Illinois Data Bank Dataset Search Results
Results
published:
2025-05-01
Wang, Weiwei; Khanna, Madhu
(2025)
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.
keywords:
BEPAM; Energy crops; direct and indirect land use change; soil carbon sequestration; fossil fuel displacement; economic incentives
published:
2025-12-09
Hsu, Felicity Ting-Yu; Smith-Bolton, Rachel
(2025)
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.
keywords:
Drosophila; regeneration; Myc; Tor; blastema; translation; cell competition
published:
2025-11-03
Blake-Bradshaw, Abigail; Bradshaw, Therin; Beilke, Elizabeth; Gilbert, Andrew; Osborn, Joshua; Fournier, Auriel M.V.
(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.
keywords:
hunting; shotgun; waterfowl; acoustics
published:
2024-02-16
Mohasel Arjomandi, Hossein; Korobskiy, Dmitriy; Chacko, George
(2024)
This dataset contains five files. (i) open_citations_jan2024_pub_ids.csv.gz, open_citations_jan2024_iid_el.csv.gz, open_citations_jan2024_el.csv.gz, and open_citation_jan2024_pubs.csv.gz represent a conversion of Open Citations to an edge list using integer ids assigned by us. The integer ids can be mapped to omids, pmids, and dois using the open_citation_jan2024_pubs.csv and open_citations_jan2024_pub_ids.scv files. The network consists of 121,052,490 nodes and 1,962,840,983 edges. Code for generating these data can be found https://github.com/chackoge/ERNIE_Plus/tree/master/OpenCitations.
(ii) The fifth file, baseline2024.csv.gz, provides information about the metadata of PubMed papers. A 2024 version of PubMed was downloaded using Entrez and parsed into a table restricted to records that contain a pmid, a doi, and has a title and an abstract. A value of 1 in columns indicates that the information exists in metadata and a zero indicates otherwise. Code for generating this data: https://github.com/illinois-or-research-analytics/pubmed_etl. If you use these data or code in your work, please cite https://doi.org/10.13012/B2IDB-5216575_V1.
keywords:
PubMed
published:
2025-09-22
Anand, Mohit; Miao, Ruiqing; Khanna, Madhu
(2025)
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.
keywords:
Sustainability;Economics;Modeling;Software
published:
2025-10-30
Yang, Boming; Yang, Pan; Golub, Emma; Cai, Ximing
(2025)
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.
keywords:
Sustainability;Economics
published:
2025-10-03
Singh, Vijay; Altpeter, Fredy; Shanklin, John; Liu, Hui; Kannan, Baskaran; Woodruff, William; Nenavath, Mounika Durga; Deshavath, Narenda Naik
(2025)
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.
keywords:
biomass analytics; energycane; feedstock bioprocessing; inter-BRC; lipids; oilcane; sugarcane
published:
2025-10-10
Clemente, Tom; Long, Stephen; Leakey, Andrew; Guo, Ming; McCoy, Scott; Sato, Shirley; Nersesian, Natalya; Ge, Zhengxiang; Quach, Truyen; Jaikumar, Nikhil
(2025)
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.
keywords:
Genome Engineering; Photosynthesis; Sorghum; Water Use Efficiency
published:
2025-10-03
McClelland, Daniel J.; Wang, Bo-Xun; Cordell, William T.; Cortes-Peña, Yoel R.; Gilcher, Elise B.; Zhang, Lifeng; Guest, Jeremy; Pfleger, Brian; Huber, George; Dumesic, James
(2025)
Base catalysts were studied for the dehydration of fatty alcohols to linear alpha olefins (LAOs). For the gas phase dehydration of 1-octanol to 1-octene, 15% Cs/SiO2 catalyst was 56% selective at 10% conversion. Diluting a feed of C8, C10, and C14 fatty alcohols to 50% in undecane increased the selectivity to alpha olefins to 77–99%. 15% Cs/SiO2 was further investigated for the gas phase dehydration of a 4.2 g L−1 mixed C8–C14 fatty alcohol in tridecane feed and showed linear alpha olefin selectivities of 78–100% at initial conversions of 51–91% with the conversion lowering to 32–77% over 30 h. Catalytic activity was totally regenerated through calcination. A feed of biologically derived alcohols was produced with E. coli strain CM24 transformed with three plasmids (pBTRCk–pVHb–maACR, pACYC–pVHb–seFadBA, pTRC99A–pVHb–tdTER–fdh) which yielded a 5.5 g L−1 of C8–C14 fatty alcohol in tridecane. This biologically-derived feed was successfully dehydrated to linear alpha olefins over 15% Cs/SiO2 at selectivities of 60–100% with initial conversions of 35–75% which decreased to 22–55% over 30 h. Techno-economic analysis (TEA) of the integrated process for fatty alcohol production and subsequent dehydration to alpha olefins was conducted across the potential fermentation TRY (titer, rate, yield) landscape. Baseline fermentation performance resulted in a minimum product selling price (MPSP) double the market price for LAOs due to low titers and high costs associated with managing water and tridecane solvent flows through the system. However, targeted improvements in fermentation performance (e.g., achieving 40 g L−1 titer, 0.5 g L−1 h−1 productivity, 80% theoretical yield) can enable financially viable production of biologically derived LAOs.
keywords:
Conversion;Sustainability;Catalysis;Modeling
published:
2025-09-11
Ng, Yee Man Margaret; Goncalves, Alexandre
(2025)
We present a three-year archival, longitudinal dataset of YouTube Trending videos, collected from July 1, 2022, to June 30, 2025, four retrieval per day. This collection, a unique historical record of digital culture in transition, includes 446,971 snapshots from 104 countries, encompassing 726,627 unique videos and their associated metadata. Each record includes collection timestamp, geographic region, video ranking, core identifiers (video ID, channel ID, category), content metadata (title, description, tags, localization), language information, live status, view and comment counts. Full documentation: https://arxiv.org/abs/2510.23645
Unlike previous datasets with limited geographic scope or short timeframes, our data offers exceptional coverage for cross-national and longitudinal analyses of digital culture. This non-personalized data corpus provides an irreplaceable baseline for understanding crisis communication, platform governance or temporal shifts in content popularity.
keywords:
YouTube; Trending Videos; Digital Culture; Global Trend
published:
2025-09-08
Zinnen, Jack; Chase, Marissa; Charles, Brian; Harmon-Threatt, Alexandra; Matthews, Jeffrey
(2025)
This is the data set for the article entitled "Pollinator seed mixes are phenologically dissimilar to prairie remnants," a manuscript pending publication in Restoration Ecology. This represents the core phenology data of prairie remnant and pollinator seed mixes that were used for the main analyses. Note that additional data associated with the manuscript are intended to be published as a supplement in the journal.
* In this V2, a second tab was added to the Rest.Ecol.data.xlsx file. This new sheet listed original data source citations that match the RELIX data base, a sister project.
keywords:
native plants; ecological restoration; tallgrass prairie; native plant materials
published:
2025-10-31
Lopes, Daiane; Dien, Bruce; Hector, Ronald; Singh, Vijay; Thompson, Stephanie R.; Slininger, Patricia J.; Boundy-Mills, Kyria; Jagtap, Sujit; Rao, Christopher V.
(2025)
Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33–9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032–0.131 (g/g) and lipid contents were 13.5–53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature.
keywords:
Conversion;Hydrolysate;Lipidomics
published:
2025-09-22
The files in this dataset include the now-public domain full raw text and illustrations for the novel Gentlemen Prefer Blondes (GBP) by Anita Loos, and files comparing the two published versions of the novel in 1925, one in Harper's Bazar magazine and the other in book format by Boni & Liveright. These files comprise the underlying data for the scholarly digital edition of the novel edited by Daniel G. Tracy. The full citation for the publication, including the DOI link for those wishing access the text, is: Loos, Anita. Gentlemen Prefer Blondes. Edited by Daniel G. Tracy, Critical Edition. Windsor & Downs Press, 2025. https://doi.org/10.21900/wd.13
keywords:
literature; textual collation; digital editions; American Literature
published:
2017-02-28
Leesburg, VA to Indianapolis, Indiana:
Sampling Rate: 0.1 Hz
Total Travel Time: 31100007 ms or 518 minutes or 8.6 hours
Distance Traveled: 570 miles via I-70
Number of Data Points: 3112
Device used: Samsung Galaxy S4
Date Recorded: 2017-01-15
Parameters Recorded:
* ACCELEROMETER X (m/s²)
* ACCELEROMETER Y (m/s²)
* ACCELEROMETER Z (m/s²)
* GRAVITY X (m/s²)
* GRAVITY Y (m/s²)
* GRAVITY Z (m/s²)
* LINEAR ACCELERATION X (m/s²)
* LINEAR ACCELERATION Y (m/s²)
* LINEAR ACCELERATION Z (m/s²)
* GYROSCOPE X (rad/s)
* GYROSCOPE Y (rad/s)
* GYROSCOPE Z (rad/s)
* LIGHT (lux)
* MAGNETIC FIELD X (microT)
* MAGNETIC FIELD Y (microT)
* MAGNETIC FIELD Z (microT)
* ORIENTATION Z (azimuth °)
* ORIENTATION X (pitch °)
* ORIENTATION Y (roll °)
* PROXIMITY (i)
* ATMOSPHERIC PRESSURE (hPa)
* Relative Humidity (%)
* Temperature (F)
* SOUND LEVEL (dB)
* LOCATION Latitude
* LOCATION Longitude
* LOCATION Altitude (m)
* LOCATION Altitude-google (m)
* LOCATION Altitude-atmospheric pressure (m)
* LOCATION Speed (kph)
* LOCATION Accuracy (m)
* LOCATION ORIENTATION (°)
* Satellites in range
* GPS NMEA
* Time since start in ms
* Current time in YYYY-MO-DD HH-MI-SS_SSS format
Quality Notes:
There are some things to note about the quality of this data set that you may want to consider while doing preprocessing. This dataset was taken continuously but had multiple stops to refuel (without the data recording ceasing). This can be removed by parsing out all data that has a speed of 0. The mount for this dataset was fairly stable (as can be seen by the consistent orientation angle throughout the dataset). It was mounted tightly between two seats in the back of the vehicle. Unfortunately, the frequency for this dataset was set fairly low at one per ten seconds.
keywords:
smartphone; sensor; driving; accelerometer; gyroscope; magnetometer; gps; nmea; barometer; satellite; temperature; humidity
published:
2025-09-19
Xue, Pu; Si, Tong; Mishra, Shekhar; Zhang, Linzixuan; Choe, Kisurb; Sweedler, Jonathan; Zhao, Huimin
(2025)
Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs) as key components of crucial nutrients, soaps, industrial chemicals, and fuels. However, our ability to control the composition of microbially synthesized FFAs is still limited, particularly, for producing medium‐chain fatty acids (MCFAs). This is mainly due to the lack of high‐throughput approaches for FFA analysis to engineer enzymes with desirable product specificity. Here we report a mass spectrometry (MS)‐based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. In particular, matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and a higher m/z peak ratio at 730 and 758 was used as an indication for improved MCFA production. This colony‐based method can be performed at a rate of ~2 s per sample, representing a substantial improvement over gas chromatography‐MS (typically >30 min per sample) as the gold standard method for FFA detection. To demonstrate the power of this method, we performed site‐saturation mutagenesis of the yeast fatty acid synthase and identified nine missense mutations that resulted in improved MCFA production relative to the wild‐type strain. Colony‐based MALDI‐ToF MS screening provides an effective approach for engineering microbial fatty acid compositions in a high‐throughput manner.
keywords:
Conversion;Lipidomics;Metabolomics
published:
2025-12-02
Zhou, Yu; Mirts, Evan N.; Yook, Sangdo; Waugh, Matthew; Martini, Rachel; Jin, Yong-Su; Lu, Yi
(2025)
Engineering enzymes with novel reactivity and applying them in metabolic pathways to produce valuable products are quite challenging due to the intrinsic complexity of metabolic networks and the need for high in vivo catalytic efficiency. Triacetic acid lactone (TAL), naturally generated by 2-pyrone synthase (2PS), is a platform molecule that can be produced via microbial fermentation and further converted into value-added products. However, these conversions require extra synthetic steps under harsh conditions. We herein report a biocatalytic system for direct generation of TAL derivatives under mild conditions with controlled chemoselectivity by rationally engineering the 2PS active site and then rewiring the biocatalytic pathway in the metabolic network of E. coli to produce high-value products, such as kavalactone precursors, with yields up to 17 mg/L culture. Computer modeling indicates sterics and hydrogen-bond interactions play key roles in tuning the selectivity, efficiency, and yield.
keywords:
Conversion;Metabolomics
published:
2017-05-01
Indianapolis Int'l Airport to Urbana:
Sampling Rate: 2 Hz
Total Travel Time: 5901534 ms or 98.4 minutes
Number of Data Points: 11805
Distance Traveled: 124 miles via I-74
Device used: Samsung Galaxy S6
Date Recorded: 2016-11-27
Parameters Recorded:
* ACCELEROMETER X (m/s²)
* ACCELEROMETER Y (m/s²)
* ACCELEROMETER Z (m/s²)
* GRAVITY X (m/s²)
* GRAVITY Y (m/s²)
* GRAVITY Z (m/s²)
* LINEAR ACCELERATION X (m/s²)
* LINEAR ACCELERATION Y (m/s²)
* LINEAR ACCELERATION Z (m/s²)
* GYROSCOPE X (rad/s)
* GYROSCOPE Y (rad/s)
* GYROSCOPE Z (rad/s)
* LIGHT (lux)
* MAGNETIC FIELD X (microT)
* MAGNETIC FIELD Y (microT)
* MAGNETIC FIELD Z (microT)
* ORIENTATION Z (azimuth °)
* ORIENTATION X (pitch °)
* ORIENTATION Y (roll °)
* PROXIMITY (i)
* ATMOSPHERIC PRESSURE (hPa)
* SOUND LEVEL (dB)
* LOCATION Latitude
* LOCATION Longitude
* LOCATION Altitude (m)
* LOCATION Altitude-google (m)
* LOCATION Altitude-atmospheric pressure (m)
* LOCATION Speed (kph)
* LOCATION Accuracy (m)
* LOCATION ORIENTATION (°)
* Satellites in range
* GPS NMEA
* Time since start in ms
* Current time in YYYY-MO-DD HH-MI-SS_SSS format
Quality Notes:
There are some things to note about the quality of this data set that you may want to consider while doing preprocessing. This dataset was taken continuously as a single trip, no stop was made for gas along the way making this a very long continuous dataset. It starts in the parking lot of the Indianapolis International Airport and continues directly towards a gas station on Lincoln Avenue in Urbana, IL. There are a couple parts of the trip where the phones orientation had to be changed because my navigation cut out. These times are easy to account for based on Orientation X/Y/Z change. I would also advise cutting out the first couple hundred points or the points leading up to highway speed. The phone was mounted in the cupholder in the front seat of the car.
keywords:
smartphone; sensor; driving; accelerometer; gyroscope; magnetometer; gps; nmea; barometer; satellite
published:
2025-08-08
Bhatnagar, Nikita; Chung, Sarah S.; Hodge, John; Kim, Sang Yeol; Sands, Mia; Leakey, Andrew D. B.; Ort, Donald R.; Burgess, Steven J.
(2025)
Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.
keywords:
photosynthesis; sorghum
published:
2025-10-16
Trinklein, Timothy; Lam, Fan; Sweedler, Jonathan
(2025)
This dataset contains MALDI imaging and fluorescence imaging data of 5xFAD mice and control animals. Processed data are provided at either MATLAB arrays or Bruker .slx / .sbd files compatible with SCiLS Lab.
- Animal_1_5xFAD_s1 and s2 : A MATLAB file of 50 micron spatial resolution imaging of whole brain slice from a 5xFAD animal.
- Slide28_Animal1_stitch_channels__Thioflavin S : A PNG file of the corresponding Thioflavin S- stained fluorescence image obtained post-MSI from the same section.
- Slide28_Animal1_stitch_merged : A PNG file of the corresponding merged imaged including brightfield, Thioflavin S (GFP channel) and Hoechst staining (DAPI channel) used for image registration
- mz_bins_use_neg.mat : A MATLAB array of the m/z channels all MSI images (whole brain slice, 50 micron spatial resolution) were binned to in order to enable comparison
- Animal3_S18_HR.mat : A MATLAB array of high-spatial-resolution (5 micron) imaging of a 5xFAD mouse hippocampus and cortex. Due to the large dataset, 22 m/z channels are included.
- Animal5_S17_HR.mat : A MATLAB array of high-spatial-resolution (5 micron) imaging of a wildtype mouse hippocampus and cortex
- mz_features_22.mat : A MATLAB array of the 22 m/z channels included in the high spatial resolution imaging data
- MALDI_Animal03_5xFAD_10um_neg.zip : A folder containing .slx and .sbd MALDI imaging data of a 5xFAD mouse (whole-brain section) at a 10 micron pitch (used in Figure 5)
- MALDI_animal3_5xFAD_5um_neg.zip : A folder containing .slx and .sbd MALDI imaging data of a 5xFAD mouse (region of interest) at a 5
micron pitch (used in Figure 4)
- TIMS_animal1_20um_5xfad_neg.zip : A folder containing .slx and .sbd MALDI TIMS imaging data of a 5xFAD mouse (region of interest) at a 20 micron pitch (used in Figure 7)
- TIMS_animal5_s13_20um_wt_neg.zip : A folder containing .slx and .sbd MALDI TIMS imaging data of a wild typemouse (region of interest) at a 20 micron pitch (used in Figure 7)
- Region Masks BMC.zip : A folder containing masks from brain regions of spatial transcriptomics data from the BMC Genomics data set
- Region Masks Cell.zip : A folder containing masks from brain regions of spatial transcriptomics data from the Cell data set
keywords:
amyloid beta; 5xfad, lipids; maldi;
published:
2025-12-23
Crawford, Reed; Dodd, Luke; O'Keefe, Joy
(2025)
This dataset contains the raw skin temperature data recorded from female Indiana bats (Myotis sodalis) recorded in Indiana and Kentucky from April through August of 2021. This dataset also contains the raw daily heterothermic response variable data that were used in this analysis. This dataset also includes the raw ambient temperature weather data recorded at our Indiana and Kentucky field sites. Lastly, this dataset contains the R script needed to analyze the above dataset.
keywords:
Artificial roost; bat box; conservation; physiology; thermoregulation; torpor
published:
2025-12-29
Wu, Yulun; Kudeki, Erhan
(2025)
Arecibo ISR CLP ion-line spectra obtained from RI receiver with 500 kHz bandwidth and 120-640 km altitude range, experiment dates September 23-26, 2016. Used for Mitigation of ion-temperature/composition ambiguity in the inversion of F-region ion-line spectra measured at Arecibo using coded long pulses.
keywords:
Remote sensing; Incoherent scatter radar; Arecibo Observatory
published:
2024-11-13
Tang, Zhichu; Chen, Wenxiang; Yin, Kaijun; Busch, Robert; Hou, Hanyu; Lin, Oliver; Lyu, Zhiheng; Zhang, Cheng; Yang, Hong; Zuo, Jian-Min ; Chen, Qian
(2024)
These datasets are for the four-dimensional scanning transmission electron microscopy (4D-STEM) and electron energy loss spectroscopy (EELS) experiments for cathode nanoparticles at different states. The raw 4D-STEM experiment datasets were collected by TEM image & analysis software (FEI) and were saved as SER files. The raw 4D-STEM datasets of SER files can be opened and viewed in MATLAB using our analysis software package of imToolBox available at https://github.com/flysteven/imToolBox. The raw EELS datasets were collected by DigitalMicrograph software and were saved as DM4 files. The raw EELS datasets can be opened and viewed in DigitalMicrograph software or using our analysis codes available at https://github.com/chenlabUIUC/OrientedPhaseDomain. All the datasets are from the work "Nanoscale Stacking Fault Engineering and Mapping in Spinel Oxides for Reversible Multivalent Ion Insertion" (2024).
The 4D-STEM experiment data include four example datasets for cathode nanoparticles collected at pristine and discharged states. Each dataset contains a stack of diffraction patterns collected at different probe positions scanned across the cathode nanoparticle.
1. Pristine untreated nanoparticle: "Pristine U-NP.ser"
2. Pristine 200ºC heated nanoparticle: "Pristine H200-NP.ser"
3. Untreated nanoparticle after first discharge in Zn-ion batteries: "Discharged U-NP.ser"
4. 200ºC heated nanoparticle after first discharge in Zn-ion batteries: "Discharged H200-NP.ser"
The EELS experiment data includes six example datasets for cathode nanoparticles collected at different states (in "EELS datasets.zip") as described below. Each EELS dataset contains the zero-loss and core-loss EELS spectra collected at different probe positions scanned across the cathode nanoparticle.
1. Pristine untreated nanoparticle: "Pristine U-NP EELS.zip"
2. Pristine 200ºC heated nanoparticle: "Prisitne H200-NP EELS.zip"
3. Untreated nanoparticle after first discharge in Zn-ion batteries: "Discharged U-NP EELS.zip"
4. Untreated nanoparticle after first charge in Zn-ion batteries: "Charged U-NP EELS.zip"
5. 200ºC heated nanoparticle after first discharge in Zn-ion batteries: "Discharged H200-NP EELS.zip"
6. 200ºC heated nanoparticle after first charge in Zn-ion batteries: "Charged H200-NP EELS.zip"
The details of the software package and codes that can be used to analyze the 4D-STEM datasets and EELS datasets are available at: https://github.com/chenlabUIUC/OrientedPhaseDomain. Once our paper is formally published, we will update the relationship of these datasets with our paper.
keywords:
4D-STEM; EELS; defects; strain; cathode; nanoparticle; energy storage
published:
2025-06-26
Zhang, Ruolin; Kontou, Eleftheria
(2025)
This dataset supports the analysis presented in the study on curbside electric vehicle (EV) charging infrastructure planning in San Francisco and the published paper titled "Urban electric vehicle infrastructure: Strategic planning for curbside charging." It includes spatial data layers and tabular data used to evaluate location suitability under multiple criteria, such as demand, accessibility, and environmental benefits. This dataset can be used to replicate the multi-criteria decision-making framework, perform additional spatial analyses, or inform policy decisions related to EV infrastructure siting in urban environments. The paper's DOI is https://doi.org/10.1016/j.jtrangeo.2025.104328.
keywords:
Electric Vehicles; Curbside Charging Stations; Multi-Criteria Decision-Making; Suitability Analysis; Urban Infrastructure
published:
2025-09-08
Lee, DoKyoung; Heaton, Emily; Umar, Muhammad; Jang, Chunhwa; Namoi, Nictor
(2025)
Purpose-grown perennial herbaceous species are nonfood crops specifically cultivated for bioenergy production and have the potential to secure bioenergy feedstock resources while enhancing ecosystem services. This study assessed soil greenhouse gas emissions (CO2 and N2O), nitrate (NO3-N) leaching reduction potential, evapotranspiration (ET), and water-use efficiency (WUE) of bioenergy switchgrass (Panicum virgatum L.) in comparison to corn (Zea mays L.). The study was conducted on field-scale plots in Urbana, IL, during the 2020–2022 growing seasons. Switchgrass was established in 2020 and urea-fertilized at 56 kg N ha−1 year−1. Corn management followed best management practices for the US Midwest, including no-till and 202 kg N ha−1 year−1 fertilization, applied as urea–ammonium nitrate (32%). Our results showed lower direct N2O emissions in switchgrass compared to corn. Although soil CO2 emissions did not differ significantly during the establishment year, emissions in subsequent years were over 50% higher in switchgrass than in corn, likely due to increased belowground biomass, which was over five times higher in switchgrass. Nitrate-N leaching decreased as the switchgrass stand matured, reaching 80% lower than in corn by the third year. Differences in ET and WUE between corn and switchgrass were not significant; however, results indicate a trend toward reduced WUE in switchgrass under drought, driven by lower aboveground biomass production. Our study demonstrates that switchgrass can be implemented at a commercial scale without negatively impacting the hydrological cycle, while potentially reducing N losses through nitrate-N leaching and soil N2O emissions, and enhancing belowground C storage.
keywords:
field data; perennial bioenergy grasses; soil; switchgrass
published:
2025-12-23
Aly, Abdallah; A. Saif, M. Taher
(2025)
The uploaded data is part of the paper titled: Self-Modifying Percolation Governs Detachment in Soft Suction Wet Adhesion, which shows the detachment mechanism of liquid suction-based adhesion.