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Raw data from a survey of para-veterinary workers in Pakistan regarding knowledge, attitudes, and practices around ticks and tick-borne diseases. Between March and August 2023, we conducted a web-based survey among para-veterinarians recruited via email, text message, and face-to-face conversations.

Glucose and xylose are the major sugars present in cellulosic hydrolysates. The cellulosic sugars can be used for the production of platform chemicals. In this study, productions of lipid and ethanol by yeasts were compared for concentrated bioenergy sorghum syrup. Bioenergy sorghum was hydrothermally pretreated at 50% w/w solids in a continuous industrial reactor and sequentially mechanically refined using a burr mill to improve biomass accessibility for hydrolysis. Fed-batch enzymatic hydrolysis was conducted with 50% w/v solids loading and cellulase cocktail (50 FPU/g biomass) to achieve 230 g/L sugar concentration. Various strains of Rhodosporidium toruloides were evaluated for converting sugars into lipids, and strain Y-6987 had the highest lipid titer (9.2 g/L). The lipid titer was improved to 19.0 g/L by implementing a two-stage culture scheme, where the first stage was optimized for yeast growth and the second for lipid production. For ethanol production, the engineered Saccharomyces cerevisiae SR8ΔADH6 was used to coferment glucose and xylose. Ethanol fermentation was optimized for media nutrients (YP, YNB/urea, and urea), cellulosic sugar concentration, and sulfite conditioning to maximize the ethanol concentration from sorghum syrups. Fermentation of 70% v/v concentrated hydrolysate conditioned with sulfite produces 50.1 g/L ethanol from 141 g/L of sugars.

This dataset is part of a genome annoucement. The main folder PROKKA_results contain nine Prokka v.1.14.6 annotation files from nine Clostridium scindens genome sequences. Each file provide 12 output files including predicted protein sequences (.faa), nucleotide sequences of the predicted coding regions (.ffn), nucleotide sequence of the genome (.fna and .fsa), annotated genome in GenBank format (.gbk), steps recording performed during the annotation process (.log), error messages or warnings (.err), annotations in Sequin format (.sqn), summary of the annotations in tabular (.tbl), tab-separated values (.tsv) and plain text (.txt) formats.

The International Registry of Reproductive Pathology Database is part of pioneering work done by Dr. Kenneth McEntee to comprehensively document thousands of disease cases studies. His large and comprehensive collection of case reports and physical samples was complimented by development of the International Registry of Reproductive Pathology Database in the 1980s. The original FoxPro Database files and a migrated access version were completed by the College of Veterinary Medicine in 2016. Access CSV files were completed by the University of Illinois Library in 2017.

This dataset includes data on soil nitrous oxide fluxes, soil properties, and climate presented in the manuscript, "A conceptual model explaining spatial variation in soil nitrous oxide emissions in agricultural fields," published in Commucations Earth & Environment. Please refer to that publication for details about methodologies used to generate these data and for the experimental design.

This supporting information file contains codes related to pending publication Ge et al. Proc. Nat. Acad. Sci. USA, (revisions in review). The contents include a Mathematica code that solves the Laplace transformed equations and generates figures from the paper. A python code is included for generation of Figure 5 in the main text.

Count histories from camera traps and remotely sensed covariate data used in N-mixture modeling to assess the site use intensity of raccoons in Illinois.

Includes two files (.csv) behind all analyses and results in the paper published with the same title. <b>1) 'sites.species.counts'</b> is the raw 2018-2022 data from Angella Moorehouse (Illinois Nature Preserves Commission) including her 456 identified pollinator species and her raw counts per site (there may be a few errors of identification or naming, and there will always be name changes over time). Headers in columns F through Q correspond to the remnant-site labels in Figure 1 and Table 1 of the paper. Columns R to AB are the “nonremnant” sites, which have not been uniquely labelled since the specific sites aren't referenced anywhere in the manuscript. <b>2) 'C.scores'</b> has the 265 species assigned empirical C values (empirical.C) along with the four sets of expert C values and their confidence ranks (low, medium, high), and the Illinois/Indiana conservation ranks (S-ranks), following the methods described in the paper. Other headers in these files: - taxa.code: four-letter abbreviation for genus and specific name - genus: genus name - species: specific epithet - common.name: English name - group: general pollinator taxa group - empirical.C: empirically estimated conservatism score - expert#.C: conservatism score assigned by each of four experts - expert#.conf: expert's confidence in their conservatism score Blank cells in the site-species abundance matrix indicates species absence (or non-detection) Blank cells in C.scores.csv indicates missing S-ranks and unassigned C-scores (with associated missing confidence ranks) where experts lacked knowledge or confidence

The dataset is for a study conducted to understand genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single nucleotide polymorphisms (SNPs).

This study advances the production of potassium sorbate (KS) from triacetic acid lactone (TAL) utilizing food-grade solvents, ethanol (EtOH) and isopropyl alcohol (IPA). We have previously demonstrated the route to produce KS from TAL in tetrahydrofuran (THF) as the main solvent, but the use of THF is associated with environmental and health risks especially for food applications. The process employs a catalytic approach in food-grade solvents and includes three main steps: hydrogenation, etherification and hydrolysis, and ring-opening hydrolysis to produce KS from TAL. In the synthesis of KS from TAL, the use of IPA leads to higher yields and reduced reaction times compared to EtOH. As a result, the overall reaction time in IPA was reduced to 35.7 h, compared to 42.1 h in our previous study using THF and EtOH, while achieving a comparable KS yield of 84% from TAL. The synthesized KS exhibits a trans-2, trans-4 geometrical configuration, identical to that of commercially available KS. Through techno-economic analysis (TEA) and life cycle assessment (LCA), we estimated full-scale production of KS from sugarcane with the developed process in IPA could achieve a minimum product selling price (MPSP) of $8.27 per kg with a range of $7.06–10.16 per kg [5th–95th percentiles from 6000 Monte Carlo simulations] and a carbon intensity (CI) of 13.7 [9.6–18.6] kg CO2-eq per kg. This study highlights the synthesis of KS from TAL using food-grade solvents, demonstrating improved economic viability and environmental sustainability compared to our previous research (MPSP of $9.68 per kg [$8.47–11.45 per kg] and CI of 16.2 [12.0–21.2] kg CO2-eq per kg), as the total required reaction decreases while achieving the comparable overall yield of KS from TAL.

Nucleotide sequences from wild parsnip CYP71AJ4 (angelic in synthase. <a href ="https://www.ncbi.nlm.nih.gov/nuccore/EF191021">Genbank EF191021</a>) were obtained by Sanger sequencing. Seeds from individual plants from different populations were harvested to obtain corresponding cDNA. The cDNA was cloned and directly sequenced. Aminoacid translations were obtained using standard codon usage. Alignments of CYP71AJ4 sequences (involved in angular furanocoumarin biosynthesis) with as the reference sequence. Consistent amino acid variabilities were found between some populations. The relationship between sequencing variability and selective pressure is not yet known.

This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.

Bioenergy sorghum (Sorghum bicolor L. Moench) is a promising crop for contributing to the United States bioenergy supply. However, the varying limitations of the marginal lands targeted for its cultivation present a management challenge. This two-year study aimed to investigate how the limitations associated with marginal cropland impact the effects of nitrogen fertilization on the yield of bioenergy sorghum and the uptake of 11 macro- (N, P, K, Ca, Mg, and S) and micronutrients (Fe, Mn, Zn, Cu, and B). The study contrasted prime cropland in central Illinois (Urbana) with three marginal cropland sites in southern (Ewing) and central Illinois (Fairbury and Pesotum). These marginal cropland sites are characterized by varying limitations, including low soil fertility (P and K limitations), leaching and erosion, and flooding, respectively. Four nitrogen rates (0, 56, 112, and 168 kg N ha−1) were tested under eight environments. The average yields and ranges of sorghum biomass were 20.2 (17.0–23.2) Mg ha−1 in Urbana, 18.1 (13.1–19.8) Mg ha−1 in Ewing, 13.8 (9.0–17.3) Mg ha−1 in Fairbury, and 23.3 (14.6–33.0) Mg ha−1 in Pesotum. Optimal N rates were 56 N in Pesotum and 112 N in Urbana, Ewing, and Fairbury. Tissue macronutrient contents in Urbana were generally higher than in the marginal croplands, while micronutrient contents did not show discernible trends. Increasing N rate generally correlated with the macronutrient removal except in Ewing. Comparable sorghum biomass yields were observed between prime and marginal croplands (averaging 18.3 Mg ha−1), but optimal N rates varied between 56 N and 112 N. This suggests that yield gaps can be narrowed by applying the optimal N rates for the respective locations. However, increased removals of macronutrients, especially P and K, with increasing yields indicate the need to revise fertilizer recommendations, particularly for soils deficient in these nutrients. Our study suggests that while sorghum production on marginal cropland is feasible, N management needs to be adapted to the unique limitations associated with various types of marginal cropland.

This dataset consists of the secondary ion mass spectrometry (SIMS) depth profiling data that was collected with a Cameca NanoSIMS 50 instrument from a 10 micron by 10 micron region on a Madin-Darby canine kidney (MDCK) cell that had been metabolically labeled so most of its sphingolipids and cholesterol contained the rare nitrogen-15 oxygen-18 isotopes, respectively.

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.