Dataset Search Results

Global assessments of climate extremes typically do not account for the unique characteristics of individual crops. A consistent definition of the exposure of specific crops to extreme weather would enable agriculturally-relevant hazard quantification. We introduce the Agriculturally-Relevant Exposure to Shocks (ARES) model, a novel database of both the temperature and moisture extremes facing individual crops by explicitly accounting for crop characteristics. Specifically, we estimate crop-specific temperature and moisture shocks during the growing season for a 0.25-degree spatial grid and daily time scale from 1961-2014 globally for 17 crops. The resulting database presented here provides annual crop- and event-specific exposure rates. Both gridded and country-level exposure rates are provided for each of the 17 crops. Our results provide new insights into the changes in the magnitude as well as spatial and temporal distribution of extreme events that impact crops over the past half-century. For additional information, please see the related paper by Jackson et al. (2021) in Environmental Research Letters.

Provides RNASim-VS2 datasets used in Gillian's Master's thesis.

A set of species entity mentions derived from an NERC dataset analyzing 900 synthetic biology articles published by the ACS. This data is associated with the Synthetic Biology Knowledge System repository (https://web.synbioks.org/). The data in this dataset are raw mentions from the NERC data.

Related to the raw entity mentions, this dataset represents the effects of the data cleaning process and collates all of the entity mentions which were too ambiguous to successfully link to the NCBI's taxonomy identifier system.

This dataset represents the results of manual cleaning and annotation of the entity mentions contained in the raw dataset (https://doi.org/10.13012/B2IDB-4950847_V1). Each mention has been consolidated and linked to an identifier for a matching concept from the NCBI's taxonomy database.

Conjugate photoelectron energy spectra derived from coincident FUV and radio measurements. These are outputs of simulations from the semi-empirical SAMI2-PE (Varney et al. 2012) for the night of January 4, 2020.

*Updates for this V3: added a few more records and rearranged the sequence of the tables in order to support our new paper "Evaluation of Indirect and Direct Scoring Methods to Relate Biochemical Soil Quality Indicators to Ecosystem Services" accepted by the Soil Science Society of America Journal. We summarize peer reviewed literature reporting associations between for three soil quality indicators (SQIs) (β-glucosidase (BG), fluorescein diacetate (FDA) hydrolysis, and permanganate oxidizable carbon (POXC)) and crop yield and greenhouse gas emissions. Peer-reviewed articles published between January of 1990 and May 2018 were searched using the Thomas Reuters Web of Science database (Thomas Reuters, Philadelphia, Pennsylvania) and Google Scholar to identify studies reporting results for: “β-glucosidase”, “permanganate oxidizable carbon”, “active carbon”, “readily oxidizable carbon”, or “fluorescein diacetate hydrolysis”, together with one or more of the following: “crop yield”, “productivity”, “greenhouse gas’, “CO2”, “CH4”, or “N2O”. Meta-data for records include the following descriptor variables and covariates useful for scoring function development: 1) identifying factors for the study site (location, duration of the experiment), 2) soil textural class, pH, and SOC, 3) depth of soil sampling, 4) units used in published works (i.e.: equivalent mass, concentration), 5) SQI abundances and measured ecosystem functions, and 6) summary statistics for correlation between SQIs and functions (yield and greenhouse gas emissions). *Note: Blank values in tables are considered unreported data.

This dataset is provided to support the statements in Kim, H., and R.Y. Makhnenko. 2022. "Evaluation of CO2 sealing potential of heterogeneous Eau Claire shale". Journal of the Geological Society. In geologic carbon dioxide (CO2) storage in deep saline aquifers, buoyant CO2 tends to float upwards in the reservoirs overlaid by low permeable formations called caprocks. Caprocks should serve as barriers to potential CO2 leakage that can happen through a diffusion loss and permeation through faults, fractures, or pore spaces. The leakage through intact caprock would mainly depend on its permeability and CO2 breakthrough pressure, and is affected by the heterogeneities in the material. Here, we study the sealing potential of a caprock from Illinois Basin - Eau Claire shale, with sandy and shaly fractions distinguished via electron microscopy and grain/pore size and surface area characterization. The direct measurements of permeability of sandy shale provides the values ~ 10-15 m2, while clayey specimens are three orders of magnitude less permeable. The CO2 breakthrough pressure under in-situ stress conditions is 0.1 MPa for the sandy shale and 0.4 MPa for the clayey counterpart – these values are higher than those predicted by the porosimetry methods performed on the unconfined specimens. Sandy Eau Claire shale would allow penetration of large CO2 volumes at low overpressures, while the clayey formation can serve as a caprock in the absence of faults and fractures in it.

Dataset for "Spatial drivers of wetland bird occupancy within an urbanized matrix in the Upper Midwestern United States" manuscript contains occupancy data for ten wetland bird species used in single-species occupancy models at four spatial scales and four wetland habitat types. Data were collected from 2017-2019 in NE Illinois and NW Indiana. Dataset includes wetland bird occupancy data, habitat parameter values for each survey location, and R code used to run analyses.

Simulated sequences provide a way to evaluate multiple sequence alignment (MSA) methods where the ground truth is exactly known. However, the realism of such simulated conditions often comes under question compared to empirical datasets. In particular, simulated data often does not display heterogeneity in the sequence lengths, a common feature in biological datasets. In order to imitate sequence length heterogeneity, we here present a set of data that are evolved under a mixture model of indel lengths, where indels have an occasional chance of being promoted to long indels (emulating large insertion/deletion events, e.g., domain-level gain/loss). This dataset is otherwise (e.g., in GTR parameters) analogous to the 1000M condition as presented in the SATe paper (doi: 10.1126/science.1171243) but with 5000 sequences and simulated with INDELible (http://abacus.gene.ucl.ac.uk/software/indelible/). For more information, see README.txt. For the INDELible control files, see https://github.com/ThisBioLife/5000M-234-het.

This is a dataset from a choice experiment survey on family forest landowner preferences for managing invasive species.

This dataset contains all the necessary information to recreate the study presented in the paper entitled "Learning coagulation processes with combinatorially-invariant neural networks". This consists of (1) the aggregated output files used for machine learning, (2) the machine learning codes used to learn the presented models, (3) the PartMC model source code that was used to generate the simulation data and (4) the Python scripts used construct the scenario library for training and testing simulations. This data was used to investigate a method (combinatorally-invariant neural network) for learning the aerosol process of coagulation. This data may be useful for application of other methods.

This dataset was created based on the publicly available microdata from PNS-2019, a national health survey conducted by the Instituto Brasileiro de Geografia e Estatistica (IBGE, Brazilian Institute of Geography and Statistics). IBGE is a federal agency responsible for the official collection of statistical information in Brazil – essentially, the Brazilian census bureau. Data on selected variables focusing on biopsychosocial domains related to pain prevalence, limitations and treatment are available. The Fundação Instituto Oswaldo Cruz has detailed information about the PNS, including questionnaires, survey design, and datasets (www.pns.fiocruz.br). The microdata can be found on the IBGE website (https://www.ibge.gov.br/estatisticas/downloads-estatisticas.html?caminho=PNS/2019/Microdados/Dados).

The data files are for the paper entitled: Long-lifetime spin excitations near domain walls in 1T-TaS2 to be published in PNAS. The data was obtained on a 300 mK custom designed Unisoku scanning tunneling microscope using the Nanonis module. All the data files have been named based on the Figure numbers that they represent.

An Atlas.ti dataset and accompanying documentation of a thematic analysis of problems and opportunities associated with retracted research and its continued citation.

This dataset contains daily and hourly temperature measurements in twenty different bat box designs deployed in central Indiana, USA from May to September 2018. Daily and hourly environmental data (temperature, solar radiation, wind speed and direction) are also included for days and hours sampled. Bat box temperature data were reclassified to cool (</= 30°C), permissive (30.1–39.9°C), and stressful (>/= 40°C) categories according to known temperature tolerances of temperate-zone bats.

This dataset includes mass spectrometry, library screening, and gas chromatography data used for creating a high-throughput screening in metabolic engineering.

The dataset consists of two types of data: the estimate of land productivity (the maximum productivity, MP) and the estimate of land that has low productivity for any major crops planted in the Contiguous United States and then may be available for growing bioenergy crops (the marginal land, ML). All data items are in GeoTiff format, under the World Geodetic System (WGS) 84 project, and with a resolution of 0.0020810045 degree (~250 m). The MP values are calculated based on machine learning model estimated yields of major crops in the CONUS, and its expected value (MP_mean.tif), and associated uncertainty (MP_IDP.tif). The ML availability data have two versions: a deterministic version and a version with uncertainty. The deterministic MLs are determined as the land pixels with expected MP values falling in the range defined in the following criteria, and the MLs with uncertainty are determined as the probability that the MP value of a land pixel falls in the range defined in the following criteria: Criteria_____Description S1________ Current crop and pasture land with MP <= P50 S2________ Current crop and pasture land with MP <= P25 S3________ S1 + current grass and shrub land with P25 < MP < P50 S4________ S2 + current grass and shrub land with P10 < MP < P25 Economic__ Current crop and pasture land with potential profitability < 0 Here P10, P25 and P50 are the 10th, 25th and 50th percentile of crop MP values

This data set contains survey results from a 2021 survey of University of Illinois University Library patrons who identify as transgender or gender non-conforming conducted as part of the Becoming a Trans Inclusive Library Project to assess the experiences of transgender patrons seeking information and services in the University Library. Survey instruments are available in the IDEALS repository: http://hdl.handle.net/2142/110081.

This repository includes datasets for the paper "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling" accepted for RECOMB2021 and submitted to Journal of Computational Biology. Each zipped file contains a README.

This dataset contains all the data for the results section in the study presented in the paper entitled "Chemistry Across Multiple Phases (CAMP) version 1.0: An integrated multi-phase chemistry mode" submitted to Geoscientific Model Development (GMD). In this paper, two sets of simulations were run to test CAMP with this results included here. This consists of (1) box model inputs and outputs presented in Section 4.2 for modal, binned and particle-resolved simulations to compare the application of identical chemical mechanisms to different aerosol representations and (2) the 3D Eulerian output presented in Section 4.3.

This dataset contains nucleotide sequences of 16S rRNA gene from phytoplasmas and other bacteria detected in phloem-feeding insects (Hemiptera, Auchenorrhyncha). The datasets were used to compare traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas in insect DNA samples. The file “Trivellone_etal_SangerSequencing.fas”, comprising 1397 positions (the longest sequence), includes 35 not aligned bacterial 16S rRNA sequences (16 phytoplasmas and 19 other bacterial strains) yielded using Sanger sequencing. The file “Trivellone_etal_AHEmethod1.fas” includes 34 not aligned bacterial 16S rRNA sequences (28 phytoplasmas and 6 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled using assembled based on ABySS v2.1.0 pipeline. The file “Trivellone_etal_AHEmethod2.fas” includes 31 not aligned bacterial 16S rRNA sequences (27 phytoplasmas and 4 other bacterial strains) and it contains 1530 positions (the longest sequence). Each sequence was assembled based on the HybPiper v2.0.1 pipeline . Additional details in the "read_me_trivellone.txt" file attached below.

These data represent the raw data from the paper “Evaluating the ability of wetland mitigation banks to replace plant species lost from destroyed wetlands” published in Journal of Applied Ecology in 2023 by Stephen C. Tillman and Jeffrey W. Matthews.

Agriculture has substantial socioeconomic and environmental impacts that vary between crops. However, information on how the spatial distribution of specific crops has changed over time across the globe is relatively sparse. We introduce the Probabilistic Cropland Allocation Model (PCAM), a novel algorithm to estimate where specific crops have likely been grown over time. Specifically, PCAM downscales annual and national-scale data on the crop-specific area harvested of 17 major crops to a global 0.5-degree grid from 1961-2014. The resulting database presented here provides annual global gridded likelihood estimates of crop-specific areas. Both mean and standard deviations of grid cell fractions are available for each of the 17 crops. Each netCDF file contains an individual year of data with an additional variable ("crs") that defines the coordinate reference system used. Our results provide new insights into the likely changes in the spatial distribution of major crops over the past half-century. For additional information, please see the related paper by Jackson et al. (2019) in Environmental Research Letters (https://doi.org/10.1088/1748-9326/ab3b93).