a uniform constant wind, a 2D rotational flow and a 3D time-evolving WRF simulated flow.

Curated networks and clustering output from the manuscript: Well-Connected Communities in Real-World Networks https://arxiv.org/abs/2303.02813

Use of cellulosic biofuels from non-feedstocks are modeled using the BEPAM (Biofuel and Environmental Policy Analysis Model) model to quantifying the uncertainties about induced land use change effects, net greenhouse gas saving potential, and economic costs. The code is in GAMS, general algebraic modeling language. NOTE: Column 3 is titled "BAU" in "merged_BAU.gdx", "merged_RFS.gdx", and "merged_CEM.gdx", but contains "RFS" data in "merged_RFS.gdx" and "CEM" data in "merged_CEM.gdx".

Provides RNASim-VS2 datasets used in Gillian's Master's thesis.

Traces created using DeathStarBench (https://github.com/delimitrou/DeathStarBench) benchmark of microservice applications with injected failures on containers. Failures consist of disk/CPU/memory failures.

Simulation trajectory data and scripts for Nature manuscript "The structure and physical properties of a packaged bacteriophage particle" that reports the all-atom structure of a complete HK97 virion, including its entire 39,732 base pair genome, obtained through multi-resolution simulations.

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.

Simulation trajectory data and scripts for Nature Nanotechnology manuscript "A DNA turbine powered by a transmembrane potential across a nanopore" that demonstrates a rationally designed nanoscale DNA-origami turbine with three chiral blades that uses a transmembrane electrochemical potential across a nanopore to drive a DNA bundle into sustained unidirectional rotations of up to 10 revolutions/s. Driven by the asymmetric mobility of a DNA duplex, the rotation direction of the turbine is set by its designed chirality and the salinity of the solvent.

This dataset was created based on the publicly available microdata from PNS-2019, a national health survey conducted by the Instituto Brasileiro de Geografia e Estatistica (IBGE, Brazilian Institute of Geography and Statistics). IBGE is a federal agency responsible for the official collection of statistical information in Brazil – essentially, the Brazilian census bureau. Data on selected variables focusing on biopsychosocial domains related to pain prevalence, limitations and treatment are available. The Fundação Instituto Oswaldo Cruz has detailed information about the PNS, including questionnaires, survey design, and datasets (www.pns.fiocruz.br). The microdata can be found on the IBGE website (https://www.ibge.gov.br/estatisticas/downloads-estatisticas.html?caminho=PNS/2019/Microdados/Dados).

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.