Illinois Data Bank Dataset Search Results
Results
published:
2025-10-29
Zhang, Zhengyi; Feng, Jianqiang; Yang, Chao; Cui, Haiyang (Ocean); Harrison, Wesley; Zhong, Dongping; Wang, Binju; Zhao, Huimin
(2025)
Since the discovery of Hofmann–Löffler–Freytag reaction more than 130 years ago, both the structure and reactivity of nitrogen-centred radicals have been widely studied. Nevertheless, catalytic enantioselective intermolecular radical hydroamination remains a challenge due to the existence of side reactions, the short lifetime of nitrogen-centred radicals and lack of understanding of the fundamental catalytic steps. In the laboratory, nitrogen-centred radicals are produced with radical initiators, photocatalysts or electrocatalysts. In contrast, their generation and reaction are unknown in nature. Here we report a pure biocatalytic system for the photoenzymatic production of nitrogen-centred radicals and enantioselective intermolecular radical hydroaminations by successfully repurposing an ene-reductase through directed evolution. These reactions progress efficiently at room temperature under visible light without any external photocatalysts and exhibit excellent enantioselectivities. A detailed mechanistic study reveals that the enantioselectivity originates from the radical-addition step while the reactivity originates from the ultrafast photoinduced electron transfer from reduced flavin mononucleotide to nitrogen-containing substrates.
keywords:
Conversion;Catalysis
published:
2025-10-22
Lane, Stephan; Turner, Timothy L.; Jin, Yong-Su
(2025)
Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing the Rhizopus oryzae lactic acid dehydrogenase (LdhA). While the membrane glucose sensors Snf3 and Rgt2 did not play any direct role in the option of predominant product, the sugar assimilation rate was strongly correlated to the partition of flux at pyruvate: fast sugar assimilation favors ethanol production while slow sugar assimilation favors lactic acid. Applying this knowledge, we created an engineered yeast capable of simultaneously converting glucose and xylose into lactic acid, increasing lactic acid production to approximately 17 g L−1 from the 12 g L−1 observed during sequential consumption of sugars. This work elucidates the carbon source-dependent effects on product selection in engineered yeast.
keywords:
Conversion;Metabolomics;Transcriptomics
published:
2021-05-26
Wang, Yu; Chan, Kher Xing; Long, Stephen P.
(2021)
Steady-state and dynamic gas exchange data for maize (B73), sugarcane (CP88-1762) and sorghum (Tx430)
keywords:
C4 plants; gas exchange
published:
2026-01-01
Iacaruso, Nicholas J.; Myers, Jared T.; Seider, Michael J.; Davis, Mark
(2026)
This dataset contains the data related to Chapter 2 of Iacaruso, N. (2026) "EVALUATING ENVIRONMENTAL DNA AS AN EARLY DETECTION METHOD FOR AQUATIC INVASIVE SPECIES". Doctoral Dissertation. University of Illinois Urbana-Champaign. This chapter will also be represented in Iacaruso et al. (2025) "Environmental DNA metabarcoding for monitoring fish biodiversity in remote lakes". North American Journal of Fisheries Management. (Forthcoming). The files contain the eDNA metabarcoding sequences from sampling Isle Royale lakes in 2021 and 2022, species read counts for each eDNA sample, and other information collected at each site.
keywords:
eDNA; Fish; Management; Cisco
published:
2020-11-14
Hoover, Jeffrey; Schelsky, Wendy
(2020)
Dataset includes temperature data (local average April daily temperatures), first egg dates and reproductive output of Prothonotary Warblers breeding in southernmost Illinois, USA. Also included are arrival dates for warblers returning to breeding grounds from wintering grounds, and global temperature anomaly data for comparison with local temperatures. These data were used in the manuscript entitled "Warmer April Temperatures on Breeding Grounds Promote Earlier Nesting in a Long-Distance Migratory Bird, the Prothonotary Warbler" published in Frontiers in Ecology and Evolution. A rich text file is included with explanations of each variable in the dataset.
keywords:
first egg dates; global warming; local temperature effects; long-distance migratory bird; prothonotary warbler; protonotaria citrea; reproductive output
published:
2020-12-16
Althaus, Scott; Bajjalieh, Joseph; Jungblut, Marc; Shalmon, Dan; Ghosh, Subhankar; Joshi, Pradnyesh
(2020)
Terrorism is among the most pressing challenges to democratic governance around the world. The Responsible Terrorism Coverage (or ResTeCo) project aims to address a fundamental dilemma facing 21st century societies: how to give citizens the information they need without giving terrorists the kind of attention they want. The ResTeCo hopes to inform best practices by using extreme-scale text analytic methods to extract information from more than 70 years of terrorism-related media coverage from around the world and across 5 languages. Our goal is to expand the available data on media responses to terrorism and enable the development of empirically-validated models for socially responsible, effective news organizations.
This particular dataset contains information extracted from terrorism-related stories in the Foreign Broadcast Information Service (FBIS) published between 1995 and 2013. It includes variables that measure the relative share of terrorism-related topics, the valence and intensity of emotional language, as well as the people, places, and organizations mentioned.
This dataset contains 3 files:
1. "ResTeCo Project FBIS Dataset Variable Descriptions.pdf"
A detailed codebook containing a summary of the Responsible Terrorism Coverage (ResTeCo) Project Foreign Broadcast Information Service (FBIS) Dataset and descriptions of all variables.
2. "resteco-fbis.csv"
This file contains the data extracted from terrorism-related media coverage in the Foreign Broadcast Information Service (FBIS) between 1995 and 2013. It includes variables that measure the relative share of topics, sentiment, and emotion present in this coverage. There are also variables that contain metadata and list the people, places, and organizations mentioned in these articles. There are 53 variables and 750,971 observations. The variable "id" uniquely identifies each observation. Each observation represents a single news article.
Please note that care should be taken when using "resteco-fbis.csv". The file may not be suitable to use in a spreadsheet program like Excel as some of the values get to be quite large. Excel cannot handle some of these large values, which may cause the data to appear corrupted within the software. It is encouraged that a user of this data use a statistical package such as Stata, R, or Python to ensure the structure and quality of the data remains preserved.
3. "README.md"
This file contains useful information for the user about the dataset. It is a text file written in mark down language
Citation Guidelines
1) To cite this codebook please use the following citation:
Althaus, Scott, Joseph Bajjalieh, Marc Jungblut, Dan Shalmon, Subhankar Ghosh, and Pradnyesh Joshi. 2020. Responsible Terrorism Coverage (ResTeCo) Project Foreign Broadcast Information Service (FBIS) Dataset Variable Descriptions. Responsible Terrorism Coverage (ResTeCo) Project Foreign Broadcast Information Service (FBIS) Dataset. Cline Center for Advanced Social Research. December 16. University of Illinois Urbana-Champaign. doi: https://doi.org/10.13012/B2IDB-6360821_V1
2) To cite the data please use the following citation:
Althaus, Scott, Joseph Bajjalieh, Marc Jungblut, Dan Shalmon, Subhankar Ghosh, and Pradnyesh Joshi. 2020. Responsible Terrorism Coverage (ResTeCo) Project Foreign Broadcast Information Service (FBIS) Dataset. Cline Center for Advanced Social Research. December 16. University of Illinois Urbana-Champaign. doi: https://doi.org/10.13012/B2IDB-6360821_V1
keywords:
Terrorism, Text Analytics, News Coverage, Topic Modeling, Sentiment Analysis
published:
2016-11-30
Spyreas, Greg; Zaya, David N.; Pearse, Ian
(2016)
This is the dataset used in the BioScience publication of the same name.
More information about this dataset:
Interested parties can request data from the Critical Trends Assessment Program, which was the source for the data on natural areas in this study. More information on the program and data requests can be obtained by visiting the program webpage.
Critical Trends Assessment Program, Illinois Natural History Survey. http://wwx.inhs.illinois.edu/research/ctap/
These spatial datasets were used for analyses:
Illinois Natural History Survey. 2003. Illinois GAP analysis land cover classification 1999-2000, 1:100 000 Scale, Raster Digital Data, Version 2.0. Champaign, IL, USA.
Illinois State Geological Survey. 1995. Illinois Landcover Thematic Map Coverage Map 1991-1995. Champaign, IL, USA.
Illinois State Geological Survey. 2001. Illinois Landcover Thematic Map Coverage Map 1999-2000. Champaign, IL, USA.
USDA National Agricultural Statistics Service Cropland Data Layer. 1999-2015. Published crop-specific data layer [Online]. Available at https://nassgeodata.gmu.edu/CropScape/. USDA-NASS, Washington, DC.
Information on agricultural practices and landcover changes were derived from the following U.S. Department of Agriculture (USDA) resources:
USDA Economic Research Service. 2016. Adoption of Genetically Engineered Crops in the U.S. Available at http://www.ers.usda.gov/data-products/. USDA-ERS, Washington, DC.
USDA Natural Resources Conservation Service. 2015. Summary Report: 2012 National Resources Inventory. https://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcseprd396218.pdf. USDA-NRCS, Washington, DC, and Center for Survey Statistics and Methodology, Iowa State University, Ames, Iowa.
keywords:
Milkweed; Monarch Butterfly; CTAP Critical Trends Assessment Program; BioScience
published:
2020-10-11
Narang, Kanika; Sundaram, Hari; Chung, Austin; Chaturvedi, Snigdha
(2020)
This dataset contains the publication record of 6429 computer science researchers collected from the Microsoft Academic dataset provided through their Knowledge Service API (http://bit.ly/microsoft-data).
published:
2020-12-30
Bolmin, Ophelia; Socha, John; Alleyne, Marianne; Dunn, Alison; Fezzaa, Kamel; Wissa, Aimy
(2020)
High-speed X-ray videos of four E. abruptus specimens recorded at the Advanced Photron Source (Argonne National lab) in the Summer of 2018 and corresponding position data of landmarks tracked during the motion. See readme file for more details.
published:
2026-01-15
Huang, Xiaoqiang; Jiang, Guangde; Harrison, Wesley; Wang, Binju; Zhao, Huimin
(2026)
Exploiting nature’s catalysts for non-natural transformations that are inaccessible to chemocatalysis is highly desirable but challenging. On the one hand, the widespread nicotinamide-dependent oxidoreductases have not been utilized for single-electron-transfer-induced bimolecular cross-couplings; on the other, the addition of catalytic asymmetric radical conjugate to terminal alkenes remains a challenge owing to strong racemic background reaction and unselective termination of prochiral radical species. Here we report a chemomimetic biocatalysitic approach for construction of alpha-carbonyl stereocentres via an unnatural intermolecular conjugate addition of N-(acyloxy)phthalimides-derived radicals with acceptor-substituted terminal alkenes, by combination of visible-light excitation and nicotinamide-dependent ketoreductases (KREDs). Based on protein crystal structure, we engineered KREDs via a semi-rational mutagenesis strategy to improve reaction outcomes with a small and high-quality variants library. Mechanistic investigations combining wet experiments, crystallographic studies and computational simulations demonstrate that the repurposed biocatalyst can suppress racemic background reaction and unselected side reactions, yielding enantioselectivity that is challenging to achieve by chemocatalysis.
keywords:
Catalysis
published:
2025-09-25
Moore, Caitlin E.; von Haden, Adam C.; Burnham, Mark B.; Kantola, Ilsa B.; Gibson, Christy; Blakely, Bethany; Dracup, Evan; Masters, Michael D.; Yang, Wendy; DeLucia, Evan H.; Bernacchi, Carl
(2025)
Perennial crops have been the focus of bioenergy research and development for their sustainability benefits associated with high soil carbon (C) and reduced nitrogen (N) requirements. However, perennial crops mature over several years and their sustainability benefits can be negated through land reversion. A photoperiod‐sensitive energy sorghum (Sorghum bicolor) may provide an annual crop alternative more ecologically sustainable than maize (Zea mays) that can more easily integrate into crop rotations than perennials, such as miscanthus (Miscanthus × giganteus). This study presents an ecosystem‐scale comparison of C, N, water and energy fluxes from energy sorghum, maize and miscanthus during a typical growing season in the Midwest United States. Gross primary productivity (GPP) was highest for maize during the peak growing season at 21.83 g C m−2 day−1, followed by energy sorghum (17.04 g C m−2 day−1) and miscanthus (15.57 g C m−2 day−1). Maize also had the highest peak growing season evapotranspiration at 5.39 mm day−1, with energy sorghum and miscanthus at 3.81 and 3.61 mm day−1, respectively. Energy sorghum was the most efficient water user (WUE), while maize and miscanthus were comparatively similar (3.04, 1.75 and 1.89 g C mm−1 H2O, respectively). Maize albedo was lower than energy sorghum and miscanthus (0.19, 0.26 and 0.24, respectively), but energy sorghum had a Bowen ratio closer to maize than miscanthus (0.12, 0.13 and 0.21, respectively). Nitrous oxide (N2O) flux was higher from maize and energy sorghum (8.86 and 12.04 kg N ha−1, respectively) compared with miscanthus (0.51 kg N ha−1), indicative of their different agronomic management. These results are an important first look at how energy sorghum compares to maize and miscanthus grown in the Midwest United States. This quantitative assessment is a critical component for calibrating biogeochemical and ecological models used to forecast bioenergy crop growth, productivity and sustainability.
keywords:
Sustainability;Field Data
published:
2020-05-04
Althaus, Scott; Bajjalieh, Joseph; Carter, John; Peyton, Buddy; Shalmon, Dan
(2020)
The Cline Center Historical Phoenix Event Data covers the period 1945-2019 and includes 8.2 million events extracted from 21.2 million news stories. This data was produced using the state-of-the-art PETRARCH-2 software to analyze content from the New York Times (1945-2018), the BBC Monitoring's Summary of World Broadcasts (1979-2019), the Wall Street Journal (1945-2005), and the Central Intelligence Agency’s Foreign Broadcast Information Service (1995-2004). It documents the agents, locations, and issues at stake in a wide variety of conflict, cooperation and communicative events in the Conflict and Mediation Event Observations (CAMEO) ontology.
The Cline Center produced these data with the generous support of Linowes Fellow and Faculty Affiliate Prof. Dov Cohen and help from our academic and private sector collaborators in the Open Event Data Alliance (OEDA).
For details on the CAMEO framework, see:
Schrodt, Philip A., Omür Yilmaz, Deborah J. Gerner, and Dennis Hermreck. "The CAMEO (conflict and mediation event observations) actor coding framework." In 2008 Annual Meeting of the International Studies Association. 2008. http://eventdata.parusanalytics.com/papers.dir/APSA.2005.pdf
Gerner, D.J., Schrodt, P.A. and Yilmaz, O., 2012. Conflict and mediation event observations (CAMEO) Codebook. http://eventdata.parusanalytics.com/cameo.dir/CAMEO.Ethnic.Groups.zip
For more information about PETRARCH and OEDA, see: http://openeventdata.org/
keywords:
OEDA; Open Event Data Alliance (OEDA); Cline Center; Cline Center for Advanced Social Research; civil unrest; petrarch; phoenix event data; violence; protest; political; conflict; political science
published:
2020-09-18
Clark, Lindsay; Njuguna, Joyce; Jin, Xiaoli; Petersen, Karen; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens B.; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik
(2020)
Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.
keywords:
variant call format (VCF); genotyping-by-sequencing (GBS); single nucleotide polymorphism (SNP); grass; genetic diversity; biomass
published:
2021-02-28
Ghosh, Sudipta; Riemer, Nicole; Giuliani, Graziano; Giorgi , Filippo; Ganguly, Dilip; Dey, Sagnik
(2021)
This dataset contains the RegCM4 simulations used in the article " Implementation of dynamic ageing of carbonaceous aerosols in regional climate model RegCM". This dataset was used to investigate the impact of a new aging parameterisation scheme implemented in a regional climate model RegCM4. The dataset contains two sets of simulations: Expt_fix and Expt_dyn. It consists of the seasonal mean and daily mean values of the variables that were used to create the visualizations of this study. The Expt_fix and Expt_dyn dataset contain 34 and 38 NetCDF files, respectively. The CERES_vs_2expts_new.mat file is the comparison between CERES shortwave downward flux at the surface and same model outputs from two experiments for clear sky and all sky conditions.
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The following information about the dataset was generated on 2021-01-08 by SUDIPTA GHOSH
<b>GENERAL INFORMATION</b>
<i>1. Date of data collection (single date, range, approximate date):</i> 2019-01-01 to 2019-12-31
<i>2. Geographic location of data collection:</i> Urbana-Champaign,Illinois, USA
<i>3. Information about funding sources that supported the collection of the data:</i> This work is supported by the MoEFCC under the NCAP-COALESCE project [Grant No. 14/10/2014-CC]. The first author acknowledges DST-INSPIRE fellowship [IF150055] and Fulbright-Kalam Climate Doctoral fellowship. N. R. acknowledges funding from NSF AGS-1254428 and DOE grant DE-SC0019192. Department of Science and Technology, Funds for Improvement of Science and Technology infrastructure in universities and higher educational institutions (DST-FIST) grant (SR/FST/ESII-016/2014) are acknowledged for the computing support.
<b>DATA & FILE OVERVIEW</b>
<i>1. File List:</i> Expt_fix and Expt_dyn datasets contain the analysed seasonal means and daily means of the variables that have been used to create the visualizations of this study. Each of the Expt_fix and Expt_dyn datasets contains 34 and 38 NetCDF files, respectively.
<i>2. Relationship between files, if important:</i> NA
<i>3. Additional related data collected that was not included in the current data package:</i> No
<b>METHODOLOGICAL INFORMATION</b>
<i>1. Description of methods used for collection/generation of data: </i>
The model RegCM4 code is freely available online from <a href="http://gforge.ictp.it/gf/project/regcm/">http://gforge.ictp.it/gf/project/regcm/</a>.
The anthropogenic aerosol emissions considered for the simulations are taken from IIASA inventory. The data used can be easily accessed online <a href="http://clima-dods.ictp.it/regcm4/">http://clima-dods.ictp.it/regcm4/</a> website.
TRMM observed precipitation data can be assessed from <a href="https://giovanni.gsfc.nasa.gov/giovanni/">https://giovanni.gsfc.nasa.gov/giovanni/</a> website.
CRU temperature data is available at <a href="https://crudata.uea.ac.uk/cru/data/hrg/">https://crudata.uea.ac.uk/cru/data/hrg/</a>.
CERES satellite surface shortwave downward fluxes are available at <a href="https://ceres.larc.nasa.gov/data/">https://ceres.larc.nasa.gov/data/</a> website.
Input files for the RegCM4 model are archived in <a href="http://clima-dods.ictp.it/regcm4/">http://clima-dods.ictp.it/regcm4/</a> website.
This dataset contains the RegCM4 simulations used in the article " Implementation of dynamic ageing of carbonaceous aerosols in regional climate model RegCM ". Two sets of simulations: Expt_fix and Expt_dyn consists of the output data . This dataset only contains the analysed seasonal mean and daily mean of the variables that have been used to create the visualizations of this study. Each of Expt_fix and Expt_dyn contains 34 and 38 NetCDF files respectively. This dataset was used to investigate the impact of a new aging parameterisation scheme implemented in a regional climate model RegCM4.
<i>2. Methods for processing the data:</i> Seasonal Mean and daily average values were extracted from 6-hourly model output.
<i>3. Instrument- or software-specific information needed to interpret the data:</i> CDO-1.7.1, Grads-2.0.a9, Matlab2016b
<i>4. Standards and calibration information, if appropriate:</i> NA
<i>5. Environmental/experimental conditions:</i> NA
<i>6. Describe any quality-assurance procedures performed on the data:</i> NA
<i>7. People involved with sample collection, processing, analysis and/or submission:</i> Sudipta Ghosh, Nicole Riemer, Graziano Giuliani, Filippo Giorgi, Dilip Ganguly, Sagnik Dey
<b>DATA-SPECIFIC INFORMATION FOR: Expt_fix_data.tar.gz</b>
<i>1. Number of variables:</i> 29
<i>2. Number of cases/rows:</i> NA
<i>3. Variable List:</i> Mass concentration (Kg m-3) of BC, BC_HB, BC_HL, OC, OC_HB, OC_HL; Columnar burden (mg m-2)] of BC, BC_HL, BC_HB, OC; Dry deposition flux (mg m-2 day-1) of BC_HB, BC_HL, OC_HB, OC_HL; Wet deposition flux due washout (mg m-2 day-1) of BC_HB, BC_HL, OC_HB, OC_HL; Wet deposition flux due to rainout (mg m-2 day-1) of BC_HB, BC_HL OC_HB, OC_HL; AOD (unit less), precipitation (Kg m-2 s-1), temperature (K) , v-wind (m s-1), u-wind (m s-1), Surface shortwave downward flux (W m-2), Shortwave radiative forcing at the surface and top of atmosphere (W m-2)
<b>DATA-SPECIFIC INFORMATION FOR: Expt_dyn_data.tar.gz</b>
<i>1. Number of variables:</i> 30
<i>2. Number of cases/rows:</i> NA
<i>3. Variable List:</i> Mass concentration (Kg m-3) of BC, BC_HB, BC_HL, OC, OC_HB, OC_HL; Columnar burden (mg m-2)] of BC, BC_HL, BC_HB, OC; Dry deposition flux (mg m-2 day-1) of BC_HB, BC_HL OC_HB, OC_HL; Wet deposition flux due washout (mg m-2 day-1) of BC_HB, BC_HL OC_HB, OC_HL; Wet deposition flux due to rainout (mg m-2 day-1) of BC_HB, BC_HL OC_HB, OC_HL; AOD (unit less); precipitation (Kg m-2 s-1); temperature (K); v-wind (m s-1); u-wind (m s-1); Surface shortwave downward flux (W m-2); Shortwave radiative forcing at the surface and top of atmosphere (W m-2); ageingscale (s-1)
<b>DATA-SPECIFIC INFORMATION FOR: CERES_vs_2expts_new.mat</b>
<i>1. Number of variables:</i> 12
<i>2. Number of cases/rows:</i> NA
<i>3. Variable List:</i> Surface shortwave downward flux for clear sky (W/m-2) for CERES, Expt_fix, Expt_dyn (for winter JF and monsoon JJAS seasons); Surface shortwave downward flux for all sky conditions (W/m-2) for CERES, Expt_fix, Expt_dyn (for winter JF and monsoon JJAS seasons).
<b>NOTE:</b> The following information applies for all three (3) files:
<i> Missing data codes:</i> NA
<i>Specialized formats or other abbreviations used:</i> NA
keywords:
Carbonaceous aerosols; ageing parameterisation scheme; regional climate model; NetCDF
published:
2025-08-21
Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ∼0.6 to ∼1.5 kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. An excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.
keywords:
gene editing; genome engineering; plant transformation
published:
2025-07-23
Dalling, James William
(2025)
Supplementary data and code associated with the Biogeosciences paper published by Cecilia Prada et al. "Soil and Biomass Carbon Storage is Much Higher in Central American than Andean Montane Forests". There are 16 files associated with this paper
(1) AGB.csv providing the site, plot, treeID, mnemn, family, agb, and AGcarbon for each tree in the dataset. Column headings are described in the file AGB_metadata.csv
(2) AGB_metadata.csv Metadata (column descriptions) for AGB.csv
(3) CWD_D.csv Complete information on the downed coarse woody debris (CWD) measured in each plot
(4) CWD_D_metadata.csv Metadata (column descriptions) for CWD_D.csv
(5) CWD_S.csv Complete information on the standing coarse woody debris measured in each plot
(6) CWD_S_metadata.csv Metadata (column descriptions) for CWD_S.csv
(7) SoilC.csv Estimated soil carbon storage (Mg C) at each sampling location in each plot
(8) SoilC_metadata.csv Metadata (column descriptions) for SoilC.csv
(9) Table.csv Data source, soil carbon value (Mg C) and elevation from published data sources
(10) Table_metadata.csv Metadata (column descriptions) for Table.csv
(11) TableS1.csv Data source, above ground carbon value (Mg C) and elevation from published data sources
(12) TableS1_metadata.csv Metadata (column descriptions) for TableS1.csv
(13) RScript.R Annotated code for data analysis and figures
(14)Full_dataset.csv Full set of environmental data and carbon data by plot
(15) Full_dataset_metadata.csv Metadata (column descriptions) for Full_dataset.csv
(16) Species list and species codes.csv Full family, genus and species names for the species codes (column mnemn in AGB.csv)
keywords:
tropical forest; carbon storage
published:
2025-11-24
Li, Maolin; Harrison, Wesley; Zhang, Zhengyi; Yuan, Yujie; Zhao, Huimin
(2025)
Strategies for achieving asymmetric catalysis with azaarenes have traditionally fallen short of accomplishing remote stereocontrol, which would greatly enhance accessibility to distinct azaarenes with remote chiral centres. The primary obstacle to achieving superior enantioselectivity for remote stereocontrol has been the inherent rigidity of the azaarene ring structure. Here we introduce an ene-reductase system capable of modulating the enantioselectivity of remote carbon-centred radicals on azaarenes through a mechanism of chiral hydrogen atom transfer. This photoenzymatic process effectively directs prochiral radical centres located more than six chemical bonds, or over 6 Å, from the nitrogen atom in azaarenes, thereby enabling the production of a broad array of azaarenes possessing a remote γ-stereocentre. Results from our integrated computational and experimental investigations underscore that the hydrogen bonding and steric effects of key amino acid residues are important for achieving such high stereoselectivities.
keywords:
Conversion;Catalysis
published:
2025-10-01
Schetter, August; Lin, Cheng-Hsien; Zumpf, Colleen; Jang, Chunhwa; Hoffmann Jr., Leo; Rooney, William; Lee, DoKyoung
(2025)
Recently introduced photoperiod-sensitive (PS) biomass sorghum (Sorghum bicolor L. Moench) needs to be investigated for yield potential under different cultivation environments with reasonable nitrogen (N) inputs. The objectives of this study were to (1) evaluate the biomass yield and feedstock quality of four sorghum hybrids with different levels of PS ranging from very PS (VPS) hybrids and to moderate PS (MPS) hybrids, and (2) determine the optimal N inputs (0~168 kg N ha−1) under four environments: combinations of both temperate (Urbana, IL) and subtropical (College Station, TX) regions during 2018 and 2019. Compared to TX, the PS sorghums in central IL showed higher yield potential and steady feedstock production with an extended day length and with less precipitation variability, especially for the VPS hybrids. The mean dry matter (DM) yields of VPS hybrids were 20.5 Mg DM ha−1 and 17.7 Mg DM ha−1 in IL and TX, respectively. The highest N use efficiency occurred at a low N rate of 56 kg N ha−1 by improving approximately 33 kg DM ha−1 per 1.0 kg N ha−1 input. Approximately 70% of the PS sorghum biomass can be utilized for biofuel production, consisting of 58-65% of the cell-wall components and 4-11% of the soluble sugar. This study demonstrated that the rainfed temperate area (e.g., IL) has a great potential for the sustainable cultivation of PS energy sorghum due to their observed high yield potential, stable production, and low N requirements.
keywords:
Sustainability;Biomass Analytics;Field Data
published:
2023-07-01
Tonks, Adam; Hwang, Jeongwoo
(2023)
This is the data used in the paper "Assessment of spatiotemporal flood risk due to compound precipitation extremes across the contiguous United States".
Code from the Github repository https://github.com/adtonks/precip_extremes can be used with the data here to reproduce the paper's results. v1.0.0 of the code is also archived at https://doi.org/10.5281/zenodo.8104252
This dataset is derived from NOAA-CIRES-DOE 20th Century Reanalysis V3. The NOAA-CIRES-DOE Twentieth Century Reanalysis Project version 3 used resources of the National Energy Research Scientific Computing Center managed by Lawrence Berkeley National Laboratory which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and used resources of NOAA's Remotely Deployed High Performance Computing Systems.
keywords:
spatiotemporal; CONUS; United States; precipitation; extremes; flooding
published:
2025-05-27
Rani, Sonia; Cao, Xi; Baptista, Alejandro E.; Hoffmann, Axel; Pfaff, Wolfgang
(2025)
This dataset contains all raw and processed data used to generate the figures in the main text and supplementary material of the paper "High dynamic-range quantum sensing of magnons and their dynamics using a superconducting qubit." The data can be used to reproduce the plots and validate the analysis. Accompanying Jupyter notebooks provide step-by-step analysis pipelines for figure generation. The dataset also includes drawings for the mechanical samples used to perform the experiment. In addition, the dataset provides ANSYS HFSS electromagnetic simulation files used to design and analyze the resonator structures and estimate field distributions.
keywords:
superconducting qubit; magnon sensing; hybrid quantum systems; spin-photon coupling; magnon decay; cavity QED
published:
2025-12-14
Fraterrigo, Jennifer; Chen, Weile
(2025)
This dataset contains information about absorptive roots from 170 plots along a latitudinal and temperature gradient in northern Alaska, including tussock sedges and deciduous alder, birch, and willow shrubs. This dataset accompanies the paper "Impacts of Arctic Shrubs on Root Traits and Belowground Nutrient Cycles Across a Northern Alaskan Climate Gradient," which was published in Frontiers in Plant Sciences.
<b>*Note:</b> in the "patch coordinates" tab, the same coordinates/elevation ("Long", "Lat", and "Elev (m)") apply to all patches that share a number. For ex: "Patch" W1, B1, and G1 share the same "Long", "Lat", and "Elev (m)" values as "Patch" A1.
keywords:
absorptive root traits; shrub expansion; Arctic; Alaskan tundra
published:
2020-01-31
Bradshaw, Therin M.; Blake-Bradshaw, Abigail G.; Fournier, Auriel M.V.; Lancaster, Joseph D. ; O'Connell, John; Jacques, Christopher N.; Eicholtz, Michael W.; Hagy, Heath M
(2020)
Data inputs, and scripts for the analysis detailed in Bradshaw et al, published in PlosONE 2020.
keywords:
Marsh birds; wetlands
published:
2025-07-31
Gibson, Jared; Jiang, Zhanzhi; Kou, Angela
(2025)
This repository includes data files and analysis and plotting codes for reproducing the figures in the paper "A scanning resonator for probing quantum coherent devices" arXiv:2506.22620
published:
2025-08-04
Hartman, Theodore; Studt, Jacob; VanLoocke, Andy; McDaniel, Marshall; Howe, Adina; Masters, Michael D. ; Mitchell, Corey; DeLucia, Evan H.; Heaton, Emily
(2025)
This dataset contains the data used for the publication “Aboveground rather than belowground productivity drives variability in Miscanthus x giganteus net primary productivity”. This dataset contains Miscanthus x giganteus biomass, carbon, and nitrogen tissue data for aboveground and belowground plant parts collected in 2021 for three different sites in Iowa with three different nitrogen application rates. Data at the Iowa sites were collected via biometric hand harvesting, belowground excavations, and soil coring both in-clump and beside-clump. Data were collected at two collection timepoints to calculate the contributions of belowground parts to Miscanthus x giganteus net primary productivity. This dataset also includes Miscanthus x giganteus and Switchgrass soil coring and excavation data collected in 2012 at the University of Illinois Urbana Champaign Energy Farm.
keywords:
Miscanthus; Net Primary Productivity; Excavation; Nitrogen fertilization; Translocation; Belowground Biomass; Carbon
published:
2025-09-06
4D-STEM datasets for solution-treated (CrCoNi)93Al4Ti2Nb MEA in [111], [112], and [114] zone. Data used for Ultramicroscopy article "Differentiating electron diffuse scattering via 4D-STEM spatial fluctuation and correlation analysis in complex FCC alloys". Experiment details can be found in the paper. Data-specific details are listed in the Readme file.
keywords:
4D-STEM; MEA; Electron Diffuse-Scattering; FluCor