Response of Soil Quality Indictors including β-glucosidase, Fluorescein Diacetate Hydrolysis and Permanganate Oxidizable CarbonYushu Xia & Michelle Wander
Dataset compiled by Yushu Xia and Michelle Wander for the Soil Health Institute. Data were recovered from peer reviewed literature reporting results for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) in terms of their relative response to management where soils under grassland cover, no-tillage, cover crops, residue return and organic amendments were compared to conventionally managed controls. Peer-reviewed articles published between January of 1990 and May...
MapAffil 2018 dataset -- PubMed author affiliations mapped to cities and their geocodes worldwide with extracted disciplines, inferred GRIDs, and assigned ORCIDsVetle Torvik
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...
Data for: An Examination of Data Reuse Practices within Highly Cited Articles of Faculty at a Research UniversityHeidi J Imker, Hoa Luong, William H Mischo, Mary C Schlembach & Chris Wiley
This dataset was developed as part of a study that assessed data reuse. Through bibliometric analysis, corresponding authors of highly cited papers published in 2015 at the University of Illinois at Urbana-Champaign in nine STEM disciplines were identified and then surveyed to determine if data were generated for their article and their knowledge of reuse by other researchers. Second, the corresponding authors who cited those 2015 articles were identified and surveyed to ascertain whether they...
Datasets for \"Phylogenomics of flavobacterial insect nutritional endosymbionts with implications for the phylogeny of their hosts\"Yanghui Cao & Christopher H. Dietrich
The file “Fla.fasta”, comprising 10526 positions, is the concatenated amino acid alignments of 51 orthologues of 182 bacterial strains. It was used for the maximum likelihood and maximum parsimony analyses of Flavobacteriales. Bacterial species names and strains were used as the sequence names, host names of insect endosymbionts were shown in brackets. The file “16S.fasta” is the alignment of 233 bacterial 16S rRNA sequences. It contains 1455 positions and was used for the maximum likelihood...
A Bayesian optimal escape model reveals bird species differ in their capacity to habituate to humansNicholas Sutton, Michael Weston, Patrick Guay, Jenna Tregoweth & James O'Dwyer
The capacity to habituate to, or tolerate, the close proximity of humans varies among wildlife species and may mediate population and species viability. Some species readily habituate to human proximity while others remain sensitive. These differences are important for predicting human impact on wildlife, but can be difficult to quantify given wildlife responses are highly idiosyncratic and are often context-dependent. A general method for assimilating multiple sources of information and variation in individual responses is...
Dataset for \"The necessity of lateral channel migration in the evolution of non-dendritic drainage networks to full dendricity and the persistence of dynamic networks\"Jeffrey S. Kwang, Abigail L. Langston & Gary Parker
*This is the third version of the dataset*. New changes in this 3rd version: 1.replaces simulations where the initial condition consists of a sinusoidal channel with topographic perturbations with simulations where the initial condition consists of a sinusoidal channel without topographic perturbations. These simulations better illustrate the transformation of a nondendritic network into a dendritic one. 2. contains two additional simulations showing how total domain size affects the landscape's dynamism. 3. changes dataset title to...
Simulated Land Allocation, Nitrogen Use, and Nitrogen Loss in the Mississippi Atchafalaya River Basin for Various RFS2 (Renewable Fuel Standard) Policy ScenariosKelsie Ferin, Luoye Chen, Jia Zhong, Emily Heaton, Madhu Khanna & Andy VanLoocke
Total nitrogen leaching rates were calculated over the Mississippi Atchafalaya River Basin (MARB) using an integrated economic-biophysical modeling approach. Land allocation for corn production and total nitrogen application rates were calculated for crop reporting districts using the Biofuel and Environmental Policy Analysis Model (BEPAM) for 5 RFS2 policy scenarios. These were used as input in the Integrated BIosphere Simulator-Agricultural Version (Agro-IBIS) and the Terrestrial Hydrologic Model with Biogeochemistry (THMB) to calculate the nitrogen loss. Land...
The file contains biomass and count data of food items encountered in the digestive tract of collected green-winged teal from the Illinois River Valley during spring 2016-2018. The file also contains biomass of food items collected from core samples collected at sites where the green-winged teal were collected. Together, the consumed and availability food data are used to calculate diet selection. The data also contains information on the teal, collection, sites, and other covariates used...
This dataset contains RNASim1000, Cox1-Het datasets as well as analyses of RNASim1000, Cox1-Het, and 1000M1(HF).
Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessionsJohn Ferguson, Samuel Fernandes, Brandon Monier, Nathan Miller, Dylan Allen, Anna Dmitrieva, Peter Schmuker, Roberto Lozano, Ravi Valluru, Edward Buckler, Michael Gore, Patrick Brown, Edgar Spalding & Andrew Leakey
This dataset contains the images of a photoperiod sensitive sorghum accession population used for a GWAS/TWAS study of leaf traits related to water use efficiency in 2016 and 2017. Raw images were produced by Optical topometry (nms files).
Photosynethic Performance Measurements in Biomass Sorghum Varietals in Central Illinois during Four Growing Seasons.Nikhil S. Jaikumar, Samuel B. Fernandes, Andrew D.B. Leakey, Patrick J. Brown, Samantha S. Stutz, Carl Bernacchi & Stephen P. Long
In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves...
The evolution of flapping flight is linked to the prolific success of insects. Across Insecta, wing morphology diversified, strongly impacting aerodynamic performance. In the presence of ecological opportunity, discrete adaptive shifts and early bursts are two processes hypothesized to give rise to exceptional morphological diversification. Here, we use the diverse sister-families Sphingidae and Saturniidae to answer how the evolution of aerodynamically important traits is linked to clade divergence and through what process(es) these traits evolve....
A tale of two conifers: Migration across a dispersal barrier outpaced regional expansion from refugiaMatias Fernandez, Feng Sheng Hu, Daniel Gavin, Guillaume De Lafontaine & Katy Heath
Aim: Understanding how climate refugia and migration over great distances have facilitated species survival during past climate changes is crucial for evaluating contemporary threats to biodiversity, particularly in the face of dispersal barriers. We address this longstanding question on the refugial origins and post-glacial development of mesic forests. Location: Pacific Northwest, North America. Taxon: Mountain hemlock (Tsuga mertensiana) and western redcedar (Thuja plicata) Methods: Range-wide genotyping-by-sequencing (ddRADseq) of both study species and a pollen reconstruction...
The mechanisms that govern thalamocortical transmission are poorly understood. Recent data have shown that sensory stimuli elicit activity in ensembles of cortical neurons that recapitulate stereotyped spontaneous activity patterns. Here, we elucidate a possible mechanism by which gating of patterned population cortical activity occurs. In this study, sensory-evoked all-or-none cortical population responses were observed in the mouse auditory cortex in vivo and similar stochastic cortical responses were observed in a colliculo-thalamocortical brain slice preparation. Cortical...
Dataset for Fifty Ways to Tag your Pubtypes: Multi-Tagger, a Set of Probabilistic Publication Type and Study Design Taggers to Support Biomedical Indexing and Evidence-Based MedicineYuanxi Fu & Jodi Schneider
This dataset contains data from extreme-disagreement analysis described in paper “Aaron M. Cohen, Jodi Schneider, Yuanxi Fu, Marian S. McDonagh, Prerna Das, Arthur W. Holt, Neil R. Smalheiser, 2021, Fifty Ways to Tag your Pubtypes: Multi-Tagger, a Set of Probabilistic Publication Type and Study Design Taggers to Support Biomedical Indexing and Evidence-Based Medicine.” In this analysis, our team experts carried out an independent formal review and consensus process for extreme disagreements between MEDLINE indexing and...
Mesospheric gravity wave activity estimated via airglow imagery, multistatic meteor radar, and SABER data taken during the SIMONe–2018 campaignFabio Vargas
Airglow images and Meteor radar data used in the paper "Mesospheric gravity wave activity estimated via airglow imagery, multistatic meteor radar, and SABER data taken during the SIMONe–2018 campaign".
Dataset for \"Continued use of retracted papers: Temporal trends in citations and (lack of) awareness of retractions shown in citation contexts in biomedicine\"Tzu-Kun Hsiao & Jodi Schneider
This dataset includes five files. Descriptions of the files are given as follows: FILENAME: PubMed_retracted_publication_full_v3.tsv - Bibliographic data of retracted papers indexed in PubMed (retrieved on August 20, 2020, searched with the query "retracted publication" [PT] ). - Except for the information in the "cited_by" column, all the data is from PubMed. - PMIDs in the "cited_by" column that meet either of the two conditions below have been excluded from analyses:  PMIDs of the...
Drainage network analysis is fundamental to understanding the characteristics of surface hydrology. Based on elevation data, drainage network analysis is often used to extract key hydrological features like drainage networks and streamlines. Limited by raster-based data models, conventional drainage network algorithms typically allow water to flow in 4 or 8 directions (surrounding grids) from a raster grid. To resolve this limitation, this paper describes a new vector-based method for drainage network analysis that allows water...
Data from: The complex genetics of symbiotic extended phenotypes across environments in a model mutualismRebecca Batstone, Hanna Lindgren, Cassandra Allsup, Laura Goralka, Alex Riley, Michael Grillo, Amy Marshall-Colon & Katy Heath
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host’s own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable...
This is the 5 states 5000 cells synthetic expression file we used for validation of SimiC, a single cell gene regulatory network inference method with similarity constraints. Ground truth GRNs are stored in Numpy array format, and expression profiles of all states combined are stored in Pandas DataFrame in format of Pickle files.
Why the Stall? Using Metabolomics to Define the Lack of Upstream Movement of Invasive Bigheaded Carp in the Illinois RiverCory Suski & Jocelyn Curtis-Quick
Bigheaded Carp have spread throughout the Mississippi River basin since the 1970s. Little has stopped the spread as carp have the ability to pass through locks and dams, and they are currently approaching the Great Lakes. However, the location of the leading edge in the Illinois River has stalled for over a decade, even though there is no barrier preventing further advancement towards the Great Lakes. Defining why carp are not moving towards the Great...
These datasets provide the basis of our analysis in the paper - The Potential Impact of a Clean Energy Society On Air Quality. All datasets here are from the model output (CAM4-chem). All the simulations were run to steady-state and only the outputs used in the analysis are archived here.
Model output from the Weather Research and Forecasting model with water vapor tracers over Amazon and La Plata river basinsFrancina Dominguez & Zhao Yang
Model output dataset (6-hourly) from the Weather Research and Forecasting (WRF) model simulations over South America with the added capability of water vapor tracers to track the moisture that originates over the Amazon and the La Plata river basins. The simulations were performed for the period 2003-2013 at 20-km horizontal resolution fully coupled with the Noah-MP land surface model. Limited number of original output variables sufficient for reproducing the analyses in papers that cite this...
University of Illinois97
University of Illinois at Urbana Champaign17
University of Illinois at Urbana-Champaign8
University of Illinois Urbana-Champaign3
University of Montana2
University of Minnesota2
University of Wisconsin–Madison2
University of Leeds2
Purdue University West Lafayette2
University of Debrecen2