Illinois Data Bank Dataset Search Results
Results
published:
2016-12-12
Zhang, Qian; Chunyan, Li; Braud, Dewitt
(2016)
This dataset is about a topographic LIDAR survey (saved in “waxlake-lidar.img”) that was conducted over the Wax Lake delta, between longitudes −91.5848 to −91.292 degrees, and latitudes 29.3647 to 29.6466 degrees. Different from other elevation data, the positive value in the LIDAR data indicates land elevation, while the zero value implies riverbed without identifying specific water depth.
keywords:
LIDAR; Wax Lake delta
published:
2024-01-30
This data set includes the cochlear implant (CI) electrodograms recorded in 2 different acoustic conditions using acoustic head KEMAR. It is a part of a study intended to explore the effect of interaural asymmetry on interaural coherence after CI processing.
keywords:
cochlear implant; electrodogram; KEMAR; interaural coherence
published:
2016-12-12
Zhang, Qian; Li, Chunyan
(2016)
This dataset is the field measurements of water depth at the Wax Lake delta on the date 2012-12-01.
keywords:
Wax Lake delta; Bathymetry
published:
2022-01-30
Bakken, George; Tillman, Francis; O'Keefe, Joy
(2022)
This dataset contains temperature measurements in four different bat box designs deployed in central Indiana, USA from May to September 2018. Hourly environmental data (temperature, solar radiation, and wind speed) are also included for days and hours sampled. Bat box temperature data were used as inputs in a free program, GNU Octave, to assess design performance with respect to suitability indices for endothermic metabolism and pup development. Scripts are included in the dataset.
keywords:
bats;thermal refuge;reproduction;conservation;bat box;microclimate
published:
2023-07-11
Parulian, Nikolaus
(2023)
The dissertation_demo.zip contains the base code and demonstration purpose for the dissertation: A Conceptual Model for Transparent, Reusable, and Collaborative Data Cleaning.
Each chapter has a demo folder for demonstrating provenance queries or tools.
The Airbnb dataset for demonstration and simulation is not included in this demo but is available to access directly from the reference website.
Any updates on demonstration and examples can be found online at: https://github.com/nikolausn/dissertation_demo
published:
2023-12-06
Starbuck, Clarissa; DeSchepper, Logan; Hoggatt, Meredith; O'Keefe, Joy
(2023)
This dataset accompanies an article published in the journal Bioacoustics: "Tradeoffs in sound quality and cost for passive acoustic devices", https://doi.org/10.1080/09524622.2023.2290715. The dataset contains measurements for acoustic call files for free-flying bats simultaneously recorded on both Audiomoth and Anabat Swift passive acoustic recording devices in a conservation area in northeastern Missouri, USA. We paired calls from the two devices and compared indicators of recording quality measured in a proprietary program (Bat Call Identification Software). The dataset also contains a file enumerating the proportions of calls classified as low frequency, mid frequency, or Myotis (three phonic groups) for each type of recording device. The data were used to compare the quality and sensitivity of the two devices. The scripts for modeling procedures and figures are included in the dataset.
keywords:
Bats; echolocation; passive acoustic monitoring; sensors
published:
2023-12-08
Preza Fontes, Giovani; Greer, Kristin; Pittelkow, Cameron
(2023)
A two-year field study was conducted to test the hypothesis that biochar application increases inorganic soil N availability during maize growth, leading to higher grain yields and N recovery efficiency while reducing the risk of N leaching following harvest. Four N fertilizer rates (0, 90, 179, and 269 kg ha-1 as urea ammonium nitrate solution) were applied with or without biochar (10 Mg ha-1) before maize planting each year. This dataset contains selected summary statistics (average and standard deviation) on soil and plant measurements. This file package also includes a readme.txt file that describes the data in detail, including attribute descriptions.
keywords:
biochar; nitrogen fertilizer; nitrogen use efficiency; corn yield, soil inorganic nitrogen; nitrate leaching
published:
2025-06-05
Guan, Yingjun; Fang, Liri
(2025)
There are two files in this dataset.
File1: AffiNorm
AffiNorm contains 1,001 rows, including one header row, randomly sampled from MapAffil 2018 Dataset ([**https://doi.org/10.13012/B2IDB-2556310_V1**](https://databank.illinois.edu/datasets/IDB-2556310)). Each row in the file corresponds to a particular author on a particular PubMed record, and contains the following 26 columns, comma-delimited. All columns are ASCII, except city which contains Latin-1.
COLUMN DESCRIPTION
1. PMID: the PubMed identifier. int.
2. ORDER: the position of the author. int.
3. YEAR - The year of publication. int(4), eg: 1975.
4. affiliation - affiliation string of the author. eg: Department of Pathology, University of Chicago, Illinois 60637.
5. annotation_type: the number of institutions annotated, denoted by S, M, O, or Z, where "S" (single) indicates 1 institution was annotated; "M" (Multiple) indicates more than one institutions were annotated; "O" (Out of Vocabulary or None) indicates no institution was annotated, but an institution was apparently mentioned; "Z" indicates no institution was mentioned.
6. Institution: the standard name(s) of the annotated institution(s), according to ROR. if "S" (single institution), it is saved as a string, eg: University of Chicago; if "M", it is saved as a string that looks like a python list, eg: ['Public Health Laboratory Service'; 'Centre for Applied Microbiology and Research']; if "O" or "Z", then blank.
7. inst_type: the type of institution, according to ROR. the potential values are: education, funder, healthcare, company, archive, nonprofit, government, facility, other. An institution may have more than one type, eg: ['Education', 'Funder']
8. type_edu: TRUE if the inst_type contains "Education"; FALSE otherwise.
9. RORid: ROR identifier(s), eg: https://ror.org/05hs6h993. when multiple, the order corresponds to institution (column 6)
10. RORid_label. the standard name(s) of the annotated institution(s) according to ROR.same as institution (column 6)
11. GRIDid: GRID identifier(s). eg: grid.170205.1
12. GRIDid_label: the standard name(s) of the annotated institution(s) according to GRID. eg: University of Chicago.
13. WikiDataid: WikiData identifier(s). eg: Q131252
14. WikiDataid_label: the standard name(s) of the annotated institution(s) according to WikiData. eg: University of Chicago
15. synonyms: a comma separated list of variant names from InsVar (file 2) . format of string. eg: University of Chicago, Chicago University, U of C, UChicago, uchicago.edu, U Chicago, ...
16. MapAffil-grid: GRID from the MapAffil 2018 Dataset.
17. MapAffil-grid_label: The standard name of institution from MapAffil 2018 Dataset.
18. judge_mapA: TRUE if GRIDid (column 11) contains MapAffil-grid (column 16); FALSE otherwise.
19. MapAffiltemporal-grid: GRID from the temporal version of MapAffil, http://abel.ischool.illinois.edu/data/MapAffilTempo2018.tsv.gz
20. MapAffiltemporal-grid_label: The standard name of institution from MapAffilTemporal 2018 Dataset.
21. judge_mapT: TRUE if GRIDid (column 11) contains MapAffiltemporal-grid (column 19); FALSE otherwise.
22. RORapi_query_id: ROR from ROR api tool (query endpoint)
23. RORapi_query_id_label: The standard name of institution from ROR api tool (query endpoint). format in string.
24. judge_rorapi_affiliation: TRUE if RORid (column 9) contains RORapi_query_id (column 22); FALSE otherwise.
25. rorapi_affiliation_id: ROR from ROR api tool (affiliation endpoint).
26. judge_rorapi_affiliation: TRUE if RORid (column 9) contains RORapi_affiliation (column 25); FALSE otherwise.
File 2: insVar.json
InsVar is a supplementary dataset for AffiNorm, which includes the institution ID and its redirected aliases from wikidata. The institution ID list is from GRID, the redirected aliases are from wiki api, for example: https://en.wikipedia.org/wiki/Special:WhatLinksHere?target=University+of+Illinois+Urbana-Champaign&namespace=&hidetrans=1&hidelinks=1&limit=100
In InsVar, the data is saved in a python dictionary format. the key is the GRID identifier, for example: "grid.1001.0" (Australian National University), and the value is a list of redirected aliases strings.
{"grid.1001.0": ["ANU", "ANU College", "ANU College of Arts and Social Sciences", "ANU College of Asia and the Pacific", "ANU Union", "ANUSA", "Asia Pacific Week", "Australia National University", "Australian Forestry School", "the Australian National University", ...], "grid.1002.3": ...}
keywords:
PubMed; MEDLINE; Digital Libraries; Bibliographic Databases; Institution Names; Author Affiliations; Institution Name Ambiguity; Authority files
published:
2024-07-31
LaBonte, Nicholas R.; Zerpa-Catanho, Dessiree P.; Liu, Siyao; Xiao, Liang; Dong, Hongxu; Clark, Lindsay V.; Sacks, Erik J.
(2024)
This dataset contains all data and supplementary materials from "Improving precision and accuracy of genetic mapping with genotyping-by-sequencing data in outcrossing species". An Excel file a list of all QTLs and linkage group length (in cM) obtained with two different SNP-calling methods (Tassel-Uneak and Tassel-GBS), genetic map-construction method (linkage-only and reference order-corrected) and depth filters (12x, 20x, 30x and 40x) for genetic mapping of 18 biomass yield traits in a biparental Miscanthus sinensis population using RAD-Seq SNPs is provided as "Supplementary file 1". A Perl script with the code for filtering VCF and HapMap-formatted data files is provided as “Supplementary file 2”. Phenotype data used for QTL mapping is provided as “Supplementary File 3”. A Perl script with the code for the simulation study is provided as “Supplementary file 4”.
keywords:
HapMapParser; GenotypingSimulator
published:
2025-04-25
Tassitano, Rafael; Chakraborty, Shreyonti
(2025)
This is an Excel file containing data about the physical environments of four Brazilian schools and the average daily minutes/day of physical activity and sedentary behavior exhibited by schoolchildren during school hours.
The Following Key describes the basic variables:
Subject IDs and Characteristics
Subject_ID: ID of Subject
total_days: Total number of days subject participated in experiment
Gender : Gender of subject
Age: Age of subject
School IDs and Characteristics
ID_School = ID of School
school1 = 1 if ID_School = 1, else = 0
school2 = 1 if ID_School = 2, else = 0
school3 = 1 if ID_School = 3, else = 0
school4 = 1 if ID_School = 4, else = 0
TotalSiteArea: Total Site Area on School Campus
PatioArea: Area of Patio(s)
CourtyardArea: Area of Courtyard(s)
TotalOpenArea: Total Area of Open Spaces on Campus
Class: Number of Sections in the School
Population: Total Number of Students Enrolled in the School
keywords:
school environment; physical activity
published:
2025-11-06
Sweedler, Jonathan; Rosado Rosa, Joenisse M.
(2025)
SCiLS MSI data files, images used in the figures and table contents for the tables found in the manuscript. The figures are labeled by figure and by their title on each figure set, including those found in the Supplementary Information. The tables are in an MS Excel sheet with the corresponding contents. The tables list the metabolites found in the images. To reduce the number of images in the manuscript, the tables complete the metabolite information not observed in the images. The images can be found using the SCiLS data files. A software license is needed to open these files. The SCiLS data files contains the processed MSI data for all obtained images. All files in the corresponding SCiLS data file must be present to open the individual data file. The feature list used for MSI analysis should be saved on the attached bookmark inside the SCiLS file so it should be available once the file is opened. SCiLS files can only be opened with the Bruker SCiLS software. If using an outdated version (before Version 13.01.17218), the files may not open or show poor quality.
keywords:
Tendrils; Pyocyanin; Quinolones; Spatiochemical; Metabolomics
published:
2025-10-21
Jia, Yuyao; Maitra, Shraddha; Singh, Vijay
(2025)
Bioenergy crops have potential for being a sustainable and renewable feedstock for biofuels and various value-added bioproducts. The study utilizes recently developed transgenic sugarcane (“oilcane”) bagasse for chemical-free coproduction of high-value bioproducts, i.e., furfurals, HMF, acetic acid, cellulosic sugars, and vegetative lipids. Hydrothermal pretreatment was optimized at 210 °C for 5 min to coproduce 6.91%, 2.67%, 5.07%, 2.42% and 37.82% (w/w) furfurals, HMF, acetic acid, vegetative lipids, and cellulosic sugars, respectively from lignocellulosic biomass. Additionally, nanofiltration system in-series was successfully established to recover sugars, furfurals, HMF, and acetic acid from the pretreatment liquor. 1st nanofiltration with Duracid NF membrane rejected ∼99% sugars. Concentrated sugars with significantly reduced inhibitory products were obtained in retentate for fermentation. 2nd nanofiltration with NF90 membrane used permeate of 1st nanofiltration as feed and rejected ∼ 86% furfurals. The work demonstrates the feasibility of coproducing and recovering multiple biochemicals from lignocellulosic biomass.
keywords:
Conversion;Biomass Analytics;Hydrolysate;Metabolomics
published:
2023-10-16
Rasoarimanana, Tantely; Edmonds, Devin; Marquis, Olivier
(2023)
This dataset provides microhabitat and environmental variables collected in the habitat of the poison frog Mantella baroni from 155 1-meter square quadrats in Vohimana Reserve along forest valleys, on slopes, and on ridgelines. We also provide data from photographic capture-recapture surveys used for estimating abundance.
keywords:
occupancy; abundance; amphibian; Madagascar; microhabitat; capture-recapture
published:
2024-08-29
Li, Shuai; Montes, Christopher; Aspray, Elise; Ainsworth, Elizabeth
(2024)
Over the past 15 years, soybean seed yield response to season-long elevated O3 concentrations [O3] and to year-to-year weather conditions was studied using free-air O3 concentration enrichment (O3-FACE) in the field at the SoyFACE facility in Central Illinois. Elevated [O3] significantly reduced seed yield across cultivars and years. However, our results quantitatively demonstrate that weather conditions, including soil water availability and air temperature, did not alter yield sensitivity to elevated [O3] in soybean.
keywords:
drought, elevated O3, heat, O3-FACE, soybean, yield
published:
2022-12-05
Ng, Yee Man Margaret ; Taneja, Harsh
(2022)
These are similarity matrices of countries based on dfferent modalities of web use. Alexa website traffic, trending vidoes on Youtube and Twitter trends. Each matrix is a month of data aggregated
keywords:
Global Internet Use
published:
2024-05-13
Gopalakrishnappa, Chandana; Li, Zeqian; Kuehn, Seppe
(2024)
Supplemental data for the paper titled 'Environmental modulators of algae-bacteria interactions at scale'. Each of the excel workbooks corresponding to datasets 1, 2, and 3 contain a README sheet explaining the reported data. Dataset 4 comprising microscopy data contains a README text file describing the image files.
keywords:
Algae-bacteria interactions; high-throughput; microfluidic-droplet platform
published:
2022-12-31
Maffeo, Christopher; Wilson, Jim; Quednau, Lauren; Aksimentiev, Aleksei
(2022)
Trajectory data for Nature Nanotechnology manuscript "DNA double helix, a tiny electromotor" that demonstrates how an electric field applied along the helical axis of a DNA or RNA molecule will generate an electroosmotic flow that causes the duplex to spin about that axis, much like a turbine.
keywords:
All-atom MD simulation; DNA; nanotechnology; motors and rotors
published:
2021-05-07
Prepared by Vetle Torvik 2021-05-07
The dataset comes as a single tab-delimited Latin-1 encoded file (only the City column uses non-ASCII characters).
• How was the dataset created?
The dataset is based on a snapshot of PubMed (which includes Medline and PubMed-not-Medline records) taken in December, 2018. (NLMs baseline 2018 plus updates throughout 2018). Affiliations are linked to a particular author on a particular article. Prior to 2014, NLM recorded the affiliation of the first author only. However, MapAffil 2018 covers some PubMed records lacking affiliations that were harvested elsewhere, from PMC (e.g., PMID 22427989), NIH grants (e.g., 1838378), and Microsoft Academic Graph and ADS (e.g. 5833220). Affiliations are pre-processed (e.g., transliterated into ASCII from UTF-8 and html) so they may differ (sometimes a lot; see PMID 27487542) from PubMed records. All affiliation strings where processed using the MapAffil procedure, to identify and disambiguate the most specific place-name, as described in:
Torvik VI. MapAffil: A bibliographic tool for mapping author affiliation strings to cities and their geocodes worldwide. D-Lib Magazine 2015; 21 (11/12). 10p
• Look for Fig. 4 in the following article for coverage statistics over time:
Palmblad, M., Torvik, V.I. Spatiotemporal analysis of tropical disease research combining Europe PMC and affiliation mapping web services. Trop Med Health 45, 33 (2017). <a href="https://doi.org/10.1186/s41182-017-0073-6">https://doi.org/10.1186/s41182-017-0073-6</a>
Expect to see big upticks in coverage of PMIDs around 1988 and for non-first authors in 2014.
• The code and back-end data is periodically updated and made available for query by PMID at http://abel.ischool.illinois.edu/cgi-bin/mapaffil/search.py
• What is the format of the dataset?
The dataset contains 52,931,957 rows (plus a header row). Each row (line) in the file has a unique PMID and author order, and contains the following eighteen columns, tab-delimited. All columns are ASCII, except city which contains Latin-1.
1. PMID: positive non-zero integer; int(10) unsigned
2. au_order: positive non-zero integer; smallint(4)
3. lastname: varchar(80)
4. firstname: varchar(80); NLM started including these in 2002 but many have been harvested from outside PubMed
5. initial_2: middle name initial
6. orcid: From 2019 ORCID Public Data File https://orcid.org/ and from PubMed XML
7. year: year of the publication
8. journal: name of journal that the publication is published
9. affiliation: author's affiliation??
10. disciplines: extracted from departments, divisions, schools, laboratories, centers, etc. that occur on at least unique 100 affiliations across the dataset, some with standardization (e.g., 1770799), English translations (e.g., 2314876), or spelling corrections (e.g., 1291843)
11. grid: inferred using a high-recall technique focused on educational institutions (but, for experimental purposes, includes a few select hospitals, national institutes/centers, international companies, governmental agencies, and 200+ other IDs [RINGGOLD, Wikidata, ISNI, VIAF, http] for institutions not in GRID). Based on 2019 GRID version https://www.grid.ac/
12. type: EDU, HOS, EDU-HOS, ORG, COM, GOV, MIL, UNK
13. city: varchar(200); typically 'city, state, country' but could include further subdivisions; unresolved ambiguities are concatenated by '|'
14. state: Australia, Canada and USA (which includes territories like PR, GU, AS, and post-codes like AE and AA)
15. country
16. lat: at most 3 decimals (only available when city is not a country or state)
17. lon: at most 3 decimals (only available when city is not a country or state)
18. fips: varchar(5); for USA only retrieved by lat-lon query to https://geo.fcc.gov/api/census/block/find
keywords:
PubMed, MEDLINE, Digital Libraries, Bibliographic Databases; Author Affiliations; Geographic Indexing; Place Name Ambiguity; Geoparsing; Geocoding; Toponym Extraction; Toponym Resolution; institution name disambiguation
published:
2021-05-14
This is the complete dataset for the "Anomalous density fluctuations in a strange metal" Proceedings of the National Academy of Sciences publication (https://doi.org/10.1073/pnas.1721495115). This is an integration of the Zenodo dataset which includes raw M-EELS data.
<b>METHODOLOGICAL INFORMATION</b>
1. Description of methods used for collection/generation of data: Data have been collected with a M-EELS instrument and according to the data acquisition protocol described in the original PNAS publication and in SciPost Phys. 3, 026 (2017) (doi: 10.21468/SciPostPhys.3.4.026)
2. Methods for processing the data: Raw data were collected with a channeltron-based M-EELS apparatus described in the reference PNAS publication and analyzed according to the procedure outlined both in the PNAS paper and in SciPost Phys. 3, 026 (2017) (doi: 10.21468/SciPostPhys.3.4.026). The raw M-EELS spectra at each momentum have been subject to minor data processing involving:
(a) averaging of different acquisitions at the same conditions,
(b) energy binning,
(c) division of an effective Coulomb matrix element (which yields a structure factor S(q,\omega)),
(d) antisymmetrization (which yields the imaginary chi)
All these procedures are described in the PNAS paper.
3. Instrument- or software-specific information needed to interpret the data: These data are simple .txt or .dat files which can be read with any standard data analysis software, notably Python notebooks, MatLab, Origin, IgorPro, and others. We do not include scripts in order to provide maximum flexibility.
4. Relationship between files, if important: We divided in different folders raw data, structure factors and imaginary chi.
<b>DATA-SPECIFIC INFORMATION</b>
There are 8 folders within the Data_public_deposition_v1.zip. Each folder contain data needed to create the corresponding figure in the publication.
<b>1. Fig1:</b> This folder contains 21 DAT files needed to plot the theory data in panels C and D, following this naming conventions:
[chiA]or[chiB]or[Pi]_q_number.dat
With chiA is the imaginary RPA charge susceptibility with a Coulomb interaction of electronically weakly coupled layers
chiB is the imaginary RPA charge susceptibility with the usual 4\pi e^2/q^2 Coulomb interaction.
Pi is the imaginary Lindhard polarizability.
q is momentum in reciprocal lattice units
Number is the numerical momentum value in reciprocal lattice units
<b>2. Fig2:</b> Files needed to plot Fig. 2 of the PNAS paper. Contains 3 folders as listed below. The files in this folder are named following this convention: Bi2212_295K_(1,-1)_50eV_161107_q_number_2.16_avg.dat,
295K is the sample temperature
(1,-1) is the momentum direction in reciprocal lattice units
50 eV is the incident e beam energy
161107 is the start date of the experiment in yymmdd format
Q is the momentum
Number is the momentum in reciprocal lattice units
2.16 is the energy range covered by the data in eV
Avg identifies averaged data
ImChi: is the imaginary susceptibility obtained by antisymmetryzing the structure factor
Raw_avg_data: raw averaged M-EELS spectra
Sqw: Structure factors derived from the M-EELS spectra
<b>3. Fig3:</b> Files needed to plot Fig. 3 of the PNAS paper. OP/ OD prefix identifies optimally doped or overdosed sample data, respectively.
ImChi: is the imaginary susceptibility obtained by antisymmetryzing the structure factor
Raw_avg_data: raw averaged M-EELS spectra
Sqw: Structure factors derived from the M-EELS spectra
<b>4. Fig4:</b> Files needed to plot Fig. 4 of the PNAS paper. The _fit_parameters.dat file contains the fit parameters extracted according to the fit procedure described in the manuscript and at all momenta.
ImChi: is the imaginary susceptibility obtained by antisymmetryzing the structure factor
Raw_avg_data: raw averaged M-EELS spectra
Sqw: Structure factors derived from the M-EELS spectra
<b>5. FigS1:</b> Files needed to plot Fig. S1 of the PNAS paper. There are 5 files in this folder. DAT files are M-EELS data following the prior naming convention, while the two .txt files are digitized data from N. Nücker, U. Eckern, J. Fink, and P. Müller, Long-Wavelength Collective Excitations of Charge Carriers in High-Tc Superconductors, Phys. Rev. B 44, 7155(R) (1991), and K. H. G. Schulte, The interplay of Spectroscopy and Correlated Materials, Ph.D. thesis, University of Groningen (2002).
<b>6. FigS2:</b> Files needed to plot Fig. S2 of the PNAS paper.
ImChi: is the imaginary susceptibility obtained by antisymmetryzing the structure factor
Raw_avg_data: raw averaged M-EELS spectra
Sqw: Structure factors derived from the M-EELS spectra
<b>7. FigS3:</b> Files needed to plot Fig. S3 of the PNAS paper. There are 2 files in this folder:
20K_phi_0_q_0.dat: is a M-EELS raw intensity at zero momentum transfer on Bi2212 at 20 K
295K_phi_0_q_0.dat: is a M-EELS raw intensity at zero momentum transfer on Bi2212 at 295 K
<b>8. FigS4:</b> Files needed to plot Fig. S4 of the PNAS paper. The _fit_parameters.dat file contains the fit parameters extracted according to the fit procedure described in the manuscript and at all momenta.
ImChi: is the imaginary susceptibility obtained by antisymmetryzing the structure factor
Raw_avg_data: raw averaged M-EELS spectra
Sqw: Structure factors derived from the M-EELS spectra
keywords:
Momentum resolved electron energy loss spectroscopy (M-EELS); cuprates; plasmons; strange metal
published:
2025-10-14
Jagtap, Sujit Sadashiv; Deewan, Anshu; Liu, Jing-Jing; Walukiewicz, Hanna E.; Yun, Eun Ju; Jin, Yong-Su; Rao, Christopher V.
(2025)
Rhodosporidium toruloides is an oleaginous yeast capable of producing a variety of biofuels and bioproducts from diverse carbon sources. Despite numerous studies showing its promise as a platform microorganism, little is known about its metabolism and physiology. In this work, we investigated the central carbon metabolism in R. toruloides IFO0880 using transcriptomics and metabolomics during growth on glucose, xylose, acetate, or soybean oil. These substrates were chosen because they can be derived from plants. Significant changes in gene expression and metabolite concentrations were observed during growth on these four substrates. We mapped these changes onto the governing metabolic pathways to better understand how R. toruloides reprograms its metabolism to enable growth on these substrates. One notable finding concerns xylose metabolism, where poor expression of xylulokinase induces a bypass leading to arabitol production. Collectively, these results further our understanding of central carbon metabolism in R. toruloides during growth on different substrates. They may also help guide the metabolic engineering and development of better models of metabolism for R. toruloides.
keywords:
Conversion;Metabolomics;Transcriptomics
published:
2020-12-02
Yang, Pan; Cai, Ximing; Khanna, Madhu
(2020)
The dataset includes the survey results about farmers’ perceptions of marginal land availability and the likelihood of a land pixel being marginal based on a machine learning model trained from the survey.
Two spreadsheet files are the farmer and farm characteristics (marginal_land_survey_data_shared.xlsx), and the existing land use of marginal lands (land_use_info_sharing.xlsx).
<b>Note:</b> the blank cells in these two spreadsheets mean missing values in the survey response.
The GeoTiff file includes two bands, one the marginal land likelihood in the Midwestern states (0-1), the other the dominant reason of land marginality (0-5; 0 for farm size, 1 for growing season precipitation, 2 for root zone soil water capacity, 3 for average slope, 4 for growing season mean temperature, and 5 for growing season diurnal range of temperature). To read the data, please use a GIS software such as ArcGIS or QGIS.
keywords:
marginal land; survey
published:
2022-10-14
Zhou, Shan; Li, Jiahui; Lu, Jun; Liu, Haihua; Kim, Ji-Young; Kim, Ahyoung; Yao, Lehan; Liu, Chang; Qian, Chang; Hood, Zachary D. ; Lin, Xiaoying; Chen, Wenxiang; Gage, Thomas E. ; Arslan, Ilke; Travesset, Alex; Sun, Kai; Kotov, Nicholas A.; Chen, Qian
(2022)
This dataset is the raw data including SEM, TEM, PINEM images and FDTD simulation as well as pairwise interaction calculation results.
published:
2025-10-14
Jia, Yuyao; Kumar, Deepak; Winkler-Moser, Jill K.; Dien, Bruce S.; Rausch, Kent D.; Tumbleson, M.E.; Singh, Vijay
(2025)
Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 °C and 180 °C for 10 minutes) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.
keywords:
Conversion;Hydrolysate;Lipidomics
published:
2025-10-03
Kang, Nam Kyu; Lee, Jaewon; Ort, Donald; Jin, Yong-Su
(2025)
L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol- and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titers of malic acid from xylose than glucose. Interestingly, the engineered strain had higher malic acid yield from lower concentrations (10 g L‒1) of xylose, with no ethanol production, than from higher xylose concentrations (20 and 40 g L‒1). As such, a fed-batch culture maintaining xylose concentrations at low levels was conducted and 61.2 g L‒1 of malic acid was produced, with a productivity of 0.32 g L‒1 h. These results represent successful engineering of S. cerevisiae for the production of malic acid from xylose, confirming that that xylose offers the efficient production of various biofuels and chemicals by engineered S. cerevisiae.
keywords:
Conversion;Feedstock Production;Genome Engineering
published:
2023-12-23
Rodriguez-Zas, Sandra
(2023)
Supplemental document corresponding to a submission to Physiological Genomics (Data supplements and source materials must now be deposited in a community-recognized data repository or to a generalist public access repository if no community resource is available. See "Author/Production Requirements" for more information.) https://pg.msubmit.net/
keywords:
Supplemental, Physiological Genomics