Dataset Search

This dataset is associated with the manuscript "Transcriptional responses of detoxification genes to coumaphos in a nontarget species, Galleria mellonella (greater wax moth) (Lepidoptera: Pyralidae), in the beehive environment" This dataset includes 2 Excel files: 1) raw_data_bioassay.xlsx: this file contains the raw data for waxworm bioassay. There are 2 worksheets within this file: - LC50: raw data for measuring LC50 in the laboratory and field strain of Galleria mellonella. - RGR: Relative Growth Rate, raw data for measuring body weight of field strain of Galleria mellonella . 2) raw-data_RT-qPCR.xlsx: this file contains raw data (Ct value) of RT-qPCR.

Data sets from "Inferring Species Trees from Gene-Family with Duplication and Loss using Multi-Copy Gene-Family Tree Decomposition." It contains trees and sequences simulated with gene duplication and loss under a variety of different conditions. <b>Note:</b> - trees.tar.gz contains the simulated gene-family trees used in our experiments (both true trees from SimPhy as well as trees estimated from alignements). - sequences.tar.gz contains simulated sequence data used for estimating the gene-family trees as well as the concatenation analysis. - biological.tar.gz contains the gene trees used as inputs for the experiments we ran on empirical data sets as well as species trees outputted by the methods we tested on those data sets. - stats.txt list statistics (such as AD, MGTE, and average size) for our simulated model conditions.

This study evaluates the bioethanol potential in response to irrigation (IR) and non-irrigation (NIR) of oilcane (OC) during a seasonal drought prior harvest. The juice was extracted through mechanical pressing of stems and fermented by Ethanol Red® yeast to produce first-generation bioethanol. Hydrothermal pretreatment followed by enzymatic hydrolysis of bagasse was performed to produce monomeric sugars from structural carbohydrates. The hydrolysates were fermented with engineered yeast for second-generation bioethanol production. The irrigated oilcane juice (276.3 ± 8.9 g/L) constitutes higher sugar concentrations than non-irrigated oilcane juice (236.5 ± 2.2 g/L). The enzymatic hydrolysis of IR-OC and NIR-OC pretreated bagasse yielded similar concentrations of 247.5 ± 2.22 and 249.7 ± 4.98 g/L fermentable sugars. Industry-relevant bioethanol titers of ≥99 g/L and ≥75 g/L were achieved from juice and hydrolysates, respectively. Therefore, the non-irrigation regime did not impact the 1G and 2G bioethanol titers. However, the overall bioethanol yield can be lower due to the reduction of stem yield (8 %) per hectare.

This dataset includes neuronal development of the Caenorhabditis elegans dauer and adult.

In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves and high light transmission through the canopy are henceforth referred to as ‘erectophile’ and those with low leaf erectness, ‘planophile’. In the final year of the study, bundle sheath leakiness in erectophile and planophile accessions was also compared.

This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes". Please refer to that publication for details about methodologies used to generate these data and for the experimental design. For this verison 2, we added specific gross nitrogen mineralization rates (ugN/gOM/d), microbial biomass carbon (ugC/gdw), microbial biomass nitrogen (ugN/gdw) and microbial biomass C:N ratios to the newest version of the data set. Additionally, we updated values for gross nitrogen mineralization, microbial NO3 assimilation and microbial NH4 assimilation to reflect slight changes in data processing. Those changes are reflected in "220829_All data_repository.csv". "220829_nitrogen_mineralization_readme.txt " is updated readme for the new file. The other 2 files begin with “220426_” are older version and same as in V1.

These data were used to make a predictive model of when ornate box turtles (Terrapene ornata) are likely to be above ground and at risk from fire. The data were generated using shell temperatures, soil temperatures at 0.35 m deep from known overwintering sites, and the spring and fall soil temperature inversion dates during 2019–2022 to infer if 26 individual radio-tracked turtles were above or below ground at three sites in Illinois.

This dataset containes the images of B73xMS71 RIL population used in QTL linkage mapping for maize epidermal traits in year 2016 and 2017. 2016RIL_all_mns.rar and 2017RIL_all_mns.rar: contain raw images produced by Nanofocus lsurf Explorer Optical Topometer (Oberhausen, Germany) at 20X magnification with 0.6 numerical aperture. Files were processed in Nanofocus μsurf analysis extended software (Oberhausen,Germany). 2016RIL_all_TIF.rar and 2017RIL_all_TIF.rar: contain images processed from the Topology layer in each nms file to strengthen the edges of cell outlines, and used in downstream cell detection. 2016RIL_all_detection_result.rar and 2017RIL_all_detection_result.rar: contain images with epidermal cells predicted using the Mask R-CNN model. training data.rar: contain images used for Mask R-CNN model training and validation.

___________________________________SUMMARY This dataset contains derivative data from concurrent fMRI and scalp EEG recordings used in: Mostame Parham, Wirsich Jonathan, Alderson Thomas H, Ridley Ben, Giraud Anne-Lise, Carmichael David W, Vulliemoz Serge, Guye Maxime, Lemieux Louis, Sadaghiani Sepideh (2024) A multiplex of connectome trajectories enables several connectivity patterns in parallel eLife 13:RP98777. doi: https://doi.org/10.7554/eLife.98777.3 ___________________________________RAW DATA The data has been originally published and described as part of other studies (Morillon et al., 2010; Sadaghiani et al., 2012). Briefly, 10 minutes of eyes-closed resting state were analyzed from 26 healthy subjects (average age = 24.39 years; range: 18-31 years; 8 females) with no history of psychiatric or neurological disorders. Informed consent was given by each participant and the study was approved by the local Research Ethics Committee (CPP Ile de France III). FMRI was acquired using a 3T Siemens Tim Trio scanner with a GE-EPI pulse sequence (TR = 2 s; TE = 50 ms; 40 slices; 300 volumes; field of view: 192×192; voxel size: 3×3×3 mm3). Structural T1-weighted scan were acquired using the MPRAGE pulse sequence (176 slices; field of view: 256×256; voxel size: 1×1×1 mm3). 62-channel scalp EEG (Easycap, with an additional EOG and an ECG channel) was recorded using an MR-compatible amplifier (BrainAmp MR, Brain Products) at 5Hz sampling rate. ___________________________________PREPROCESSING fMRI and EEG data were preprocessed with standard preprocessing steps as explained in detail elsewhere (Wirsich et al., 2020). In brief, fMRI underwent standard slice-time correction, spatial realignment (SPM12, http://www.fil.ion.ucl.ac.uk/spm/software/spm12). Structural T1-weighted images were processed using Freesurfer (recon-all, v6.0.0, https://surfer.nmr.mgh.harvard.edu/) in order to perform non-uniformity and intensity correction, skull stripping and gray/white matter segmentation. The cortex was parcellated into 68 regions of the Desikan-Kiliany atlas (Desikan et al., 2006). This atlas was chosen because —as an anatomical parcellation— avoids biases towards one or the other functional data modality. The T1 images of each subject and the Desikan-Killiany were co-registered to the fMRI images (FSL-FLIRT 6.0.2, https://fsl.fmrib.ox.ac.uk/fsl/fslwiki). We extracted signals of no interest such as the average signals of cerebrospinal fluid (CSF) and white matter from manually defined regions of interest (ROI, 5 mm sphere, Marsbar Toolbox 0.44, http://marsbar.sourceforge.net) and regressed out of the BOLD timeseries along with 6 rotation, translation motion parameters and global gray matter signal (Wirsich et al., 2017a). Then we bandpass-filtered the timeseries at 0.009–0.08 Hz. Average timeseries of each region was then used to calculate connectivity. EEG underwent gradient and cardio-ballistic artifact removal using Brain Vision Analyzer software (Allen et al., 1998, 2000) and was down-sampled to 250 Hz. EEG was projected into source space using the Tikhonov-regularized minimum norm in Brainstorm software (Baillet et al., 2001; Tadel et al., 2011). Source activity was then averaged to the 68 regions of the Desikan-Killiany atlas. Band-limited EEG signals in each canonical frequency band and every atlas region were then used to calculate frequency-specific connectome dynamics. Note that the MEG-ROI-nets toolbox in the OHBA Software Library (OSL; https://ohba-analysis.github.io/osl-docs/) was used to minimize source leakage in the band-limited source-localized EEG data (Colclough et al., 2015). ___________________________________FOLDER STRUCTURE The dataset includes five separate folders as described below: 1) EEGfMRI_dFC folder: connectome dynamics of scalp data This folder contains 26 single MATLAB (.mat) files for each subject. Inside each `.mat` is a structure with fields `A`, `B`, and `C`, corresponding to fMRI, amplitude-coupling, and phase-coupling connectome dynamics, respectively. The fMRI data are 3-dimensional (ROI × ROI × timepoints). The EEG data are stored in a 1×5 cell array (Delta, Theta, Alpha, Beta, Gamma), each cell containing a 3-D ROI × ROI × timepoints matrix. 2) EEGfMRI_dFC_SourceOrtho foldeR: connectome dynamics of source-orthogonalized scalp data Same format as above, except that EEG connectome dynamics are derived from source-orthogonalized signals. The MEG-ROI-nets toolbox in the OHBA Software Library (OSL; https://ohba-analysis.github.io/osl-docs/) was used to minimize source leakage in the band-limited, source-localized EEG data (Colclough et al., 2015). 3-5) Cross-modal Recurrence Plot (CRP) data Each subject has an Excel file with five sheets (Delta through Gamma), corresponding to the five frequency bands. Each sheet contains a 2-D CRP matrix (rows = fMRI timepoints, columns = band-limited EEG timepoints). - Scalp EEG–fMRI CRPs (CRP_EEGfMRI and CRP_EEGfMRI_SourceOrtho folder): two versions (with and without source-orthogonalization), each has 52 Excel files, including amplitude- and phase-coupling CRPs. - Intracranial EEG–fMRI CRPs (CRP_iEEGfMRI folder): one version, 27 Excel files, containing three cases: amplitude coupling, HRF-convolved amplitude coupling, and phase coupling.

This data and code accompany the manuscript "Small population size and possible extirpation of the threatened Malagasy poison frog Mantella cowanii". The data were collected using photograph capture-recapture at three sites in the central highlands of Madagascar. In Part 1, the script implements robust design capture-mark-recapture models in program MARK through the RMark interface to estimate population sizes and annual survival probabilities. In Part 2, it estimates the number of surveys needed to infer absence at sites where we did not detect the frog.

This data set contains data used for “Improved Net Carbon Budgets in the US Midwest through Direct Measured Impacts of Enhanced Weathering.” Data include biomass, soil bulk densities, soil respiration measurements, soil lanthanide element analysis, plant tissue analysis for major cations, and eddy covariance fluxes.

Zika virus (ZIKV) infection has been linked to neurological disorders such as microcephaly in children. Cases of Guillain-Barré Syndrome (GBS), a peripheral nervous system (PNS) disorder, have been reported in adults with ZIKV infection. These ZIKV-related GBS cases often exhibit atypical clinical features compared to classic GBS, including central nervous system (CNS) involvement. This dataset comprises two patient groups and a healthy control group. The first patient group includes adults with confirmed ZIKV infection, presenting both PNS-related GBS symptoms and CNS manifestations. The second group consists of adults with GBS but without ZIKV infection. The final group includes healthy, unaffected individuals.

A novel process applying high solids loading in chemical-free pretreatment and enzymatic hydrolysis was developed to produce sugars from bioenergy sorghum. Hydrothermal pretreatment with 50% solids loading was performed in a pilot scale continuous reactor followed by disc refining. Sugars were extracted from the enzymatic hydrolysis at 10% to 50% solids content using fed-batch operations. Three surfactants (Tween 80, PEG 4000, and PEG 6000) were evaluated to increase sugar yields. Hydrolysis using 2% PEG 4000 had the highest sugar yields. Glucose concentrations of 105, 130, and 147 g/L were obtained from the reaction at 30%, 40%, and 50% solids content, respectively. The maximum sugar concentration of the hydrolysate, including glucose and xylose, obtained was 232 g/L. Additionally, the glucose recovery (73.14%) was increased compared to that of the batch reaction (52.74%) by using two-stage enzymatic hydrolysis combined with fed-batch operation at 50% w/v solids content.

This data set is related to a SoyFACE experiment conducted in 2004, 2006, 2007, and 2008 with the soybean cultivars Loda and HS93-4118. The experiment looked at how seed elements were affected by elevated CO2 and yield. In this V2, 2 new files were added per journal requirement. Total there are 5 data files in text format within the digrado_et_al_gcb_data_V2 and 1 readme file. The name of files are listed below. Details about headers are explained in the readme.txt file. <b>1. ionomic_data.txt file</b> contains the ionomic data (mg/kg) for the two cultivars. The file contains all six technical replicates for each plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>2. yield_data.txt file</b> contains the yield data for the two cultivars (seed yield in kg/ha, seed yield in bu/a, Protein (%), Oil (%)). The file contains yield data for every plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>3. mineral_pro_oil_yield.txt file</b> contains the yield per hectare for each mineral (g/ha) along with the yield per hectare for protein and oil (t/ha). This was obtained by multiplying the seed content of each element (minerals, protein, and oil) by the total seed yield. The file contains yield data for every plots. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>4. economic_assessment.txt file</b> contains data used to assess the financial impact of altered seed oil content on soybean oil production. <b>5. meteorological_data.txt file</b> contains the meteorological data recorded by a weather station located ~ 3km from the experimental site (Willard Airport Champaign). Data covering the period between May 28 and September 24 were used for 2004; between May 25 and September 24 were used in 2006; between May 23 and September 17 in 2007; and between June 16 and October 24 in 2008.

This dataset includes a total of 16 images of 2 extant species of Podocarpus (Podocarpaceae) and 23 images of fossil specimens of the morphogenus Podocarpidites. The images were taken using a Zeiss LSM 880 microscope with Airyscan confocal superresolution 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 open microscopy software, such as ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/software/zeiss-zen/czi-image-file-format.html] For Podocarpus (modern specimens): Each folder is labelled by genus and contain all images corresponding to that genus. Detailed information about the folders, files, and specimens can be found in the Excel file "METADATA_Podocarpus_extant.csv". This file includes metadata on: species, slide ID, collection, folder name file name and notes. Images are of pollen grains from slides in the Florida Museum of Natural History collections. For Podocarpidites (fossil specimens): Each image is named after the sample from which it was derived. Detailed information about the specimens can be found in the Excel file "METADATA_ Podocarpidites_fossil.csv". This file includes metadata: the fossil type (Taxon), the slide and sample name (Slide Info), the location of the sample locality (Country, Latitude, Longitude), the age of the sample (Min age, Max age), the location of the specimen on the sample slide (England Finder coordinates), and the image file name. Images are of fossil pollen from slides in Smithsonian Tropical Research Institute collections. Please cite this dataset and listed publications when using these images.

In this study, the economics of producing biofuels from an industrial hemp (Cannabis sativa) genotype – 19m96136 was investigated. A lignocellulosic biofuel plant, hourly consuming 85 metric tons of hemp biomass was modeled in SuperPro Designer®. The integrated bioenergy plant produced hemp biodiesel and bioethanol from lipids and carbohydrates, respectively. The structural composition of the industrial hemp plant was analyzed in a previous study. The data obtained was used to simulate feedstock composition in SuperPro Designer®. The simulation results indicated that Hemp containing 2% lipids can yield up to 3.95 million gallons of biodiesel annually. On improving biomass lipid content to 5 and 10%, biodiesel production increased to 9.88 and 19.91 million gallons, respectively. The breakeven unit production cost of hemp biodiesel with 2, 5, and 10% lipid containing hemp was $18.49, $7.87, and $4.13/gallon, respectively. The biodiesel unit production cost when utilizing 10% lipid-containing hemp was comparable to soybean biodiesel at $4.13/gallon. Furthermore, sensitivity analysis revealed the possibility of a 7.80% reduction in unit production cost upon a 10% reduction in hemp feedstock cost. Furthermore, industrial hemp was capable of producing between 307.80 and 325.82 gallons of total biofuels per hectare of agricultural land than soybean.

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 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.