cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25675/10217/233940
title: Data associated with "Improved methods for single-molecule fluorescence in situ hybridization and immunofluorescence in Caenorhabditis elegans embryos"

description: This repository contains the data set associated with the Current Protocols publication "Improved methods for single-molecule fluorescence in situ hybridization and immunofluorescence in Caenorhabditis elegans embryos." This data includes the raw images associated with each figure, the complete data sets for both antifade and buffer quantification, and sample output data from both quantification pipelines. In addition, the associated README file describes each file in more detail, including which embryos from the raw data were analyzed and how files were generated.
description: Visualization of gene products in Caenorhabditis elegans has provided insights into the molecular and biological functions of many novel genes in their native contexts. Single-molecule Fluorescence In Situ Hybridization (smFISH) and Immunofluorescence (IF) visualize the abundance and localization of mRNAs and proteins, respectively, allowing researchers to elucidate the localization, dynamics, and functions of the corresponding genes. Whereas both smFISH and immunofluorescence have been foundational techniques in molecular biology, each protocol has challenges in the C. elegans embryo. smFISH protocols suffer from high initial costs and can photobleach rapidly. Immunofluorescence requires technically challenging permeabilization and slide preparation. Most importantly, published smFISH and IF protocols have predominantly been mutually exclusive, preventing the exploration of relationships between an mRNA and a relevant protein in the same sample. Here, we describe protocols to perform immunofluorescence and smFISH in C. elegans embryos either in sequence or simultaneously. We also present protocols to perform smFISH or immunofluorescence alone, including several improvements and optimizations to existing approaches. These protocols include 1) improved fixation and permeabilization steps to preserve cellular morphology while maintaining probe and antibody accessibility in the embryo, 2) a streamlined, in-tube approach for antibody staining that negates freeze-cracking, 3) a previously validated protocol to perform the cost-reducing smiFISH (single molecule inexpensive FISH) adaptation, 4) slide preparation using empirically determined optimal antifade products, and 5) straightforward quantification and data analysis methods. Figure 1 shows a schematic workflow for each protocol. Finally, we discuss tricks and tips to help the reader optimize and troubleshoot individual steps in each protocol. Together, these protocols and optimizations simplify existing protocols for single-molecule RNA and protein detection. Moreover, simultaneous, high-resolution imaging of proteins and RNAs of interest will permit analysis, quantification, and comparison of protein and RNA distributions, furthering our understanding of the relationship between RNAs and their protein products or cellular markers in early development.
DOI: 10.25675/10217/205802
title: Source code associated with "Shear-parallel tropical convective systems: importance of cold pools and wind shear"

description: This dataset contains source code for the RAMS model simulations and Matlab analysis documented and described in the associated publication, "Shear-Parallel Tropical Convective Systems: Importance of Cold Pools and Wind Shear."
description: The impact of cold pools on line-orientated convective systems is assessed using idealized simulations of tropical oceanic convection under weak, moderate, and strong wind shear regimes. Cold pools are weakened by suppressing evaporation in the shallow sub-cloud layer. Analysis of objectively-identified convective systems reveals that the convection with weaker cold pools is more often oriented parallel, rather than perpendicular, to the wind shear. The cold pool-induced orientation changes are most pronounced in the strong shear environment. Interactions between convective orientation and the tropical atmosphere are assessed. Simulations with shear-parallel convection demonstrate more top-of-atmosphere upwelling longwave radiation and less reflected shortwave radiation due to changes in convective anvils, faster-propagating larger-scale gravity waves, narrower cross-shear moisture distributions, and differences in convective momentum fluxes. The results highlight critical interactions across convective scales, mesoscales, and climate scales, as well as avenues for parameterizing structural modes of mesoscale-organized convection in global models.
DOI: 10.25675/10217/234029
title: Dataset associated with the manuscript: “Divergent belowground allocation patterns of winter wheat shape rhizosphere microbial communities and nitrogen cycling activities”

description: Purpose and scope: The purpose of this research was to investigate the role of wheat root exudation/rhizodeposition on the cycling and availability of added plant residue nitrogen. The purpose of this dataset is to provide the raw data collected from the experiment. This dataset includes biogeochemical values, mainly soil and plant carbon and nitrogen concentrations. Time period: This dataset deals with the data from one greenhouse experiment conducted in the spring of 2018. The experiment lasted ~ 50 days, and the data provided here was collected from destructive sampling of the experimental pots at the completion of the experiment. Areas of Investigation: Plant biomass, nitrogen cycling, enzyme activities, stable isotopes, biogeochemistry, exudation, soil organic matter priming, crop nutrition, root architecture, exudation, microbial biomass carbon, soil carbon, inorganic nitrogen, residue decomposition, nitrogen cycling, belowground plant carbon allocation.
description: Plant roots add carbon (C) -rich rhizodeposits to the soil, which can alter microbial activity and nitrogen (N) cycling with implications for N availability and uptake by plants. We evaluated root architecture, rhizodeposit C, and microbial community structure and function across a breeding gradient of twelve winter wheat genotypes and examined how these rhizosphere traits were related to the availability and uptake of N from fresh cover crop residues in the soil. We traced wheat-derived C into soil and microbial pools using continuous isotopic labelling (13C-CO2) and applied 15N labelled plant residues to quantify plant and microbial uptake of residue-derived N. Wheat genotypes differed in root C allocation patterns, influencing N cycling. Thicker roots released more C into soil, which enhanced N mineralization through stimulation of the microbial biomass. Microbial biomass increased N-cycling enzyme activity and residue N-uptake by wheat. Microbial communities did not differ between wheat genotypes but were strongly related to patterns in root C allocation, and several genera showed strong relationships with root C deposition and N uptake. The microbial community associated with extractable root-derived C was structurally different from the community associated with residue N uptake, indicating the N-cycling response to exudation was not necessarily carried out by the same microbial community members as those stimulated by rhizosphere C inputs. Our results indicate that differential patterns of rhizodeposition and associated belowground C allocation strategies in winter wheat can alter microbial communities and influence cycling and plant availability of residue N. Ecologically-based nutrient management in agricultural systems should consider the role of crop root traits and associated microbiomes to optimize soil nutrient dynamics.
DOI: 10.25675/10217/195227
title: Dataset associated with "The landscape of North American rangeland social science: a systematic map"

description: The dataset contains information of journal articles that meet the following criteria: 1) a geographic focus on North America, 2) a social science component, 3) focus on rangeland or ranching systems, and 4) a scientific article published in a peer-reviewed journal from 1970 to 2017 in English or Spanish. The data are analyzed and published in a systematic map to characterize this literature by 1) the research objectives and questions, 2) who was studied, 3) where research was conducted, 4) which theories, methodologies, and methods were applied, and 5) how these research characteristics have changed from 1970 to 2017.
description: Rangeland scientists have made substantial progress in understanding ecological dynamics of rangelands, but the social factors have received less attention in North America. A body of North American rangeland social science has developed over the past four decades, with the number of studies increasing each decade. However, these works have not been systematically reviewed to assess the state of rangeland social science in North America and to identify research gaps. We developed a systematic map to characterize this literature by 1) the research objectives and questions, 2) who was studied, 3) where research was conducted, 4) which theories, methodologies, and methods were applied, and 5) how these research characteristics have changed from 1970 to 2017. We found that most (81%) North American rangeland social science has studied ranchers, farmers, and/or landowners, with limited consideration of other stakeholders (e.g., ranch workers, youth). Although age (43% of the studies) and education (40%) are often considered, other demographic attributes and identities, such as gender (28%) and race or ethnicity (18%), are less frequently included. The most commonly used research method is surveys (52%) and much of rangeland social science does not make explicit connections to either specific methodological or theoretical frameworks. The limited application of theories, methodologies, and a diversity of methods has potentially constrained who and what has been studied in North America. The lack of consideration of gender and race in rangeland social science is echoed in the limited number of studies that have accounted for the effects of social identities and power relationships on people's connection to and management of rangelands. This review highlights the need for more North American research that 1) is informed by social theory, 2) applies a diversity of methods, 3) considers a broader diversity of stakeholders, and 4) draws from multiple social science disciplinary traditions.
DOI: 10.25675/10217/176162
title: Plant level browse intensity on observation plots in Yellowstone's Northern Range, 2009-2013

description: Zip file includes: data and metadata file.
description: Data file and metadata sheet for column fields.
DOI: 10.25675/10217/232461
title: Data associated with “Adapting the COSP Radar Simulator to Compare GCM Output and GPM Precipitation Radar Observations”

description: This dataset includes the global 2° and 1° CAM5 output variables for June 2017 that were used as input into our version of the COSP simulator package as described in the publication. A README file is included to describe the unix scripts used to prepare the data files for input into COSP.
description: Comparisons of precipitation between general circulation models (GCMs) and observations are often confounded by a mismatch between model output and instrument measurements, including variable type and temporal and spatial resolution. To mitigate these differences, the radar-simulator Quickbeam within the Cloud Feedback Model Intercomparison Project (CFMIP) Observation Simulator Package (COSP) simulates reflectivity from model variables at the sub-grid scale. This work adapts Quickbeam to the dual-frequency Precipitation Radar (DPR) onboard the Global Precipitation Measurement (GPM) satellite. The longer wavelength of the DPR is used to evaluate moderate-to-heavy precipitation in GCMs, which is missed when Quickbeam is used as a cloud radar simulator. Latitudinal and land/ocean comparisons are made between COSP output from the Community Atmospheric Model version 5 (CAM5) and DPR data. Additionally, this work improves the COSP sub-grid algorithm by applying a more realistic, non-deterministic approach to assigning GCM grid box convective cloud cover when convective cloud is not provided as a model output. Instead of assuming a static 5% convective cloud coverage, DPR convective precipitation coverage is used as a proxy for convective cloud coverage. For example, DPR observations show that convective rain typically only covers about 1% of a 2°grid box, but that the median convective rain area increases to over 10% in heavy rain cases. In our CAM5 tests, the updated sub-grid algorithm improved the comparison between reflectivity distributions when the convective cloud cover is provided versus the default 5% convective cloud cover assumption.
DOI: 10.25675/10217/232637
title: Dataset associated with “Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America”

description: VCF file from UNEAK on RAD-Seq data containing 4,659 SNPs that can be used to reproduce all analyses, with a bit of formatting for STRUCTURE, smartpca, PLINK, and BA3.
description: The global invasion, and subsequent spread and evolution of weeds provides unique opportunities to address fundamental questions in evolutionary and invasion ecology. Amaranthus palmeri is a widespread glyphosate-resistant (GR) weed in the USA. Since 2015, GR populations of A. palmeri have been confirmed in South America, raising questions about introduction pathways and the importance of pre- versus post-invasion evolution of GR traits. We used RAD-Seq genotyping to characterize genetic structure of populations from Brazil, Argentina, Uruguay and the USA. We also quantified gene copy number of the glyphosate target, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS) and the presence of an extra-chromosomal circular DNA (eccDNA) replicon known to confer GR in USA populations. Populations in Brazil, Argentina, and Uruguay were only weakly differentiated (pairwise FST  0.043) in comparison to USA populations (mean pairwise FST = 0.161, range = 0.068-0.258), suggesting a single major invasion event. However, elevated EPSPS copy number and the EPSPS replicon were identified in all populations from Brazil and Uruguay, but only in a single Argentinean population. These observations are consistent with independent in situ evolution of glyphosate resistance in Argentina, followed by some limited recent migration of the eccDNA based mechanism from Brazil to Argentina. Taken together, our results are consistent with an initial introduction of A. palmeri into South America sometime before the 1980s, and local evolution of GR in Argentina, followed by a secondary invasion of GR A. palmeri with the unique eccDNA based mechanism from the USA into Brazil and Uruguay during the 2010’s.
DOI: 10.25675/10217/194364
title: Successful process evaluation provides insight into team development and goal attainment: science of team science

description: Data set includes three components: 1. Social network data; 2. Turn-taking Data; 3. Outcome Metrics. See Readme Files for more details.
description: The Science of Team Science (SciTS) emerged as a field of study because scientists are increasingly charged with solving complex and large-scale societal, health, and environmental challenges. The SciTS field seeks to develop both methods for assessing teams and a knowledge base of effective practices in team science. What makes interdisciplinary scientific teams successful? Many early studies of team science success drew on existing data like bibliometrics and patent applications to examine the patterns of successful teams. However, these metrics have several shortcomings: they can only be used to characterize teams that were successful enough to produce publications, patents or grant proposals; and their creation lags years behind team formation. Studies which rely exclusively on existing data are not able explain the differences between successful and unsuccessful teams in their formation, interaction, and development. This study asks the questions: "How are team processes and interactions related to goal accomplishment in transdisciplinary teams? Can process metrics be used to predict team success and team outcomes?" This study aims to fill the gap in SciTS literature by longitudinally observing eight scientific transdisciplinary teams and correlating process metrics to outcome metrics. From 2015 through 2017, we used participant observation, informal interviews, turn-taking assessments, and social network surveys to follow teams through their first two years of formation. We then examined which metrics of team interaction and team processes are correlated with traditional team-defined outcome metrics such as conference presentations, grant proposals, journal articles, and invention disclosures. We found that the strength of relationships, role of women, and even participation were the biggest predictors of team success. We discuss how process evaluation can be used to assess team success in the early stages of team development and which measures are more strongly associated with team success.
DOI: 10.6084/m9.figshare.23608593
title: oats yield estimator code

description: Oats yield machine learning model, <br> <br> <br>
DOI: 10.25675/10217/184640
title: Precipitationshed data for the moisture recycling analysis within the article "Megacity precipitationsheds reveal tele-connected water security challenges"

description: These data are the output of a global moisture tracking model. There are output files for 29 megacities from the original analysis. Each file contains a globally gridded dataset of evaporation that eventually falls as precipitation in each of the megacity regions, i.e. precipitationshed data. The data is in a Matlab matrix, with dimensions of [years, months, latitude, longitude]. For additional details on how the data were produces, please query the original publication.
description: Urbanization is a global process that has taken billions of people from the rural countryside to concentrated urban centers, adding pressure to existing water resources. Many cities are specifically reliant on renewable freshwater regularly refilled by precipitation, rather than fossil groundwater or desalination. A precipitationshed can be considered the "watershed of the sky" and identifies the origin of precipitation falling in a given region. In this paper, we use this concept to determine the sources of precipitation that supply renewable water in the watersheds of the largest cities of the world. We quantify the sources of precipitation for 29 megacities and analyze their differences between dry and wet years. Our results reveal that 19 of 29 megacities depend for more than a third of their water supply on evaporation from land. We also show that for many of the megacities, the terrestrial dependence is higher in dry years. This high dependence on terrestrial evaporation for their precipitation exposes these cities to potential land-use change that could reduce the evaporation that generates precipitation. Combining indicators of water stress, moisture recycling exposure, economic capacity, vegetation-regulated evaporation, vegetation-regulated runoff, land-use change, and dry-season moisture recycling sensitivity reveals five highly vulnerable megacities (Karachi, Bengalaru, Delhi, Istanbul, and Wuhan). A further nine megacities were found to have medium vulnerability with regard to their water supply. We conclude that understanding how upwind landscapes affect downwind municipal water resources could be a key component for understanding the complexity of urban water security.
DOI: 10.25675/10217/198159
title: Data for "The convection connection: how ocean feedbacks affect tropical mean moisture and MJO propagation."

description: This archive contains daily mean variables from eight model simulations used to produce figures in "The Convection Connection: How ocean feedbacks affect tropical mean moisture and MJO propagation." Journal of Geophysical Research: Atmospheres, 2019. Authors: Charlotte A. DeMott, Nicholas P. Klingaman, Wan-Ling Tseng, Melissa Burt, Yingxia Gao, and David A. Randall.
DOI: 10.25675/10217/234137
title: Dataset associated with the manuscript: “Long-term compost amendment modulates wheat genotype differences in belowground carbon allocation, rhizosphere recruitment and nitrogen acquisition”

description: Format of data files – .csv; Location where data were collected – Fort Collins, CO; Time period during which data were collected - 2021; File Information – Total number of files: 3 Kelly_2021_Wheat_Genotype_Wheat.Genotype.Soil.Treatment _Datafile.csv – processed primary biogeochemical and plant data used for data analysis of referenced manuscript. README_Kelly_2021_Wheat.Genotype.Soil.Treatment.pdf – Description of data and associated publication Codebook.csv – description of variable names in Datafile.
description: The implementation of soil health-promoting practices, such as cover crops and compost additions, has important implications for nutrient cycling regimes in agroecosystems. At the same time, plant belowground carbon (C) allocation patterns can influence nutrient cycling and availability in soil, but the effects may depend on the crop genotype and management practices in place. The relationship between root exudation, rhizosphere communities and the processes they regulate is likely influenced by a range of soil conditions, including soil organic matter (SOM) content, nutrient status, and overall soil biological activity, but such interactions remain poorly understood. To better understand the potential role of long-term soil management (that alters of SOM) and crop genotype in regulating rhizosphere microbial communities and associated nitrogen (N) cycling processes, we collected soils from two treatments in a 10-year field trial, one with high compost inputs (108.7 Mg ha-1 every 2 years) and a control (no nutrient inputs). We then used stable isotopes to measure belowground C allocation patterns in two genotypes of winter wheat (Triticum aestivum) with distinct rooting and exudation strategies. We also measured microbial community structure and function in the rhizosphere and quantified uptake of residue-derived N from 15N-labeled residues. We found an interactive effect between soil management and genotype, where the high-exudation genotype modified its exudation more in response to soil management and was relatively better at accessing residue N in the compost-amended soils than the low-exudation genotype. The high-exudation genotype also demonstrated selection of specific rhizosphere microbial taxa, with several taxa conserved across soil treatments. Our results suggest that the high-exudation strategy influences the microbial community, and this strategy is more successful in soils with higher SOM. Understanding the relationship between crop genotype, soil management, and microbial function can help inform crop production and breeding strategies in systems seeking to leverage improved soil health and biological nutrient cycling.