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This work evaluates the consistency and reliability of the title flag, i.e., retraction labeling that appears in the title of retracted publications, using 925 sampled retracted publications indexed in the Crossref only (Lee & Schneider, 2023), that are indexed in three other sources, Retraction Watch, Scopus, and Web of Science as of April 2023. We presume the retraction status of an item based on its title flag. For example, the flag "removal notice" is a retraction notice, and "retracted article" is a retracted paper. We compared the item's likely retraction status from the flag with the item's actual retraction status from the publisher's website.

Conversion of corn fiber to ethanol in the dry grind process could increase ethanol yields, reduce downstream processing costs and improve overall process profitability. This work investigates the in-situ conversion of corn fiber into ethanol (cellulase addition during simultaneous saccharification and fermentation) during dry grind process. Addition of 30 FPU/g fiber cellulase resulted in 4.6% increase in ethanol yield compared to the conventional process. Use of excess cellulase (120 FPU/g fiber) resulted in incomplete fermentation and lower ethanol yield compared to the conventional process. Multiple factors including high concentrations of ethanol and phenolic compounds were responsible for yeast stress and incomplete fermentation in excess cellulase experiments.

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted 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). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus. This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus.

Lipids produced using oleaginous yeast cells are an emerging feedstock to manufacture commercially valuable oleochemicals ranging from pharmaceuticals to lipid-derived biofuels. Production of biofuels using oleaginous yeast is a multistep procedure that requires yeast cultivation and harvesting, lipid recovery, and conversion of the lipids to biofuels. The quantitative recovery of the total intracellular lipid from the yeast cells is a critical step during the development of a bioprocess. Their rigid cell walls often make them resistant to lysis. The existing methods include mechanical, chemical, biological and thermochemical lysis of yeast cell walls followed by solvent extraction. In this study, an aqueous thermal pretreatment was explored as a method for lysing the cell wall of the oleaginous yeast Rhodotorula toruloides for lipid recovery. Hydrothermal pretreatment for 60 min at 121 °C with a dry cell weight of 7% (w/v) in the yeast slurry led to a recovery of 84.6 ± 3.2% (w/w) of the total lipids when extracted with organic solvents. The conventional sonication and acid-assisted thermal cell lysis led to a lipid recovery yield of 99.8 ± 0.03% (w/w) and 109.5 ± 1.9% (w/w), respectively. The fatty acid profiles of the hydrothermally pretreated cells and freeze-dried control were similar, suggesting that the thermal lysis of the cells did not degrade the lipids. This work demonstrates that hydrothermal pretreatment of yeast cell slurry at 121 °C for 60 min is a robust and sustainable method for cell conditioning to extract intracellular microbial lipids for biofuel production and provides a baseline for further scale-up and process integration.

This dataset contains all raw data corresponding to the figures in the main text and appendices of the paper "Dispersion Engineering of Planar Sub-millimeter Wave Waveguides and Resonators with Low Radiation Loss."

Data for 'Atomic-scale imaging and charge state manipulation of NV centers by scanning tunneling microscopy' to be published in Nature Communications.

Most native producers of ribosomally synthesized and post-translationally modified peptides (RiPPs) utilize N-terminal leader peptides to avoid potential cytotoxicity of mature products to the hosts. Unfortunately, the native machinery of leader peptide removal is often difficult to reconstitute in heterologous hosts. Here we devised a general method to produce bioactive lanthipeptides, a major class of RiPP molecules, in Escherichia coli colonies using synthetic biology principles, where leader peptide removal is programmed temporally by protease compartmentalization and inducible cell autolysis. We demonstrated the method for producing two lantibiotics, haloduracin and lacticin 481, and performed analog screening for haloduracin. This method enables facile, high throughput discovery, characterization, and engineering of RiPPs.

Conversion of corn fiber to ethanol in the dry grind process can increase ethanol yields, improve coproduct quality and contribute to process sustainability. This work investigates the use of two physio-chemical pretreatments on corn fiber and effect of cellulase enzyme dosage to improve ethanol yields. Fiber separated after liquefaction of corn was pretreated using (1) hot water pretreatment (160°C for 5, 10 or 20 min); and (2) wet disk milling and converted to ethanol. The conversion efficiencies of hot water pretreated fiber were higher than untreated fiber, with highest increase in conversion (10.4%) achieved for 5-minute residence time at 160 °C. Disk milling was not effective in increasing conversion compared to other treatments. Hydrolysis and fermentation of untreated fiber with excess cellulase enzymes resulted in 33.3% higher conversion compared to untreated fiber. Note: in “Table1_Treatments.csv”, NA = Not applicable.

Datasheets relating to the article "Brachypodium SPEECHLESS2 promoter drives expression of a synthetic EPF to reduce stomatal density in sugarcane without pleiotropic effects" published in Plant Biotechnology Journal.

The increased awareness for eco-friendliness and sustainability has shifted the interest of stakeholders from synthetic colors to natural plant-based pigments. In this study, purple stemmed Miscanthus x giganteus was evaluated as a source of anthocyanins. Hydrothermal pretreatment was studied as a green, chemical-free process for recovering maximum anthocyanins in the pretreatment liquor. The highest recovery of 94.3 ± 1.5% w/w of the total anthocyanin concentration was obtained for a temperature and time combination of 170 °C and 10 min. The pretreatment also improved the enzymatic digestibility of the biomass and led to a 2.1-fold increase in the overall recovery of glucose (70.6 ± 0.5% w/w) at the end of 72 h. The sugar monomers obtained after the enzymatic hydrolysis of the pretreated biomass could be used for the production of biofuels or biochemicals in an integrated biorefinery based on purple-stemmed miscanthus. Overall, this study demonstrates that the clean pretreatment method developed could lead to an additional product stream (rich in anthocyanins) along with its effect in reducing the recalcitrance of miscanthus biomass.

This dataset consists of raw ADC readings from a 3 transmitter 4 receiver 77GHz FMCW radar, together with synchronized RGB camera and depth (active stereo) measurements. The data is grouped into 4 distinct radar configurations: - "indoor" configuration with range <14m - "30m" with range <38m - "50m" with range <63m - "high_res" with doppler resolution of 0.043m/s # Related code https://github.com/moodoki/radical_sdk # Hardware Project Page https://publish.illinois.edu/radicaldata

This dataset contains the following to replicate figures from "TChem-atm (v2.0.0): Scalable Performance-Portable Multiphase Atmospheric Chemistry" submitted to Geophysical Model Development (GMD). It contains (1) the simulation inputs, outputs and analysis notebook for recreating the PartMC-CAMP and PartMC-TChem-atm comparison and (2) scripts, timing results and analysis tools for recreating the performance evaluation. Users can either inspect the raw output to verify the results of the manuscript or rerun simulations using the provided inputs. Additionally, modifiying the inputs allows for for further exploration of both model simulation and performance characteristics.

The data within consist of compressed output files in the form of edgelists (*.edgelist.gz) and nodelists (*.aux.parquet) from large citation network simulations using an agent-based model. The code and instructions are available at: <a href="https://github.com/illinois-or-research-analytics/SASCA">https://github.com/illinois-or-research-analytics/SASCA</a>. In addition, we provide a distribution of citation frequencies drawn from a random sample of PubMed journal articles (pooled_50k_pubmed_unique.csv) and a table of recencies- the frequency with which citations are made to the previous year, the year before that and so on (recency_probs_percent_stahl_filled.csv). A manuscript describing the SASCA-s simulator has been submitted for review and will be referenced in a future version of this data repository if it is accepted. The prefixes sj and er refer to the real world and Erdos-Renyi random graph respectively that were used to initiate simulations. These 'seed' networks are available from the Github site referenced above.

Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae. The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an engineered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

DayCent MUVP version (Methanogenesis, UV litter degradation and Photosynthesis). DAYCENT is the daily time-step version of the CENTURY biogeochemical model (Parton et al., 1994). DAYCENT simulates fluxes of C and N among the atmosphere, vegetation, and soil (Del Grosso et al., 2001a; Parton et al., 1998). Key submodels include soil water content and temperature by layer, plant production and allocation of net primary production (NPP), decomposition of litter and soil organic matter, mineralization of nutrients, N gas emissions from nitrification and denitrification, and CH4 oxidation in non-saturated soils.

Dataset generated using the technique described in "EC-SBM synthetic network generator". This contains multiple synthetic networks with ground-truth community structure, which can be used to evaluate community detection methods. Note: * networks.zip contains the synthetic networks

Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts, and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a buffer modification workflow (BMW) in which the same sample is run by LC-MS in both liquid chromatography solvent with 14NH3–acetate buffer and in solvent with the buffer modified with 15NH3–formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Overall, it identified 26% of ∼27 000 liver LC-MS features as putative metabolites, of which ∼2600 showed HMDB or KEGG database formula match. This workflow is well suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.

BEPAM, Biofuel and Environmental Policy Analysis Model, models the agricultural sector and determines economically optimal land-use and feedstock mix at the US scale by maximizing the sum of agricultural sector consumers’ and producers’ surplus subject to various resource balances, land availability, and technological constraints under a range of biomass prices, from zero to $140 Mg-1 over the 2016-2030 period. Here BEPAM is used to model SAF production using energy crops and crop residues. BEPAM uses the GAMS format and uses yield and GHG balance projections from the biogeochemical model, DayCent.

This page contains the data for the publication "Myc and Tor drive growth and cell competition in the regeneration blastema of Drosophila wing imaginal discs" published in Development, 2025.

Data consist of 55 acoustic recordings collected using Autonomous Recording Units (ARUs) from two locations and sampling periods. Specifically, data include 60-minute WAV files (8 folders, each contains 5 WAV files) from a field trial during February 2025 whereby we shot shotguns at varying distance from ARUs at Emiquon Reserve owned by The Nature Conservancy. Data also include 60-minute WAV files (15 WAV files) from one ARU placed at Big Rice Lake State Fish and Wildlife Area on opening day of waterfowl hunting season during 10-26-2024. Filenames include the ARU ID separated by underscores and the associated date and time e.g., MINI10_20241026_060002.wav was from MINI10 on 10/26/24 at 6 AM.

We apply prospect theory to examining farmers’ economic incentives to divert a share of their land to bioenergy crops (miscanthus and switchgrass in this study). Numerical simulation is conducted for 1,919 rain‐fed U.S. counties to identify the impact of loss aversion on bioenergy crop adoption, and how this impact is influenced by biomass price, discount rate, credit constraint status, and policy instruments. Results show that ignoring farmer’s loss aversion causes overestimation of miscanthus production but underestimation of switchgrass production, particularly when farmers are credit constrained and have a high discount rate. We find that establishment cost subsidy induces more miscanthus production whereas subsidized energy crop insurance induces more switchgrass production. The efficacy of these two policy instruments, measured by biomass production increased by per dollar of government outlay, depends on the magnitude of farmers’ loss aversion and discount rate.

The lack of farmers’ willingness to grow perennial bioenergy crops (PBCs) presents a critical barrier to the emergence of cellulosic biofuel production. The willingness relies on a complex network of economic, environmental, and social drivers, among which the influence of social factors (e.g., the influence of neighborhood, community, and communication) is less understood. This study addresses this knowledge gap via a survey analysis of midwestern farmers. The survey data are analyzed through ordinary least square regression and structural equation model, which together investigate the individual and interactive impacts of multiple factors on farmers’ decisions to adopt PBCs. Based on a farm-scale analysis, six statistically significant predictors of farmer willingness to grow PBCs are identified: perception of PBCs’ environment benefits, education level, willingness to take risks, familiarity with PBCs, portion of peers already growing PBCs, and support of biorefineries locating in the local community. Among these, the latter three predictors are social support variables. It is found that familiarity with the crops is the most significant predictor of willingness; familiarity is also an important intermediate variable that mediates the influence of many other predictors. In addition, peer adoption can both directly and indirectly affect willingness via its influence on familiarity. These findings suggest that it is a pressing need to improve farmers’ knowledge of PBCs to promote the adoption of such crops.

The selection of pretreatment methods is critical to achieving high product yields during bioconversion of lignocellulosic biomass. Hydrothermal, soaking-in-aqueous ammonia, and ionic liquid pretreatment methods are viable candidates for minimizing sugar decomposition, permitting the effective hydrolysis of structural carbohydrates, and producing a fermentable substrate suitable for achieving industrial ethanol titers and yields. In this study, the effect of these three pretreatment methods on non-modified sugarcane cultivar CP88-1762 and two transgenic lipid-accumulating sugarcane lines, oilcane 1565 and oilcane 1566, were investigated and compared in terms of lipid recovery, sugar yield, and ethanol yields within the lignocellulosic biomass conversion pipeline. Fed-batch enzymatic hydrolysis at high solid loading yielded hydrolysates capable of supporting industrial bioethanol titers across all conditions. The highest sugar yields were obtained on ammonia-pretreated biomass hydrolysate (253.73 g L−1), followed by hydrothermally pretreated hydrolysate (213.10 g L−1) and ionic liquid-pretreated hydrolysate (154.20 g L−1). Commercially viable ethanol titers of 100.62 g L−1, 64.47 g L−1, and 52.95 g L−1 were achieved from ammonia, hydrothermal, and ionic liquid pretreated hydrolysate with the corresponding ethanol productivities of 2.08 g L−1 h−1, 0.53 g L−1 h−1, and 0.36 g L−1 h−1. The lower acetic acid concentration in ammonia-pretreated hydrolysate may have enhanced its fermentability relative to the hydrothermal pretreatment condition, as indicated by the differences in ethanol titer and productivity. Lower sugar yields and ethanol productivities under the ionic liquid conditions likely resulted from the inhibitory effect of cholinium lysinate. Oilcane 1565 and oilcane 1566 bagasse accumulated over 16- and 3 times higher lipids than the non-modified sugarcane CP88-1762. The total fatty acid content in the oilcane samples was reduced in ammonia and ionic liquid-pretreated bagasse relative to the hydrothermal pretreatment condition. While all pretreatment techniques tested are industrially viable, the observed differences in titer, productivity, and lipid content indicate that careful selection and validation of upstream processing methods can contribute to improved economic and environmental outcomes.

Plant architecture influences the microenvironment throughout the canopy layer. Plants with a more erect leaf architecture allow for an increase in planting densities and allow more light to reach lower canopy leaves. This is predicted to increase crop carbon assimilation. Frictional resistance to wind reduces air movement in the lower canopy, resulting in higher humidity. By increasing the proportion of canopy photosynthesis in the more humid lower canopy, gains in the efficiency of water use might be expected, although this may be slightly offset by the more open erectophile form canopy. An anatomical feature in members of the Poaceae family that impacts leaf angle is the articulated junction of the sheath and blade, which also bares the ligule and auricles. Mutants, which lack ligules and auricles, show no articulation at this junction, resulting in leaves that are near vertical. In maize, these phenotypes termed liguleless result from null mutations of genes: ZmLG1 (Zm00001eb67740) and ZmLG2 (Zm00001eb147220). In sorghum, SbiRTx430.06G264300 (SbLG1) and SbiRTx430.03G392300 (SbLG2) are annotated as the respective maize homologues. A hair-pin element designed to down-regulate both SbLG1 and SbLG2 was introduced into the grain sorghum genotype RTx430. Derived transgenic events harbouring the hair-pin failed to develop ligules and displayed reduced leaf angles to the vertical, but less vertical than in null mutations. Under field settings, plots sown with these sorghum events having an erect architecture phenotype displayed an increase in photosynthesis in lower canopy levels, which led to increases in above-ground biomass and seed yield, without an increase in water use.