Dataset Search

This dataset includes supporting data for our article 'Assessing long-term impacts of cover crops on soil organic carbon in the central U.S. Midwestern agroecosystems'. The dataset contains carbon fluxes and SOC benefits from cover crops at six cover crop experiment sites in Illinois with three rotation systems: (1) without-cover-crop (maize-soybean rotations), (2) non-legume-preceding-maize (maize-annual ryegrass-soybean-annual ryegrass rotations), and (3) legume-preceding-maize (maize-cereal rye-soybean-hairy vetch rotations). <b>*NOTE:</b> there should be 13 files + 1 readme file, instead of 15 files as mentioned in readme.

Femoral skeletal traits (cross-sectional properties, maximum distal metaphyseal breadth of the femur, and maximum superior/inferior femoral head diameter) of 219 Taiwanese subadult individuals (aged 0 to 17) as used in the manuscript "Allometric scaling and growth: evaluation and applications in subadult body mass estimation."

This data set documents bat activity (counts per detector-night per phonic group) and bat diversity (number of bat species per detector-night) in relation to distance to the nearest forested corridor in a row crop agriculture dominated landscape and in relation to relative crop pest abundance. This data set was used to assess if bats were homogeneously distributed over a near-uninterrupted agricultural landscape and to assess the importance of forested corridors and the presence of pest species on their distribution across the landscape. Data was collected with 50 AudioMoth bat detectors along 10 transects, with each transect having 5 detectors. The transects started at a forest corridor and extended out for 4 km into uninterrupted row crop agriculture. Pest abundance was extrapolated from data collected in the same county during the same time as the study. Potentially important weather covariates were extracted from the nearest operational weather station.

This dataset contains the amino acid and nucleotide alignments corresponding to the phylogenetic analyses of South et al. 2020 in Systematic Entomology. This dataset also includes the gene trees that were used as input for coalescent analysis in ASTRAL.

The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

This dataset contains raw data of plasma glucose, insulin, c-peptide, GLP-1, and FGF21 collected as part of a study aimed to study alcohol pharmacokinetics in women who underwent metabolic surgery.

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.

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.

Data from census of peer-reviewed papers discussing nosZ and published from 2013 to 2019. These data were reported in the manuscript titled, "Beyond denitrification: the role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions" published in Global Change Biology as an Invited Report.

The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".

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.

Video footage of an Eastern Box Turtle (Terrapene carolina carolina) partially predating a Field Sparrow nest (Spizella pusilla) at 0845 h on the 31 of May 2020. Please note that the date on the video footage is incorrect due to user error, but the time is correct.

A mechanistic functional structural plant model. The .gsz file includes a parameterised maize and soybean to be used in GRoIMP software https://grogra.de/. The current model is parameterised to maize cultivar DKC63-21RIB and soybean cultivar AG36X6 for the 2019 growing season in Champaign, IL USA.

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.

Raw data of Auchenorrhyncha (Hemiptera) species presence and abundance from samples collected as part of Morgan Brown's M.S. thesis entitled "Investigating changes in Auchenorrhyncha (Hemiptera) communities in Illinois prairies over 25 years." Collection_Events_MBrown.pdf contains information that corresponds to each collection event code listed in the raw data files, including coordinates, date of collection, collection method, and name of collector. Each CSV file contains Auchenorrhyncha species presence and abundance data from each sampling area in Illinois: Route 45 Railroad Prairie, Richardson Wildlife Foundation, Mason County nature preserves, and Twelve Mile Prairie. Variables included in the CSV files include: Family: Taxonomic family to which each species belongs Subfamily: Taxonomic subfamily to which each species belongs Tribe: Taxonomic tribe to which each species belongs Species: Lowest taxonomic level to which individuals were identified The first row of column 5 to the end are collection event codes which correspond to each code listed in the PDF * New in V2: The CSV files originally uploaded in V1 contained outdated species names. V2 provides updated CSV files with the corrected names. * New in V3: There were some inconsistencies in the collection event codes listed in the PDF and CSV files uploaded in V1 and V2. V3 provides updated PDF and CSV files with the corrected codes. File update status: Collection_Events_MBrown_V2.pdf -> updated in this V3 (in V2 it remained the same as in V1 but now is updated in V3) MasonCounty_RawData_V3.csv -> updated in this V3 RichardsonWildlifeFoundation_RawData_V2.csv -> remains the same as in V2 Route45_RawData_V3.csv -> updated in this V3 TwelveMilePrairie_RawData_V3.csv -> updated in this V3

This is a general description of the datasets included in this upload; details of each dataset can be found in the individual README.txt in each compressed folder. We have: 1. ROSE-HF.tar.gz 2. ROSE-LF.tar.gz HF (high fragmentary): 50% of the sequences are made fragmentary, which have average lengths of 25% of the original lengths with a standard deviation of 60 bp. LF (low fragmentary): 25% of the sequences are made fragmentary, which have average lengths of 50% of the original lengths with a standard deviation of 60 bp. The seven ROSE datasets made fragmentary are: 1000L1, 1000L3, 1000L4, 1000M3, 1000S1, 1000S2 and 1000S4. "ROSE-HF.tar.gz" contains HF versions of the seven ROSE datasets. "ROSE-LF.tar.gz" contains LF versions of the seven ROSE datasets.

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.

Data are from a long-term fire manipulation experiment in the Missouri Ozarks, USA. Data include the raw, annual ring-width increment (rwl), basal area increment (BAI), population-level annual growth resistance (Drs) and resilience (Drl) to drought, intrinsic water use efficiency values (WUEi) and oxygen isotopic composition of individual radial growth rings (δ18O) from southern red oak (Quercus falcata) and post oak (Q. stellata) trees. ---------------------- TITLE: Data for "Sixty-five years of fire manipulation reveals climate and fire interact to determine growth rates of Quercus spp." ---------------------- FILE OVERVIEW: This dataset contains four (4) CSV files as described below: Refsland_et_al_ECS20-0465_BAI.csv: annual basal area increment between 1948-2015 for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_DroughtIndices.csv: population-level drought resistance and resilience of trees during each target drought period Refsland_et_al_ECS20-0465_WUEi.csv: carbon isotope indicators of drought stress for trees across the fire manipulation experiment Refsland_et_al_ECS20-0465_d18Or.csv: oxygen isotope indicators of drought stress for trees across the fire manipulation experiment ---------------------- VARIABLE EXPLANATION: All the variables in those four files are explained as below: treeID: unique character string that identifies subject tree block: integer (1, 2) that identifies the study block plot: integer (1-12) that identifies the plot nested within each study block trt: character string (Annual, Control, Periodic) that identifies the fire treatment of a given plot species: character string (Quercus falcata, Quercus stellata) that identifies species of subject tree year: integer (1948-2015) that identifies the dated year of each tree ring rwl_mm: numerical value representing the annual tree ring-width, in mm bai_cm2: numerical value representing the annual basal area increment, in cm2 timeperiod: integer value (1953, 1964, 2007, 2012) representing the periods encompassing target dry and wet years Drs_2yr: numerical value representing the drought resistance, defined as the population-level annual growth of trees during drought years relative to pre-drought years for a given time period Drl_2yr: numerical value representing the drought resilience, defined as the population-level annual growth of trees following drought years relative to pre-drought years for a given time period stand_ba_m2ha: numerical value representing the total basal area of a given plot, in m2 per ha stand_density_stems_ha: numerical value representing the total stem density of a given plot, in stems per ha pool: numerical value (1-40) identifying the set of tree ring samples pooled for analysis. Samples were pooled by block, plot, year and species period: integer value (1953, 1964, 1980, 2007, 2012) representing the periods encompassing target dry and wet years type: character string (Dry, Wet) indicating the water availability of a given year d13C: numerical value representing the carbon isotopic composition of radial growth rings within a given sample pool, in per mil WUEi: numerical value representing the annual intrinsic water use efficiency of radial growth rings within a given sample pool d18O: numerical value representing the oxygen isotopic composition of radial growth rings within a given sample pool, in per mil

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.

Data files and R code to replicate the econometric analysis in the journal article: B Chen, BM Gramig and SD Yun. “Conservation Tillage Mitigates Drought Induced Soybean Yield Losses in the US Corn Belt.” Q Open. https://doi.org/10.1093/qopen/qoab007

These data are the result of analyses of the metagenome of North American bats, including 18s and 16s barcode genes designed to target microorganisms of the gut. These files are Phyloseq import files created by the DADA2 program. Each barcode gene is uploaded separately as the four files required to build a phyloseq object. For each barcode gene, the files include amplicon sequence variant (ASV) sequences, sequence tables (seqtab) which connect individual samples to the ASVs, tax tables (taxtab) which identify the taxa present as determined by a Bayesian RDP classifier, and rooted phylogenetic trees for the ASVs. Additionally, we have included a "sample_data" file which is necessary for sorting of samples across all four sequence analysis data sets by study and species. Some sample information which could identify the location of endangered species has been restricted. Multiple studies are represented in the data which can be accessed using standard methods in the Phyloseq program (e.g. For a study of bats, parasites, and gut microbiome dysregulation by Bennett, Suski, and OKeefe 2024 [in prep March 2024], study specific data can be accessed using the Study variable "DYSBIOMICS." File names include reference to the primer set used to generate them (18s primer sets: G3, G4, G6; 16s primer set: 341F3_806R5).

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)

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.

Dataset includes maternal antigen treatment and early-life antigen treatment for male zebra finches. Also includes data on beak coloration, measures of song complexity for each male, and female responses to treated males. Male beak color and song metadata: * MATID= Maternal Identity * MATTRT=Maternal antigen treatment prior to egg laying (KLH=keyhole limpet hemocyanin, LPS= lipopolysaccharide, PBS=phosphate buffered saline) * YGTRT= Young antigen treatment post-hatch (KLH=keyhole limpet hemocyanin, LPS= lipopolysaccharide, PBS=phosphate buffered saline)) * NESTBANDNUM= Nestling band number * Haptoglobin=haptoglobin levels at day 28 (mg/ml) * Mean TE= Mean number of total elements in that male's song * TE (z)= Z-transformed total elements * Mean UE=Mean number of unique elements in the song * UE (z)= z-transformed unique elements * mean phrases= Mean number of song phrases * Phrases (z)= z-transformed song phrases * Mean D= Mean song duration in seconds * D (z)=z-transformed song duration * B2 standard=beak brightness standardized so that lower values reflect less bright beaks * B2 (z)=z-transformed brightness * S1R standard= beak saturation at high wavelengths standardized so that lower values reflect less red beaks * S1R (z)=z-transformed S1R * S1U standard= beak saturation at low wavelengths standardized so that lower values reflect less red beaks * S1U (z)=z-transformed S1U * H4B standard= beak hue standardized so that lower values reflect less red beaks * H4B (z)=z-transformed H4B Female choice metadata: * Control Bird=PBS denotes that all control males received phosphate buffered saline * Treatment Bird= Treatment the male received (keyhole limpet hemocyanin (KLH) or lipopolysaccharide (LPS)) * Beak Wipes Control=# of beak wipes the female performed when on the control male side * Beak Wipes Treatment=# of beak wipes the female performed when on the "treatment male" side * Hops Control=# of hops female performed when on the control male side * Hops Treatment=# of hops female performed when on the treatment male side * Time Spent Near Control=amount of time (sec) female spent on the control male side * Time Spent Near Treatment=amount of time (sec) the female spent on the treatment male side

Raw gas exchange data for photosynthetic induction in 6 rice accession flag leaves. Photosynthetic induction and point measurements were made at ambient [CO2]. Two accessions (AUS 278 and IR64) were selected to screen in greater detail in which photosynthetic induction was measured at six [CO2].