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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 scripts and data developed as a part of the research manuscript titled “Spatial and Temporal Allocation of Ammonia Emissions from Fertilizer Application Important for Air Quality Predictions in U.S. Corn Belt”. This includes (1) Spatial and temporal factors for ammonia emissions from agricultural fertilizer usage developed using the hybrid ISS-DNDC method for the Midwest U.S., (2) CAMx job scripts and outputs of predictions of ambient ammonia and total and speciated PM2.5, (3) Observation data used to statistically evaluate CAMx predictions, and (4) MATLAB programs developed to pair CAMx predictions with ground-based observation data in space and time.

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.

These data support Ruess et al (2025) "Drought impacts to water footprints and virtual water transfers of counties of the United States", Water Resources Research, 61, e2024WR037715, https://doi.org/10.1029/2024WR037715. The dataset contains estimates for Virtual Water Content (VWC) and Virtual Water Trade (VWT) for nine unique combinations of three crop categories (cereal grains, produce, and animal feed) and three water sources (surface water withdrawals, groundwater withdrawals, and groundwater depletion) for the years 2012 and 2017 within the Continental United States. The VWC is calculated by dividing irrigation withdrawal estimates (m3) by the production (tons) at the county resolution. The VWT is calculated by multiplying the VWC by the estimated county level food flows (tons) from Karakoc et al. (2022). All VWC estimates are provided at the county resolution according to county GEOID and are given in units of m3/ton. All VWT estimates are given in pairs of origin and destination GEOID’s and provided in units of m3. When using, please cite as: Ruess, P.J., Hanley, J., and Konar, M. (2025) "Drought impacts to water footprints and virtual water transfers of counties of the United States", Water Resources Research, 61, e2024WR037715, doi: 10.1029/2024WR037715.

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.

The plant-sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2-pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl-CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP-citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl-CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12-ACL1-ACC1 using fed-batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl-CoA-derived polyketides from low-cost carbon sources.

This dataset contains genotypic and phenotypic data, R scripts, and the results of analysis pertaining to a multi-location field trial of Miscanthus sinensis. Genome-wide association and genomic prediction were performed for biomass yield and 14 yield-component traits across six field trial locations in Asia and North America, using 46,177 single-nucleotide polymorphism (SNP) markers mined from restriction site-associated DNA sequencing (RAD-seq) and 568 M. sinensis accessions. Genomic regions and candidate genes were identified that can be used for breeding improved varieties of M. sinensis, which in turn will be used to generate new M. xgiganteus clones for biomass.

Data and code supporting the paper titled "Estimating the Electric Vehicle Charging Demand of Multi-Unit Dwelling Residents in the United States" by Xi Cheng and Eleftheria Kontou at the University of Illinois Urbana-Champaign. The data and the code enable analytics and assessment of multi-unit dwelling residents travel patterns and their electric vehicle charging demand.

Dataset used for the paper entitled "Morphological differences between wild and game-farm Mallards in North America". Large-scale releases of domesticated, game-farm Mallards to supplement wild populations have resulted in wide-spread introgressive hybridization that changed the genetic constitution of wild populations in eastern North America. The resulting gene flow is well-documented between game-farm and wild Mallards, but the mechanistic consequences from such interactions remain unknown in North America. We provide the first study to characterize and investigate potential differences in morphology between genetically known, wild and game-farm Mallards in North America. We used nine morphological measurements to discriminate between wild and game-farm Mallards with 96% accuracy. Compared to their wild counterparts, game-farm Mallards had longer bodies and tarsi, shorter heads and wings, and shorter, wider, and taller bills. The nail on the end of the bill of game-farm Mallards was longer, and game-farm Mallard bills had a greater lamellae:bill length ratio than wild Mallards. Differences in body morphologies between wild and game-farm Mallards are consistent with an artificial, terrestrial life whereby game-farm Mallards are fed pelleted foods resulting in artificial selection for a more “goose-like” bill. We posit that 1) game-farm Mallards have diverged from their wild ancestral traits of flying and filter feeding towards becoming optimized to run and peck for food; 2) game-farm morphological traits optimized over the last 400 years in domestic environments are likely to be maladaptive in the wild; and 3) the introgression of such traits into wild populations is likely to reduce fitness. Understanding effects of game-farm Mallard introgression requires analysis of various game-farm × wild hybrid generations to determine how domestically-derived traits persist or diminish with each generation.

Elevated tropospheric ozone concentration (O3) significantly reduces photosynthesis and productivity in several C4 crops including maize, switchgrass and sugarcane. However, it is unknown how O3 affects plant growth, development and productivity in sorghum (Sorghum bicolor L.), an emerging C4 bioenergy crop. Here, we investigated the effects of elevated O3 on photosynthesis, biomass and nutrient composition of a number of sorghum genotypes over two seasons in the field using free-air concentration enrichment (FACE), and in growth chambers. We also tested if elevated O3 altered the relationship between stomatal conductance and environmental conditions using two common stomatal conductance models. Sorghum genotypes showed significant variability in plant functional traits, including photosynthetic capacity, leaf N content and specific leaf area, but responded similarly to O3. At the FACE experiment, elevated O3 did not alter net CO2 assimilation (A), stomatal conductance (gs), stomatal sensitivity to the environment, chlorophyll fluorescence and plant biomass, but led to reductions in the maximum carboxylation capacity of phosphoenolpyruvate and increased stomatal limitation to A in both years. These findings suggest that bioenergy sorghum is tolerant to O3 and could be used to enhance biomass productivity in O3 polluted regions.

Environmental DNA metabarcoding data for fish communities at 50 sites in the Tennessee River watershed of northern Alabama, United States collected in summer 2018 used in the calculation of an Index of Biotic Integrity for biological monitoring. * New in this V2: In response to peer review at a journal and associated revised statistical analyses, we have added four variables to the file Curtis_etal_IBImetrics.csv and edited the Curtis_etal_readme.txt to explain these variables. The files Curtis_etal_FishDetections.csv and Curtis_etal_FishReadsbySite.csv remain unchanged. - 4 new variables in Curtis_etal_IBImetrics.csv are: fishIBI_noDELT, MaxHab, Stressor, and Distance.

The dataset contains processed model fields used to generate data, figures and tables in the Journal of Geophysical Research article "Investigating the linear dependence of direct and indirect radiative forcing on emission of carbonaceous aerosols in a global climate model." The processed data are monthly averaged cloud properties (CCN, CDNC and LWP) and forcing variables (DRF and IRF) at original CAM5 spatial resolution (1.9° by 2.5°). Raw model output fields from CAM5 simulations are available through NERSC upon request. Please find more detailed information in the ReadMe file.

Supplementary data tables for the dissertation "Hybridization dynamics and population genomics of a Manacus hybrid zone." This work focuses on the dynamics of hybridization over time in two species of tropical birds, the golden-collared manakin (Manacus vitellinus) and white-collared manakin (Manacus candei) comparing data from historical museum samples and contemporary wild-caught birds. Table A1 contains the sample metadata for the Manacus Restriction site-associated DNA sequencing dataset used in the dissertation with associated NCBI Biosample Accession numbers, Smithsonian Museum of Natural History number (where applicable), sample IDs, sampling site locations, and sample information of year the sample was taken, age, and sex. Table A6 contains phenotypic measurements of male plumage traits of manakins used in cline analyses to assess hybrid zone movement over time in historical and contemporary datasets, including beard length (mm), epaulet width (mm), tail length (mm), collar color (nm), and belly color (nm). Table A7 contains a summary of male plumage measurements across the hybrid zone. Table C1 contains a list of annotated protein coding genes in candidate regions of interest in Manacus genomes using outlier regions of genomic divergence, linkage disequilibrium, and enrichment of parental private alleles.

This data set includes information on mixing metric values and distances to determine the average length scale, rates and variability of mixing downstream of 43 river confluences for 150 mixing events. The file "pmx_all data.csv" contains confluence names, the number of events per confluence site, and Pmx values measured at various actual and dimensionless downstream distances. The file "pmx_binned data.csv" provides mean Pmx values within 0.5-unit dimensionless distance bins.

The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C12 products. Of the four mutations which conferred a specificity shift, we noted that three affected the shape of the binding pocket, while one occurred on the positively charged acyl carrier protein landing pad. Finally, we fused the maltose binding protein (MBP) from E. coli to the N – terminus of BTE-MMD19 to improve enzyme solubility and achieve a titer of 1.9 g per L of twelve-carbon fatty acids in a shake flask.

Wikipedia category tree embeddings based on wikipedia SQL dump dated 2017-09-20 (<a href="https://archive.org/download/enwiki-20170920">https://archive.org/download/enwiki-20170920</a>) created using the following algorithms: * Node2vec * Poincare embedding * Elmo model on the category title The following files are present: * wiki_cat_elmo.txt.gz (15G) - Elmo embeddings. Format: category_name (space replaced with "_") <tab> 300 dim space separated embedding. * wiki_cat_elmo.txt.w2v.gz (15G) - Elmo embeddings. Format: word2vec format can be loaded using Gensin Word2VecKeyedVector.load_word2vec_format. * elmo_keyedvectors.tar.gz - Gensim Word2VecKeyedVector format of Elmo embeddings. Nodes are indexed using * node2vec.tar.gz (3.4G) - Gensim word2vec model which has node2vec embedding for each category identified using the position (starting from 0) in category.txt * poincare.tar.gz (1.8G) - Gensim poincare embedding model which has poincare embedding for each category identified using the position (starting from 0) in category.txt * wiki_category_random_walks.txt.gz (1.5G) - Random walks generated by node2vec algorithm (https://github.com/aditya-grover/node2vec/tree/master/node2vec_spark), each category identified using the position (starting from 0) in category.txt * categories.txt - One category name per line (with spaces). The line number (starting from 0) is used as category ID in many other files. * category_edges.txt - Category edges based on category names (with spaces). Format from_category <tab> to_category * category_edges_ids.txt - Category edges based on category ids, each category identified using the position (starting from 1) in category.txt * wiki_cats-G.json - NetworkX format of category graph, each category identified using the position (starting from 1) in category.txt Software used: * <a href="https://github.com/napsternxg/WikiUtils">https://github.com/napsternxg/WikiUtils</a> - Processing sql dumps * <a href="https://github.com/napsternxg/node2vec">https://github.com/napsternxg/node2vec</a> - Generate random walks for node2vec * <a href="https://github.com/RaRe-Technologies/gensim">https://github.com/RaRe-Technologies/gensim</a> (version 3.4.0) - generating node2vec embeddings from random walks generated usinde node2vec algorithm * <a href="https://github.com/allenai/allennlp">https://github.com/allenai/allennlp</a> (version 0.8.2) - Generate elmo embeddings for each category title Code used: * wiki_cat_node2vec_commands.sh - Commands used to * wiki_cat_generate_elmo_embeddings.py - generate elmo embeddings * wiki_cat_poincare_embedding.py - generate poincare embeddings

This dataset contains all the numerical results (digital elevation models) that are presented in the paper "Landscape evolution models using the stream power incision model show unrealistic behavior when m/n equals 0.5." The paper can be found at: http://www.earth-surf-dynam-discuss.net/esurf-2017-15/ The paper has been accepted, but the most up to date version may not be available at the link above. If so, please contact Jeffrey Kwang at jeffskwang@gmail.com to obtain the most up to date manuscript.

Bibliotelemetry data are provided in support of the evaluation of Internet of Things (IoT) middleware within library collections. IoT infrastructure within the physical library environment is the basis for an integrative, hybrid approach to digital resource recommenders. The IoT infrastructure provides mobile, dynamic wayfinding support for items in the collection, which includes features for location-based recommendations. A modular evaluation and analysis herein clarified the nature of users’ requests for recommendations based on their location, and describes subject areas of the library for which users request recommendations. The modular mobile design allowed for deep exploration of bibliographic identifiers as they appeared throughout the global module system, serving to provide context to the searching and browsing data that are the focus of this study.

The Empoascini_morph_data.nex text file contains the original data used in the phylogenetic analyses of Xu et al. (Systematic Entomology, in review). 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 first nine lines of the file indicate the file type (Nexus), that 110 taxa were analyzed, that a total of 99 characters were analyzed, the format of the data, and specification for symbols used in the dataset to indicate different character states. For species that have more than one state for a particular character, the states are enclosed in square brackets. Question marks represent missing data.The pdf file, Appendix1.pdf, is available here and describes the morphological characters and character states that were scored in the dataset. The data analyses are described in the cited original paper.

Dataset compiled by Yushu Xia and Michelle Wander for the Soil Health Institute. Data were recovered from peer reviewed literature reporting results for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) in terms of their relative response to management where soils under grassland cover, no-tillage, cover crops, residue return and organic amendments were compared to conventionally managed controls. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, and “fluorescein diacetate hydrolysis”, together with one or more of the following: “management practice”, “tillage”, “cover crop”, “residue”, “organic fertilizer”, or “manure”. Records were tabulated to compare SQI abundance in soil maintained under a control and soil aggrading practice with the intent to contribute to SQI databases that will support development of interpretive frameworks and/or algorithms including pedo-transfer functions relating indicator abundance to management practices and site specific factors. Meta-data include the following key descriptor variables and covariates useful for development of scoring functions: 1) identifying factors for the study site (location, year of initiation of study and year in which data was reported), 2) soil textural class, pH, and SOC, 3) depth and timing of soil sampling, 4) analytical methods for SQI quantification, 5) units used in published works (i.e. equivalent mass, concentration), 6) SQI abundances, and 7) statistical significance of difference comparisons. *Note: Blank values in tables are considered unreported data.

This dataset contains all the necessary information to recreate the study presented in the paper entitled "Learning coagulation processes with combinatorially-invariant neural networks". This consists of (1) the aggregated output files used for machine learning, (2) the machine learning codes used to learn the presented models, (3) the PartMC model source code that was used to generate the simulation data and (4) the Python scripts used construct the scenario library for training and testing simulations. This data was used to investigate a method (combinatorally-invariant neural network) for learning the aerosol process of coagulation. This data may be useful for application of other methods.

This dataset provides instructions for procedures to use heat transfer analyses to estimate thermal conditions in artificial roosts for bats. The dataset contains scripts to employ in the program GNU Octave, example meteorology data, and example text files specifying roost dimensions and material properties.

This deposit contains all raw data and analysis from the paper "In-cell titration of small solutes controls protein stability and aggregation". Data is collected into several types: 1) analysis*.tar.gz are the analysis scripts and the resulting data for each cell. The numbers correspond to the numbers shown in Fig.S1. (in publication) 2) scripts.tar.gz contains helper scripts to create the dataset in bash format. 3) input.tar.gz contains headers and other information that is fed into bash scripts to create the dataset. 4) All rawData*.tar.gz are tarballs of the data of cells in different solutes in .mat files readable by matlab, as follows: - Each experiment included in the publication is represented by two matlab files: (1) a calibration jump under amber illumination (_calib.mat suffix) (2) a full jump under blue illumination (FRET data) - Each file contains the following fields: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordleft - coordinates of cropped and aligned acceptor channel on the original image &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordright - coordinates of cropped and aligned donor channel on the original image] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataleft - a 3d 12-bit integer matrix containing acceptor channel flourescence for each pixel and time step. Not available in _calib files &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataright - a 3d 12-bit integer matrix containing donor channel flourescence for each pixel and time step. This will be mCherry in _calib files and AcGFP in data files. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;frame1 - original image size &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;imgstd - cropped dimensions &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;numFrames - number of frames in dataleft and dataright &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;videos - a structure file containing camera data. Specifically, videos.TimeStamp includes the time from each frame.

Miscanthus is a close relative of saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between miscanthus and saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of saccharum and miscanthus genotypes. We found that day length was an important factor influencing when miscanthus and saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. ×giganteus collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis, short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis, days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.