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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 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.

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)

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.

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

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

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.

These datasets contain modeling files and GIS data associated with a risk assessment study for the Cambrian-Ordovician sandstone aquifer system in Illinois from predevelopment (1863) to the year 2070. Modeling work was completed using the Illinois Groundwater Flow Model, a regional MODFLOW model developed for water supply planning in Illinois, as a base model. The model is run using the graphical user interface Groundwater Vistas 7.0. The development and technical details of the base Illinois Groundwater Flow Model, including hydraulic property zonation, boundary conditions, hydrostratigraphy, solver settings, and discretization, are described in Abrams et al. (2018). Modifications to this base model (the version presented here) are described in Mannix et al. (2018), Hadley et al. (2020) and Abrams and Cullen (2020). Modifications include removal of particular multi-aquifer wells to improve calibration, changing Sandwich Fault Zone properties to achieve calibration at production wells within and near the fault zone, and the incorporation of demand scenarios based on a participatory modeling project with the Southwest Water Planning Group. The zipped folder of model files contains MODFLOW input (package) files, Groundwater Vistas files, and a head file for the entire model run. The zipped folder of GIS data contains rasters of: simulated drawdown in the St. Peter sandstone from predevelopment to 2018, simulated drawdown in the Ironton-Galesville sandstone from predevelopment to 2018, simulated head difference between the St. Peter and Ironton-Galesville sandstone units in 2018, simulated head above the top of the St. Peter sandstone for the years 2029, 2050, and 2070, and simulated head above the top of the Ironton-Galesville sandstone for the years 2029, 2050, and 2070. Raster outputs were derived directly from the simulated heads in the Illinois Groundwater Flow Model. Rasters are clipped to the 8 county northeastern Illinois region (Cook, DuPage, Grundy, Kane, Kendall, Lake, McHenry, and Will counties). Well names, historic and current head targets, and spatial offsets for the Illinois Groundwater Flow Model are available upon request via a data license agreement. Please contact authors to set this up if needed.

Data associated with the manuscript "Eastern banded killifish (Fundulus diaphanus diaphanus) in Lake Michigan and connected watersheds: the invasion of a non-native subspecies" by Jordan H. Hartman, Jeremy S. Tiemann, Joshua L. Sherwood, Philip W. Willink, Kurt T. Ash, Mark A. Davis, and Eric R. Larson. For this project, we sampled 109 locations in Lake Michigan and connected waters and found 821 total banded killifish. Using mitochondrial DNA analysis, we found 31 eastern and 25 western haplotypes which split our banded killifish into 422 eastern banded killifish and 398 western banded killifish. This dataset provides the sampling locations, banded killifish haplotypes, frequency of those haplotypes per location, accession numbers in GenBank, and the associated mitochondrial DNA sequences.

Scripts used to computationally estimate the current through a DNA nanopore, starting from an equilibrated oxDNA configuration, in association with the manuscript "A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport".

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.

Data used in paper published in the Journal of Applied Ecology titled " Bee diversity in tallgrass prairies affected by management and its effects on above- and below-ground resources" Bee Community file contains info on bees sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the bee species name in the first row and all individuals recorded. Plant Community file contains info on plants sampled in each site. The first column contain the Tallgrass Prairie Sites sampled all additional columns contain the plant species name in the first row and all individuals recorded. Soil PC1 file contains the soil PC1 values used in the analyses. The first column contain the Tallgrass Prairie Sites sampled, the second column contains the calculated soil PC1 values.

A stochastic domination analysis model was developed to examine the effect that emerging carbon markets can have on the spatially varying returns and risk profiles of bioenergy crops relative to conventional crops. The code is written in MATLAB, and includes the calculated output. See the README file for instructions to run the code.

Data: Variation in pesticide toxicity in the western honey bee (Apis mellifera) associated with consuming phytochemically different monofloral honeys Includes: Identification and quantification of phenolic components of honeys: Raw_data_JOCE.xlsx – sheet: “HoneyPhytochemicals” Effects of honey phytochemicals on acute pesticide toxicity: Raw_data_JOCE.xlsx – sheet: “raw_LD50 Raw_data_JOCE.xlsx – sheet: “raw_LD50_hive_based”

Oxidative cleavage of alkenes and unsaturated fatty acids with hydrogen peroxide gives an efficient and sustainable process to obtain mono- and di-acids for polymers and lubricants with fewer safety risks and less environmental impact than processes that utilize ozone or other inorganic oxidizers (e.g., permanganate, dichromate, etc.). Guided by insight into the mechanisms for competing reaction pathways (i.e., epoxidation of alkene on W–(η2-O2) complexes vs. H2O2 decomposition) and the apparent kinetics derived from kinetic experiments, here, we postulate that W-based heterogeneous catalysts can provide high performance and stable operations at low H2O2 concentrations. Semi-batch reactors with continuous introduction of H2O2 solutions offer the means to maintain low H2O2 concentrations while providing sufficient quantities of H2O2 to satisfy the reaction stoichiometry. We derived simple kinetic model equations for the epoxidation, ring-opening, oxidative cleavage, and oxidation steps and fit theses equations to batch experimental data to obtain kinetic parameters. This kinetic model describes the concentration profiles of reactant, oxidant, and products well as shown by agreement with experimental data. Further predictions of the optimal H2O2 feed rate for semi-batch operation utilized by the proposed rate expressions and the reactor design equations suggest that low H2O2 feed rate increases selectivity towards oxidative cleavage products and selective use of H2O2 for oxidative cleavage pathway. Comparisons of oxidative cleavage of 4-octene in batch and semi-batch reactors show that semi-batch reactors with optimized molar feed rates of H2O2 increased oxidative cleavage product selectivities (76% to 99%; with an increase in butyric acid selectivity from 1% to 55%) and H2O2 selectivity (3% to 30%). In addition, semi-batch reaction conditions used avoid H2O2-mediated dissolution of W-atoms from the catalyst. Analysis of these findings suggest that solid oxide catalysts will be effective for continuous oxidative cleavage reactions if deployed within fixed-bed reactors that allow for distributed introduction of reactants and therefore low in situ concentrations of H2O2.

Dataset includes the dataset for estimating bat density from acoustic data and the R code. The data support a publication by Meredith L. Hoggatt, Clarissa A. Starbuck, and Joy M. O'Keefe entitled Acoustic monitoring yields informative bat population density estimates.

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.

These data obtained from the peer-reviewed literature and a public database depict the geographic expansion of the black-legged tick (Ixodes scapularis) and human cases of Lyme disease in the midwestern U.S. <b><i>Note</b></i>: There was an omission from the first version (V1) of the data set that required us to update the data. Specifically, we failed to include the data from the article "Caporale DA, Johnson CM, Millard BJ. 2005 Presence of Borrelia burgdorferi (Spirochaetales: Spirochaetaceae) in Southern Kettle Moraine State Forest, Wisconsin, and characterization of strain W97F51. J. Med. Entomol. 42, 457–472". In the second version (V2) of the data, this omission is corrected.

Detection data of carnivores and their prey species from camera traps in Fort Hood, Texas and Santa Cruz, California, USA. Non-carnivore and non-prey species (humans, domestic species, avian species, etc.) were excluded from this dataset. All detections of each species at a camera within 30 minutes have been combined to 1 detection (only first detection within that 30 minutes kept) to avoid pseudoreplication. Variable Description: Site= Study area data were collected MonitoringPeriod= year in which data was collected (data were collected at each location over multiple monitoring periods) CameraName= Unique name for each camera location Date= calendar date of detection Time= time of detection -Fort Hood= Central Time USA -Santa Cruz= Pacific Time USA Species= Common name of species detected