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This repository includes data sets and R scripts that were used to perform analysis and produce figures for the following publication: Salesse-Smith, C. E. et al. “Adapting C4 photosynthesis to atmospheric change and increasing productivity by elevating Rubisco content in sorghum and sugarcane.” Proceedings of the National Academy of Sciences 122, e2419943122 (2025) doi:10.1073/pnas.2419943122.

TBP assessment raw data files of pre- and post- motion capture velocity and center of pressure force plate data. Labels are self-explanatory. The .mat files refer to data exported from the force plate for the time-to-stabilization assessments while the .txt files are the data collected for smoothness of gait assessments. These files do not relate to one another and are from separate assessments. Version2's files are the result from using Python code Data_Bank_Cleaner.py on version1's. Please find more information in READ_ME_databank.txt.

Vector competence and survival data for Aedes albopictus mosquitoes exposed to Ross River virus

Baseline data from a multi-modal intervention study conducted at the University of Illinois at Urbana-Champaign. Data include results from a cardiorespiratory fitness assessment (maximal oxygen consumption, VO2max), a body composition assessment (Dual-Energy X-ray Absorptiometry, DXA), and Magnetic Resonance Spectroscopy Imaging. Data set includes data from 435 participants, ages 18-44 years.

Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.

Presence of free fatty acids along with glycerides poses a technical difficulty for biodiesel production. This work used a Taguchi L9 design to optimize the solvent-free enzymatic process to result in the esterification of oleic acid with glycerol. Under optimal conditions the esterification reaction temperature of 60°C, enzyme dose of 5 wt%, glycerol: oleic acid molar ratio of 5:1, and reaction time of 3 h, a 75.235 ± 2.19% conversion of oleic acid to esters was achieved. With the addition of molecular sieves, the conversion increased to 86.73% ± 1.09%. However, using the parameters predicted by Taguchi design (60°C, 5 wt%, 5:1, and 4.5 h), 88.5% ± 1.11% of oleic acid could be converted to esters derivative. Diglycerides were the major product, and the reaction equilibrium was attained after 4 h. The immobilized enzyme could be used up to seven times with only a 10% reduction in the conversion. Thus, the process can efficiently reduce the free fatty acid content of oil to make it suitable for biodiesel production.

This project investigates retraction indexing agreement among data sources: BCI, BIOABS, CCC, Compendex, Crossref, GEOBASE, MEDLINE, PubMed, Retraction Watch, Scopus, and Web of Science Core. Post-retraction citation may be partly due to authors’ and publishers' challenges in systematically identifying retracted publications. To investigate retraction indexing quality, we investigate the agreement in indexing retracted publications between 11 database sources, restricting to their coverage, resulting in a union list of 85,392 unique items. This dataset highlights items that went through a DOI augmentation process to have PubMed added as a source and that have duplicated PMIDs, indicating data quality issues.

The presence of free fatty acids interferes with the conversion of plant oils to biodiesel. Four strong and weak base resins were evaluated for the removal of free fatty acids (FFA) from oil. Amberlite FPA 51 showed the highest adsorption capacity of FFA. A resin concentration above 3% could enable a higher percentage FFA adsorption. The adsorption process fitted a pseudo-first-order kinetic model and achieved equilibrium in approximately 8 h. A full factorial design was used to optimize the resin and FFA concentrations at a fixed temperature (40° C). A ratio of resin to fatty acid concentrations above 1.875 was sufficient for 70% adsorption and the amount adsorbed continued to increase with further added resin. A two-step washing of resin using hexane and ethanol recovered approximately 67.55% ± 4.05% of the initially added fatty acid. The resin that was used was regenerated with 5% NaOH and re-used for a minimum of three consecutive cycles. However, the adsorption capacity diminished to 75% of the initial cycle in cycles 2 and 3. Thus, the work presents a resin-based process for deacidification of oil to reduce fatty acid content of oil for biodiesel production.

Data and documentation for Ornithological Applications manuscript “Integrating multiple data sources improves prediction and inference for upland game bird occupancy models” by Robert L. Emmet, Thomas J. Benson, Maximilian L. Allen, and Kirk W. Stodola We combined data from the North American Breeding Bird Survey and eBird with a targeted survey (IDNR upland game) to estimate habitat use of northern bobwhite and ring-necked pheasant in Illinois and to document the efficiency and overlap among the various data sources. Data include, eBird, USGS Breeding Bird Survey, National Land Cover Database, Upland game bird surveys, stream data)

Use of corn fractionation techniques in dry grind process increases the number of coproducts, enhances their quality and value, generates feedstock for cellulosic ethanol production and potentially increases profitability of the dry grind process. The aim of this study is to develop process simulation models for eight different wet and dry corn fractionation techniques recovering germ, pericarp fiber and/or endosperm fiber, and evaluate their techno-economic feasibility at the commercial scale. Ethanol yields for plants processing 1113.11 MT corn/day were 37.2 to 40 million gal for wet fractionation and 37.3 to 31.3 million gal for dry fractionation, compared to 40.2 million gal for conventional dry grind process. Capital costs were higher for wet fractionation processes ($92.85 to $97.38 million) in comparison to conventional ($83.95 million) and dry fractionation ($83.35 to $84.91 million) processes. Due to high value of coproducts, ethanol production costs in most fractionation processes ($1.29 to $1.35/gal) were lower than conventional ($1.36/gal) process. Internal rate of return for most of the wet (6.88 to 8.58%) and dry fractionation (6.45 to 7.04%) processes was higher than the conventional (6.39%) process. Wet fractionation process designed for germ and pericarp fiber recovery was most profitable among the processes.

DNA aptamers have been widely used as biosensors for detecting a variety of targets. Despite decades of success, they have not been applied to monitor any targets in plants, even though plants are a major platform for providing oxygen, food, and sustainable products ranging from energy fuels to chemicals, and high-value products such as pharmaceuticals. A major barrier to progress is a lack of efficient methods to deliver DNA into plant cells. We herein report a thiol-mediated uptake method that more efficiently delivers DNA into Arabidopsis and tobacco leaf cells than another state-of-the-art method, DNA nanostructures. Such a method allowed efficient delivery of a glucose DNA aptamer sensor into Arabidopsis for sensing glucose. This demonstration opens a new avenue to apply DNA aptamer sensors for functional studies of various targets, including metabolites, plant hormones, metal ions, and proteins in plants for a better understanding of the biodistribution and regulation of these species and their functions.

We present a new strategy for the production of a δ-lactam from glucose that integrates biological production of triacetic acid lactone (TAL, 4-hydroxy-6-methyl-2H-2-one) with catalytic transformation of TAL into 6-methylpiperidin-2-one (MPO) through metabolic engineering, isomerization, amination, and catalytic hydrogenation/hydrogenolysis. We developed a sustainable and antibiotic-free fed-batch fermentation using genetically modified Rhodotorula toruloides IFO0880. This process achieved a yield of 2-hydroxy-6-methyl-4H-pyran-4-one (2H4P) at 0.05 g/g of glucose, corresponding to a 9.9 g/L titer. By adjusting the pH of the fermentation broth to 2, 2H4P was quantitatively converted into TAL. The TAL in the fermentation broth was directly converted by aminolysis into 4-hydroxy-6-methylpyridin-2(1H)-one (HMPO), which achieved an 18.5% yield with 94.3% purity. The HMPO yield was lower in the fermentation broth than in a clean feedstock (32.2%), suggesting that the biological impurities are inhibitors in this reaction. Further investigation revealed that lower pH levels and reduced TAL concentrations in the fermentation broth significantly decreased HMPO yields. Subsequently, the precipitated HMPO was filtered and dried and then subjected to the final catalytic conversion in H2O solvent, achieving a MPO yield of 91.8%. This integrated approach demonstrated the direct use of TAL in the filtered aqueous fermentation broth without the need to isolate TAL.

The text file contains the original DNA sequence data used in the phylogenetic analyses of Krishnankutty et al. (2016: Systematic Entomology 41: 580–595). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The file contains five separate data blocks, one for each character partition (28S, histone H3, 12S, indels, and morphology) for 53 taxa (species). Gaps inserted into the DNA sequence alignment are indicated by a dash, and missing data are indicated by a question mark. The separate "indels1" block includes 40 indels (insertions/deletions) from the 28S sequence alignment re-coded using the modified complex indel coding scheme, as described in the "Materials and methods" of the original publication. The DIMENSIONS statements near the beginning of each block indicate the numbers of taxa (NTax) and characters (NChar). The file contains aligned nucleotide sequence data for 3 gene regions and 40 morphological characters. The file is configured for use with the maximum likelihood-based phylogenetic program GARLI but can also be parsed by any other bioinformatics software that supports the NEXUS format. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the supplementary document included as a separate pdf. The original raw DNA sequence data are available from NCBI GenBank under the accession numbers indicated in the supporting pdf file. More details on individual analyses are provided in the original publication.

This data contains bam files and transcripts in the simulated instances generated for the paper 'JUMPER: Discontinuous Transcript Assembly in SARS-CoV-2' submitted for RECOMB 2021. The folder 'bam' contained the simulated bam files aligned using STAR wile the reads were generated using the method polyester Note: in the readme file, close to the end of the document, please ignore this sentence: 'Those files can be opened by using [name of software].'

We developed a new application of isotopic gas exchange which couples a tunable diode laser absorption spectroscope (TDL) with a leaf gas exchange system, analyzing leakiness through induction of C4 photosynthesis on dark to high-light transitions. The youngest fully expanded leaf was measured on 40-45 day-old maize(B73) and sorghum (Tx430). Detail definition of each variable in raw Li-6400XT and Li-6800 (in "Original_data_AND_Data_processing_code.zip") is summarized in: <a href="https://www.licor.com/env/support/LI-6800/topics/symbols.html#const">https://www.licor.com/env/support/LI-6800/topics/symbols.html#const</a>

The dataset contains the data and code for Single-cell and Subcellular Analysis of freshly isolated cultured, uncultured P1 cells and uncultured Old cells. The .csv file named 'MagLab20220721' contains the sample and intensity information with the columns referring to the m/z values and the rows being the samples. The 'MagLabNameINdex.csv' file contains all the index information. The file named '20220721_MagLab.spydata' contains the loaded data of both the two previous files in Spyder. The .mat file contains the aligned data for the three groups.

5-hydroxymethyl furfural (HMF) and furfurals are DOE-listed platform chemicals that can be derived from the renewable carbon in the lignocellulosic biomasses and have the potential to replace petroleum-derived alternatives. High substrate cost and use of expensive solvents limit the economic feasibility of bio-based HMF production on an industrially relevant scale. The study presents an experimental optimized condition that maximizes the chemical-free production of HMF and furfurals without lowering the yield of total fermentable sugars from Saccharum bagasse. Hydrothermal pretreatment at 210 °C for 15 min yielded approximately 10%, 12%, and 46% of HMF, furfurals, and fermentable sugars per gram of dry biomass, respectively. Additionally, the study proposes a consolidated bioprocess model to produce and recover four high-value bioproducts i.e., HMF, furfurals, ethanol, and acetic acid based on the experimental results and evaluates its technoeconomic feasibility considering HMF as the main product. The minimum selling price (MSP) of HMF was estimated to be 930.6 USD/t which is competitive with its petroleum-derived precursor alternative p-xylene (1,113 USD/t). The sensitivity analysis performed for the process parameters suggests that pretreatment cost and revenues from coproducts immensely influence the MSP of HMF. The preliminary technoeconomic analysis performed on the consolidated bioprocess design indicates that additional revenue streams from diversified coproducts in biorefineries aid in lowering the MSP of high-value bioproducts.

Aerial imagery utilized as input in the manuscript "Deep convolutional neural networks exploit high spatial and temporal resolution aerial imagery to predict key traits in miscanthus" . Data was collected over M. Sacchariflorus and Sinensis breeding trials at the Energy Farm, UIUC in 2020. Flights were performed using a DJI M600 mounted with a Micasense Rededge multispectral sensor at 20 m altitude around solar noon. Imagery is available as tif file by field trial and date (10). The post-processing of raw images into orthophoto was performed in Agisoft Metashape software. Each crop surface model and multispectral orthophoto was stacked into an unique raster stack by date and uploaded here. Each raster stack includes 6 layers in the following order: Layer 1 = crop surface model, Layer 2 = Blue, Layer 3 = Green, Layer 4 = Red, Layer 5 = Rededge, and Layer 6 = NIR multispectral bands. Msa raster stacks were resampled to 1.67 cm spatial resolution and Msi raster stacks were resampled to 1.41 cm spatial resolution to ease their integration into further analysis. 'MMDDYYYY' is the date of data collection, 'MSA' is M. Sacchariflorus trial, 'MSI' is Miscanthus Sinensis trial, 'CSM' is crop surface model layer, and 'MULTSP' are the five multispectral bands.

Corbicula spp. are one of the most prolific aquatic invasive species in the world and can have negative effects on aquatic ecosystems. We performed qualitative field surveys, examined literature accounts and natural history museum holdings, and accessed citizen science data sources to document the distribution of Corbicula in Mexico and shared drainages. Through 26 publications (N = 127 records), 312 museum holdings, and 446 iNaturalist records, we documented 885 records pertaining to Corbicula in Mexico and shared drainages. The first record of the species in Mexico was in 1969, and it has since been reported from 26 of the 32 Mexican states and most of the major river basins throughout the country. However, we suggest Corbicula is more prevalent in Mexico than we report in this work as it is often under sampled / under reported.

This repository contains the the data and code to recreate the simulations in "High Costs of GHG Abatement with Electrifying the Light-Duty Vehicle Fleet with Heterogeneous Preferences of Vehicle Consumers." The model can be run by calling the bash file in the SLURM environment with parameters set for different scenarios. BEPEAM-E model details: (1) the "Main.gms" file in GAMS format that contains the initiating stage settings with input and main optimization model (2) the "output.gms" file in GAMS format that prepare the output file from BEPAM model. (3) the rest are the intermediate input files for model to generate the input and output files for the model. (4) Four bash files are the script file that call the GAMS model on the HPC that includes both HPC environment and the scenario settings. Four bash files are uploaded corresponding to 4 scenarios

The optimal flowering time for bioenergy crop miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.

Miscanthus × giganteus (Miscanthus) is a warm-season perennial grass grown for bioenergy feedstock production. Nitrogen (N) fertilizer management is crucial for the sustainability of Miscanthus production. In our two-year study (2018 and 2019), we investigated the role of vegetation indices (VIs) in evaluating N fertilization (0 N, 56 N, 112 N, and 168 N kg ha−1) impacts on Miscanthus biomass yield and stand health. The flight campaigns were conducted early, middle, and late during the summer growing season. Among the VIs, mid-summer growing season NDRE provided the best prediction of fresh biomass (R2 = 0.87 and 0.97) and dry biomass (R2 = 0.89 and 0.97) in 2018 and 2019, respectively. The VIs generally showed that it was possible to distinguish between 0 N and 168 N treatments, but neither 0 N and 56 N kg ha−1 nor 112 N and 168 N kg ha−1 could be separated. The results from this study highlight the importance of moderate application of N (112 kg N ha−1) in improving and maintaining the stand health and biomass yield of Miscanthus over time and suggest that mid-summer growing season VIs, NDRE in particular, can be useful for assessment of Miscanthus stand health and biomass yield.

This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.

The file contains biomass and count data of food items encountered in the digestive tract of collected green-winged teal from the Illinois River Valley during spring 2016-2018. The file also contains biomass of food items collected from core samples collected at sites where the green-winged teal were collected. Together, the consumed and availability food data are used to calculate diet selection. The data also contains information on the teal, collection, sites, and other covariates used in analysis. Lastly, the dataset contains biomass of food items collected in medium (#35) and small (#60) sieves for 2018 core samples.

The aim of this study was to determine carbohydrate recovery from hemp for ethanol production and quantify biodiesel from TAG (triacylglycerol) present in hemp. The structural composition of five different hemp varieties (Seward County-SC, York County-YC, Loup County-LC, 19 m96136-19 m, and CBD Hemp-CBD) were analyzed. Concentration of glucan and xylan ranged between 32.63 to 44.52% and 10.62 to 15.48% respectively. The biomass was then pretreated with Liquid hot water followed by disk milling and then hydrolyzed enzymatically to yield monomeric sugars. High glucose (63-85%) and xylose (73-88%) recovery was achieved. Lipids were extracted from hemp using hexane and isopropanol and then transesterified to produce biodiesel. Approximately, 50% of total fatty acids in SC, LC, and CBD hemp were linoleic acid. Palmitic acid was present between 32 to 50% in varieties YC and 19 m. Highest TAG concentration at 25% of total lipids was observed in CBD hemp. The analysis on lipid composition and high sugar recovery demonstrates hemp as a potential bioenergy crop for ethanol and biodiesel coproduction.