Illinois Data Bank Dataset Search Results
Results
published:
2026-03-20
Wu, Yulun; Kudeki, Erhan
(2026)
Arecibo ISR CLP/ULP/LULP ion-line spectra obtained from USRP receiver with 500 kHz bandwidth and 120-1400 km altitude range, experiment dates September 23-26, 2016. Used for Joint inversions of coded and uncoded long pulse1 F-region ISR returns measured at Arecibo.
keywords:
Remote sensing; Incoherent scatter radar; Arecibo Observatory
published:
2026-03-26
Leakey, Andrew; Fischer, James
(2026)
Includes three different types of stacks, in two folders:
"REC_RAW_STACKS.zip" contains:
(1) Raw gray-scale reconstructed microCT x-ray scans, in the form of individual stacks per sample.
"ML_STACKS.zip" contains:
(2) Stacks that have been labeled using a machine-learning mask-RCNN pipeline identifying epidermis, mesophyll, airspace, vascular bundle, and background.
(3) Stacks that have stomata locations labeled using a small point.
The three types of stacks were used to calculate a variety of anatomical and physiological traits, using ImageJ Macros provided on Github: https://github.com/leakey-lab/microCT-Macros-Fischer. Young leaves from WT and transgenic Sorghum plants.
CSV "microCT_REC2_META.csv" contains metadata, including sample/sub-sample labels.
keywords:
Stomata; microCT; Imaging; Sorghum; 3D; Gas exchange; Segmentation
published:
2025-10-01
Crawford, Reed; Wolff, Patrick; Pierce, Ellen; Braun de Torrez, Elizabeth; Pourshoushtari, Roxanne; O'Keefe, Joy
(2025)
This dataset contains the raw Florida bonneted bat echolocation calls recorded in southern Florida, USA from the years 2021 and 2022. This dataset also includes our artificial roost microclimate data (2021 only) and observations of bats recorded in our artificial roosts (2021 and 2022). Lastly, we include the R script required to analyze the Florida bonneted bat echolocation calls and the R script to produce the supplemental table and supplemental figure for our microclimate data.
keywords:
bats; roosts; acoustics
published:
2026-02-01
Xu, Xiaotian; Yao, Yu; Liu, Yicen; Curtis, Jeffrey; West, West; Riemer, Nicole
(2026)
This dataset contains simulation results from PartMC-MOSAIC and WRF-PartMC that used in the journal article: Quantifying the Impact of Surfactants on Cloud Condensation Nuclei Activity Using a Particle-Resolved Model. Two compressed folder are uploaded here, one is for the data that used in this article, the other folder is the python scripts to process the data. For more details of the uploaded files, please check the README file.
keywords:
Surfactants; CCN; Effective surface tension
published:
2026-03-13
Majeed, Fahd; Khanna, Madhu
(2026)
An economic model was developed that incorporates spatially varying joint yield and price distributions for the multiple crop choices a farmer faces when choosing between conventional and bioenergy crops. The model is developed in Matlab, and has options for no, annual and upfront payment results.
keywords:
Carbon; modeling; Sustainable Aviation Fuel
published:
2026-02-13
Frederick, Samuel; Mohebalhojeh, Matin; Curtis, Jeffrey; West, Matthew; Riemer, Nicole
(2026)
This dateset contains data files necessary to replicate figures from "Idealized Particle-Resolved Large-Eddy Simulations to Evaluate the Impact of Emissions Spatial Heterogeneity on CCN Activity" submitted to Atmospheric Chemistry and Physics.
Within the compressed folder data.zip are two subdirectories, "processed_data" and "spatial-het". The "processed_data" directory contains netCDF files which contain a subset of simulation output used in figure generation. The "spatial-het" subdirectory contains a .csv file with spatial heterogeneity values computed via an exact algorithm of the spatial heterogeneity metric described by Mohebalhojeh et al. 2025. The subdirectory "sh-patterns" contains .csv files for each emissions scenario. Each entry corresponds to a single grid cell over a domain of dimension 100x100 (lateral resolution of the computational domain employed in this paper).
Within scripts.zip are python notebooks for generating figures. Additional python modules are included which contain helper functions for notebooks. Furthermore, a Fortran version of the spatial heterogeneity metric is included alongside shells scripts for creating a python environment in which the code can be compiled and convert into a Python module. Note that the create_env.sh and compile_nsh.sh scripts must be run prior to executing cells in notebooks to make use of the spatial heterogeneity subroutines.
<b>*Note*:</b> New in this V3: During review, a bug regarding vertical diffusion of particles was discovered in WRF-PartMC which necessitated re-running simulations. We present new simulations with diffusion fixed. Furthermore, we have run additional simulations in response to reviewer comments--simulations with emissions turned off at t = 4 h to investigate reversible partitioning and simulations with the RH raised near saturation throughout the domain to model the effects of co-condensation. The README PDF has been updated to reflect changes to the dataset collection. Also, we have added a shell script in scripts_v3.zip which was used to process simulation output and create the data subsets contained in data_v3.zip. Lastly, notebooks were re-run with updated datasets to create manuscript figures and additional plotting routines were added for new figures pertaining to the requested simulations.
keywords:
Atmospheric chemistry; aerosols; Particle-resolved modeling; spatial heterogeneity
published:
2026-03-12
Acharya, Rishi; Gerber, Eli; Bielinski, Nina; Aguirre, Hannah E.; Kim, Younsik; Bernal-Choban, Camille; Tenkila, Gaurav; Sheikh, Suhas; Mahaadev, Pranav; Hoveyda-Marashi, Faren; ROYCHOWDHURY, SUBHAJIT; Shekhar, Chandra; Felser, Claudia; Abbamonte, Peter; Wieder, Benjamin; Mahmood, Fahad
(2026)
This repository contains source data for key plots presented in the manuscript "Plasmon-driven exciton formation in a non-equilibrium Fermi liquid."
Experimental data that was analyzed in Igor Pro 8 are presented as the .pxp files used to generate individual sub-plots. Electronic spectral function calculations are provided as .txt files, in which consecutive rows refer to the meshgrid x coordinate, y coordinate, spectral function (and, where relevant, axis-projected local angular momentum). We additionally include the Wannier model and DFT-obtained bulk band structure on which the Wannier model was based.
Files are named as the number of the figure in the manuscript to which they correspond, with additional details included where necessary.
<b>Details of file names:</b>
2a_DOS_Lxz_Ek_KGM_40layer_xnum_800kpt_tot.txt: Density of states, xz-axis projected local orbital angular momentum, for 800 points along the K-Gamma-M path, for a 40-layer model.
2c_composite_y.pxp: ARPES (angle-resolved photoemission spectroscopy) spectra along the ky axis, including both a scan near the Fermi level and a scan at high kinetic energies.
2d_LCP_RCP_diff_Sect_20K.pxp: difference between ARPES constant energy cuts at T=20 K at E0 + 0.23 eV taken with left- and right-circularly polarized photons. The polarization-integrated intensity at the constant energy cut is also included.
2e_DOS_L45_E11pt79_m0pt25to0pt25_xnum_800kpt_tot.txt: Density of states, xz-projected local orbital angular momentum, and corresponding k-points in two dimensions from ab-initio electronic structure calculations for a constant-energy cut.
3a_[x]_[y]ps: ARPES cut under excitation at a fluence of x uJ/cm2, measured y ps after photoexcitation. Measurements were performed at 9 K.
3b_[x]: Energy distribution curves under excitation at a fluence x uJ/cm2 at selected delay times after photoexcitation.
4a_ImSigma_vs_temperature.pxp: Imaginary self energy (extracted from ARPES linewidths) at different energies above E0 for selected lattice temperatures.
4b_EELS_lowE.pxp: Electron energy loss spectrum over a low energy range
5b_diff_55m15.pxp: Difference between momentum-integrated Tr-ARPES traces at 55 uJ/cm2 and 15 uJ/cm2 photoexcitation. Time-dependent intensity at each energy level has been normalized to a maximum of 1 for each individual fluence prior to subtraction.
5d_invtau_at_EX_vs_fluence.pxp: decay rate at a specified energy EX for different excitation fluences, from single exponential fits.
<b>NOTE: Analyses based on the Wannier model presented here should cite both the associated Article and this dataset. For all other files in the repository, citing the dataset alone is sufficient.</b>
published:
2026-03-09
Nambiar, Ananthan; Dubinkina, Veronika; Liu, Simon; Maslov, Sergei
(2026)
mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.
keywords:
Genomics; Modeling
published:
2026-03-09
Lee, Jung Woo; Vittore, Kayla Marie; Namoi, Nictor; Hwang, Soonho; Lee, DoKyoung
(2026)
Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller−1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha−1. Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.
keywords:
Miscanthus
published:
2026-03-05
Xue, Xueyi; Beuchat, Gabriel; Wang, Jiang; Yu, Ya-Chi; Moose, Stephen; Chen, Jin; Chen, Li-Qing
(2026)
Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stages post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were down regulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.
keywords:
Transcriptomics
published:
2026-03-04
Tran, Vinh; Mishra, Somesh; Sarang, Bhagwat; Shafaei, Saman; Shen, Yihui; Allen, Jayne; Tan, Shih-I; Fatma, Zia; Rabinowitz, Joshua; Guest, Jeremy; Singh, Vijay; Zhao, Huimin
(2026)
Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.
keywords:
Metabolomics; Modeling
published:
2026-03-02
Liu, Xing; Wickland, Daniel; Borges dos Santos, Lucas; Hudson, Karen; Hudson, Matthew
(2026)
Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.
keywords:
Biomass Analytics; Genomics
published:
2026-03-02
Yang, Jihoon; Sooksa-nguan, Thanwalee (JiJY); Kannan, Baskaran; Cano-Alfanar, Sofia; Liu, Hui; Kent, Angela; Shanklin, John; Altpeter, Fredy; Howe, Adina
(2026)
This project aims to study the microbial structure and potential functions of bacterial and fungal microbiomes in leaves, stems, roots, rhizospheres, and bulk soils of energy crops (oilcane) grown in greenhouses.
keywords:
Biomass Analytics; Metabolomics
published:
2026-03-02
Lee, Jae Won; Bhagwat, Sarang; Kuanyshev, Nurzhan; Cho, Young; Sun, Liang; Lee, Ye-Gi; Cortes-Pena, Yoel; Li, Yalin; Rao, Christopher; Guest, Jeremy; Jin, Yong-Su
(2026)
Rising concerns for sustainability and global climate change have driven the development of sustainable production pathways for biofuels and chemicals from lignocellulosic biomass via integrated biological and chemical processes. We constructed an engineered Saccharomyces cerevisiae capable of producing 2,3-butanediol (2,3-BDO) from glucose without accumulating ethanol and glycerol, which hinder downstream processing of 2,3-BDO, through extensive metabolic reprogramming. Specifically, we introduced heterologous 2,3-BDO biosynthetic enzymes and deleted the major isozymes of ethanol and glycerol biosynthetic enzymes. In addition, we introduced an NAD+ regenerating Pyruvate-Malate (PM) cycle and enhanced the NAD+ regenerating capability of the PM cycle to resolve the redox imbalance from the deletion of ethanol and glycerol production pathways. The resulting engineered yeast produced 109.9 g/L of 2,3-BDO with a productivity of 1.0 g/L/h and a yield of 0.36 g/g glucose in a fed-batch fermentation. We also conducted techno-economic analysis (TEA) and life cycle assessment (LCA) of the production of methyl ethyl ketone (MEK) through catalytic dehydration of 2,3-BDO. A TEA based on the experimental results indicated that the minimum product selling price (MPSP) was estimated to be $1.90/kg. Regarding cradle-to-grave LCA, 100-year global warming potential (GWP100) and fossil energy consumption (FEC) were found to be 0.37 kg CO2 eq/kg and 3.1 MJ/kg, respectively. These results demonstrated the feasibility of cost-competitive and sustainable bio-based MEK production via yeast fermentation. In addition, we explored the possibility of using the fermentation broth containing 2,3-BDO as a biostimulant inducing drought tolerance in plants. As a result, the yeast 2,3-BDO fermentation broth can induce drought tolerance in Arabidopsis thaliana without a complicated purification process.
keywords:
Economics; Metabolomics
published:
2026-03-02
Mula-Michel, Himaya; White, Paul; Hale, Anna
(2026)
Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.
keywords:
Field Data; Genomics
published:
2026-03-02
Session, Adam; Rokhsar, Daniel
(2026)
Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.
keywords:
Genomics
published:
2026-02-27
Zhang, Zhihai; Anwar, Sultana; Yafuso, Erin; Zuniga Soto, Evelyn; Luo, Guangbin; Moose, Stephen; swaminathan, kankshita; Altpeter, Fredy; Hudson, Matthew
(2026)
A new GAL4-based feed-forward loop circuit enhances β-glucuronidase (GUS) reporter gene expression in leaves and stems of stably transformed sugarcane plants.
keywords:
Bioproducts; Metabolic Engineering; Plant Transformation; Sugarcane
published:
2026-02-20
Emran, Shah-Al; Petersen, Bryan M; Roney, Heather Elizabeth ; Masters, Michael David ; Varela, Sebastian; Hedrick, Travis; Leakey, Andrew D.B. ; VanLoocke, Andy; Heaton, Emily A.
(2026)
This dataset contains biomass yield measurements and associated vegetation index data collected from commercial Miscanthus × giganteus fields in eastern Iowa during the 2022–2023 growing seasons.
The data support the analyses presented in the article:
“Yield From Iowa's First Commercial Miscanthus Fields: Implications of Spatial Variability for Productivity and Sustainability Beyond Research Plots.”
We collected 105 ground-truth biomass samples from four mature commercial fields (>4 years old) covering 92.81 ha.
Samples were taken from 3 m² quadrats that were hand-harvested in alignment with commercial harvest timing. Stem biomass (excluding leaves) was weighed, moisture-corrected, and converted to dry-matter yield expressed in Mg DM ha⁻¹.
Sampling locations were selected to capture spatial variability visible in aerial imagery and were recorded using RTK GPS.
Each biomass observation was paired with vegetation indices derived from high-resolution PlanetScope satellite imagery (3 m resolution).
Images were acquired throughout the growing season, and indices were calculated to evaluate their ability to predict end-of-season biomass yield.
Statistical and machine learning approaches were used to identify key predictors, and a linear regression model based on end-of-July Green Normalized Difference Vegetation Index (GNDVI) was developed and evaluated.
This repository includes the data used in that modeling workflow. Management practices, economic data, full imagery time series, and additional methodological details are described in the associated publication and are not included here.
The dataset consists of three comma-separated value (CSV) files:
1. Combine_Groundtruth_Yield_VI_22_23.csv
This file contains ground-truth biomass yield measurements and associated key vegetation index values collected during the 2022 and 2023 growing seasons.
Rows: 105 observations
Columns:
Year — Year of observation (2022 or 2023)
Field — Field location identifier
Sample_number — Unique sample identifier
GNDVI_End_Jul — Green Normalized Difference Vegetation Index calculated at end of July
GNDVI_End_Aug — Green Normalized Difference Vegetation Index calculated at end of August
NDRE_End_Aug — Normalized Difference Red Edge index calculated at end of August
Biomass_Stem_Yield_MgDM/ha — Measured stem biomass yield (megagrams dry matter per hectare)
2. trainData_GNDVI.csv
This file contains the subset of observations used to train the predictive relationship between July GNDVI and biomass yield.
Rows: 76 observations
Columns:
Unnamed: 0 — Row index retained from the original data processing workflow
GNDVI_End_Jul — GNDVI at end of July
Stem_Yield_MgDM/ha — Observed stem biomass yield (Mg DM ha⁻¹)
3. testData_GNDVI.csv
This file contains the test dataset used to evaluate model performance.
Rows: 29 observations
Columns:
Unnamed: 0 — Row index retained from the original data processing workflow
GNDVI_End_Jul — GNDVI at end of July
Predicted_Yield_MgDM/ha — Model-predicted stem biomass yield (Mg DM ha⁻¹)
Observed_Yield_MgDM/ha — Measured stem biomass yield (Mg DM ha⁻¹)
keywords:
Potential yield, yield gap, in-field management, yield prediction, remote sensing, spatial variability, profitability, Miscanthus × giganteus, M×g
published:
2026-02-19
Gurumoorthi, Akshay; Peters, Baron
(2026)
The dataset contains a jupyter notebook intended for anyone who wants to apply the Empirical Bayes method described in the paper titled 'Data for Improving individual committor estimates and data efficiency in reaction coordinate tests with the Empirical Bayes method' to committor data with a simple and lucid python script.
published:
2026-02-11
Hanley, David; Lee, Jongwon; Choi, Su Yeon; Bretl, Timothy
(2026)
If you use this dataset, please cite both the dataset and the associated data paper (bibtex is below).
@ARTICLE{11386847,
author={Hanley, David and Lee, Jongwon and Choi, Su Yeon and Bretl, Timothy},
journal={IEEE Transactions on Instrumentation and Measurement},
title={The MagPIE2 Dataset for Mapping, Localization, and Simultaneous Localization and Mapping Using Magnetic Fields},
year={2026},
volume={},
number={},
pages={1-1},
keywords={Magnetometers;Magnetic field measurement;Magnetic fields;Pedestrians;Location awareness;Buildings;Simultaneous localization and mapping;Measurement errors;Hardware;Calibration;Localization;mapping;SLAM;dataset;benchmark;magnetometer;magnetic field},
doi={10.1109/TIM.2026.3662919}}
We present a dataset for the evaluation of magnetic field-based robotic and pedestrian localization, mapping, and SLAM methods. This dataset contains magnetometer and inertial measurement unit data collected from inside three buildings both a pedestrian and a ground robot. Data were collected at different heights simultaneously, both with and without changes in the placement of objects that may affect magnetometer measurements. In total, approximately 689 square meters of floor space was covered by this dataset.
This dataset is archivally stored. We provide a GitHub site which is meant to serve as a forum to post issues with the dataset, share code using the dataset, and to resolve problems: <a href="https://github.com/hanley6/MagPIE2Forum">https://github.com/hanley6/MagPIE2Forum</a>
Note that while the dataset is meant to be permanently stored, this forum is not meant to guarantee perennial support and its existence will be dependent on the policies of GitHub.
<b>How is the dataset organized?</b> The data is divided into the following parts at a high level and more detailed information can be found in the Readme:
1. The walking portion of the dataset: CSL_WLK.zip, DCL_WLK.zip, Talbot_WLK.zip, and WLK_Misc.zip.
2. The robot portion of the dataset: Robot_Dataset.zip.
3. Motor interference tests: Motor_Interference_Test.zip.
4. Ground truth evaluation: Ground_Truth_Evaluation.zip.
5. Quick start results: Quick_Start_Results.zip.
<b>How is data recorded and stored?</b> Data is generally collected in the form of ROS bag files. Each ROS bag has Intel Realsense camera images, magnetometer readings, IMU readings, timestamps, and more as applicable for each file in the dataset. Each bag file has an associated metadata file written as a YAML file. This contains general information about each bag file including the start and stop time, who collected the bag file (during the pedestrian portion of the dataset), and the approximate location where data was collected. In several cases, additional comma separated (csv) files of the dataset where included either as a convenient supplement to ROS bag files (e.g., csv files of magnetometer calibration data) or because they serve as human readable quick start results.
<b>How does one set up and run files on the dataset?</b> The files are stored in ROS bags and are, therefore, meant to be run using the Robot Operating System. Information regarding how to use the Robot Operating System as well as installation instructions are available at: <a href="https://ros.org/">https://ros.org/</a>
keywords:
Localization; mapping; SLAM; dataset; benchmark; magnetometer; magnetic field
published:
2025-05-07
Reves, Olivia; Larson, Eric
(2025)
Data collected at 71 study sites from 2023 to 2024 for Reves, Olivia P. (2025): Using Environmental DNA Metabarcoding to Inform Biodiversity Conservation in Agricultural Landscapes. Master's thesis, University of Illinois Urbana-Champaign. Files include study site information, taxa by site matrices for vertebrates from environmental DNA metabarcoding using multiple mitochondrial DNA primers (COI, 12S), and bird species audibly detected by a phone app at study sites.
keywords:
agricultural conservation; biodiversity; eDNA; environmental DNA; Illinois; metabarcoding; riparian buffers; stream flow; vertebrates
published:
2026-01-22
Edmonds, Devin; Du, Jane; Stickley, Samuel; Sucre, Samuel
(2026)
This dataset contains data and R scripts used to analyze the trade of non-native pet amphibians in the United States by integrating online classified advertisements with U.S. Fish and Wildlife Service import records. The data include records of amphibian advertisements, U.S. imports, taxonomic reference lists, and conservation status information. The dataset supports analyses identifying domestically produced species, species entering U.S. markets through unrecorded or unofficial trade pathways, and price differences associated with documented and undocumented trade. The dataset supports the analyses presented in an associated peer-reviewed publication in Biological Conservation.
keywords:
amphibian; biocommerce; biosecurity; conservation; LEMIS; pet trade; species laundering; wildlife trade
published:
2026-01-23
Kaman, Bobby; Lim, Jinho; Liu, Yingkai; Hoffmann, Axel
(2026)
Data related to a publication, "Emulating 2D Materials with magnons" to be published, but also as a preprint on arXiv https://arxiv.org/abs/2601.03210.
It contains scripts for the simulation program Mumax3, and python scripts for conversion and analysis.
keywords:
micromagnetics; mumax; tight-binding; spin waves; magnons
published:
2026-01-21
Suthers, Patrick; Maranas, Costas
(2026)
Growth-coupling product formation can facilitate strain stability by aligning industrial objectives with biological fitness. Organic acids make up many building block chemicals that can be produced from sugars obtainable from renewable biomass. Issatchenkia orientalis is a yeast strain tolerant to acidic conditions and is thus a promising host for industrial production of organic acids. Here, we use constraint-based methods to assess the potential of computationally designing growth-coupled production strains for I. orientalis that produce 22 different organic acids under aerobic or microaerobic conditions. We explore native and engineered pathways using glucose or xylose as the carbon substrates as proxy constituents of hydrolyzed biomass. We identified growth-coupled production strategies for 37 of the substrate-product pairs, with 15 pairs achieving production for any growth rate. We systematically assess the strain design solutions and categorize the underlying principles involved.
keywords:
Bioproducts; Modeling
published:
2025-09-18
Chen, Maosi; Parton, William J.; Hartman, Melannie D.; Del Grosso, Stephen J.; Smith, William K.; Knapp, Alan; Lutz, Susan; Derner, Justin; Tucker, Compton; Ojima, Dennis; Volesky, Jerry; Stephenson, Mitchell B.; Schacht, Walter H.; Gao, Wei
(2025)
Productivity throughout the North American Great Plains grasslands is generally considered to be water limited, with the strength of this limitation increasing as precipitation decreases. We hypothesize that cumulative actual evapotranspiration water loss (AET) from April to July is the precipitation‐related variable most correlated to aboveground net primary production (ANPP) in the U.S. Great Plains (GP). We tested this by evaluating the relationship of ANPP to AET, precipitation, and plant transpiration (Tr). We used multi‐year ANPP data from five sites ranging from semiarid grasslands in Colorado and Wyoming to mesic grasslands in Nebraska and Kansas, mean annual NRCS ANPP, and satellite‐derived normalized difference vegetation index (NDVI) data. Results from the five sites showed that cumulative April‐to‐July AET, precipitation, and Tr were well correlated (R2: 0.54–0.70) to annual changes in ANPP for all but the wettest site. AET and Tr were better correlated to annual changes in ANPP compared to precipitation for the drier sites, and precipitation in August and September had little impact on productivity in drier sites. April‐to‐July cumulative precipitation was best correlated (R2 = 0.63) with interannual variability in ANPP in the most mesic site, while AET and Tr were poorly correlated with ANPP at this site. Cumulative growing season (May‐to‐September) NDVI (iNDVI) was strongly correlated with annual ANPP at the five sites (R2 = 0.90). Using iNDVI as a surrogate for ANPP, we found that county‐level cumulative April–July AET was more strongly correlated to ANPP than precipitation for more than 80% of the GP counties, with precipitation tending to perform better in the eastern more mesic portion of the GP. Including the ratio of AET to potential evapotranspiration (PET) improved the correlation of AET to both iNDVI and mean county‐level NRCS ANPP. Accounting for how different precipitation‐related variables control ANPP (AET in drier portion, precipitation in wetter portion) provides opportunity to develop spatially explicit forecasting of ANPP across the GP for enhancing decision‐making by land managers and use of grassland ANPP for biofuels.
keywords:
Sustainability;Field Data;Modeling