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At least 361 records · Page 20

Data for “Tree root nutrient uptake kinetics vary with nutrient availability, environmental conditions, and root traits: A global analysis”

This data package contains data and code used in the paper “Tree root nutrient uptake kinetics vary with nutrient availability, environmental conditions, and root traits: A global analysis”. The central product is a global dataset of root inorganic nutrient uptake rates and kinetics parameters covering temperate, boreal, and sub/tropical tree species, representing a collection of nutrient uptake data from published studies. This dataset enables tree investigation of root nutrient uptake rates across species, space, and experimental conditions. The data can also be combined with supplementary data on root and soil traits or with external datasets (e.g. R scripts contained within use data from FRED 3.0; (Iversen et al., 2021)). Contained within is the main nutrient data “uptake_data.csv” as well as 4 additional .csv files that link uptake data to supplementary measurements, source references, taxonomic information, and additional nutrient uptake measurements across nutrient gradients, and 1 .csv file that records meta-analysis results for plotting with the R scripts. There are seven R scripts that support data analysis and creation of the figures in the related publication.

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Vegetation Phenology in Experimental Plots from Phenocam Imagery, 2015-2020

The most recent version of these data are available https://doi.org/10.25581/spruce.100/1874948 and supersedes all previous versions. This data set consists of PhenoCam data from the SPRUCE experiment from the beginning of whole ecosystem warming (Hanson et al. 2017) in August 2015 through March 31 of 2021, with start- and end-of-season phenological transition dates derived through the end of autumn 2020. Digital cameras, or phenocams, installed in each SPRUCE enclosure track seasonal variation in vegetation “greenness”, a proxy for vegetation phenology and associated physiological activity. Three separate regions of interest (ROIs) were defined for each camera field of view, corresponding to different vegetation types and demarcating (1) Picea trees (vegetation type EN, for evergreen needleleaf); (2) Larix trees (vegetation type DN, for deciduous needleleaf); and (3) the mixed shrub layer (vegetation type SH). User note: A list of previous versions can be found in the Related Datasets section of the user guide.

54 ENVIRONMENTAL SCIENCES↗

MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data

Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.

54 ENVIRONMENTAL SCIENCES↗

ORNL FACE Tree Height, with data on height of a subset of trees measured every year, 1997-2009. Free-Air CO2 Enrichment (FACE) Experiment Synthesis Activities.

Height of 20 sweetgum trees in three rows of each of the plots in the Oak Ridge National Laboratory (ORNL) free-air CO2 enrichment (FACE) experiment was measured each year of the experiment (1997-2009). The trees were exposed to ambient or elevated CO2. Tree height data contribute to the overall project objectives to determine the integrated response of a deciduous forest to elevated CO2. Average tree height per plot was used in allometric equations to calculate tree dry mass each year and to test whether there were effects of elevated CO2 on canopy development. Height was derived from trigonometric calculation from measurements of horizontal distance of observer from the bole and the angles from observer’s eye to top and base of tree, using a Haglof sonic hypsometer. The data are presented in a csv file, with plot number in the first column, tree number in the second column, and height recorded to 0.1 m in 1997 to 2009 in remaining columns. Plots 1 and 2 had elevated CO2, and plots 3-5 were in ambient CO2. Missing data occur after the tree died. The experiment and the height measurement are described in: Norby, R. J., D. E. Todd, J. Fults, and D. W. Johnson. 2001. Allometric determination of tree growth in a CO2-enriched sweetgum stand. New Phytologist 150: 477-487. The ORNL FACE experiment is described at: https://richnorby.org/home/face-home/.

54 ENVIRONMENTAL SCIENCES↗

Processed sap flow and fine-root trait data associated with summer drought responses in temperate trees in Lisle, Illinois, USA (2019–2021)

These data support the manuscript “Acquisitive root exploration strategies help maintain higher peak sap flux rates during summer drought, but more root biomass does not”. The dataset includes processed sap flow measurements and fine-root trait data collected between 2019 and 2021 from temperate monodominant tree plots established in the 1920s to 1930s ranging in size from 0.05 to 0.8 ha at The Morton Arboretum in Lisle, IL. Sap flow was measured with ICT sap flow sensors using the heat ratio method. Fine-root traits were measured from soil cores which includes specific root length (SRL), specific root area (SRA), diameter, biomass, and length for diameter classes ≤1 mm and ≤2 mm. The package contains comma separated value (CSV) data files and associated metadata that can be viewed and analyzed using common software such as spreadsheet programs, R, and Python. These data are used to investigate how variation in fine-root traits relate to tree water use and drought response during summer drought linking belowground root traits and aboveground physiological responses.

drought↗

Machine learning to discover mineral trapping signatures due to CO 2 injection

Mineral trapping is pursued as a geological CO 2 sequestration (GCS) mechanism because it permanently stores CO 2 in solid phases or minerals. However, CO 2 mineral-trapping mechanisms are poorly understood due to (1) lack of sufficient field and laboratory data characterizing these complex processes, and (2) challenges to develop site-specific reactive-transport models coupling fluid flow and geochemical reactions occurring at various temporal (from milliseconds to years) and spatial (from pore (millimeters) to field (kilometers)) scales. Reactive transport with additional complexities such as heterogeneity can make the simulation outputs even more difficult to interpret because of complex nonlinearity and multi-scale interdependencies. Furthermore, the values of model outputs such as concentrations can vary by several orders of magnitude, making it harder to correlate and characterize the impact of the variables via traditional data interpretation techniques such as exploratory data analyses. Recently, machine learning (ML) has shown promise in feature discovery and in highlighting hidden mechanisms that cannot be obtained by existing data-analytics and statistical methods. In this study, we applied an unsupervised ML approach, non-negative matrix factorization with custom -means clustering (NMF) to the data generated by reactive-transport simulations of GCS. The reactive-transport data consisted of 19 attributes, including four physio-chemical variables (pH, porosity, aqueous CO 2 , and sequestered CO 2 ), six chemical species (K + , Na + , HCO, Ca 2+ , Mg 2+ , Fe 2+ ), and four carbonate minerals (calcite, dolomite, siderite, and ankerite), a feldspar mineral (albite), and four clay minerals (illite, clinochlore, kaolinite, and smectite) over a period of 200 years of simulation time. Furthermore, the simulation data used was for Morrow B sandstone at the Farnsworth hydrocarbon unit in Texas. Data are sampled at two locations within the model domain: (1) at the injection well and (2) 200 m west of the injection well. The injection was performed for a period of 10 years. Using NMF, we estimated the temporal interdependencies among the 19 attributes over a span of 200 years. We found that NMF was able to identify four reaction stages and their dominant attributes; these cannot be directly discerned through traditional visualization (e.g., line plots, Pareto analysis, Glyph-based visualization methods) or exploratory data analysis tools of the simulation data. The four stages were: reactions in the injection phase followed by short-, mid-, and long-term reactions. The NMF analysis also revealed that 10 among the 19 attributes are dominant. These dominant attributes for mineral trapping include calcite, dolomite at injection well, siderite at 200 m away from the injection well, clinochlore, kaolinite, Na + , K + , Ca 2+ , Mg 2+ , pH, and aqeuous CO 2 . Finally, at late times (65–200 years), our results showed that calcite plays a major role in mineral trapping with insignificant contribution from siderite, ankerite, and clay minerals. These findings make the proposed unsupervised ML-model attractive for reactive-transport sensing towards real-time GCS monitoring.

54 ENVIRONMENTAL SCIENCES↗

GAT (Grid Analysis Toolkit) [SWR-25-41]

Grid Analysis Toolkit (GAT) is a unified Python API and plotting for power system PCM and CEM results (Sienna, PLEXOS, ReEDS™). It's a toolkit for wrangling data for Bulk Grid Dispatch and Transmission Analysis. GAT aims to provide simplified access to PCM and CEM results in a standard format while also allowing raw data access to underlying datasets specific to the model. This software can also be found on PyPI at For plotting, GAT defaults to standard National Lab of the Rockies (NLR) color schemes and standard styles while allowing customization.

Webb, Micah [National Laboratory of the Rockies (N↗

Radiative transition probabilities of neutral and singly ionized Europium estimated by laser-induced breakdown spectroscopy (LIBS)

Laser-induced breakdown spectroscopy (LIBS) is a versatile technique for compositional analysis for solids, liquids, or gasses. LIBS is an asset for the quantitative or qualitative analysis of resource limited materials like actinides and rare earths because it is quasi-nondestructive. Two Eu 2 O 3 pellets were synthesized to be a test and validation set, respectively. Spectral lines identified from the National Institute of Standards and Technology database with fundamental data reported were used to form Saha-Boltzmann plots. The Saha-Boltzmann plots were used to determine the plasma temperatures and electron densities of the laser-induced plasmas for both samples. These Saha-Boltzmann plots were then used to calculate previously unreported transition probabilities associated with identified peaks. Additionally, the transition probabilities presented in this paper provide the capability for calibration free LIBS to be performed more readily on europium samples and the spectroscopic analysis of stellar bodies. Eight previously unreported transition probabilities are presented in this paper; five for Eu I and three for Eu II. The transition probabilities for Eu I ranged from 0.172 to 7.38 × 10 7 s -1 and those for Eu II ranged from 1.56 to 6.75 × 10 7 s -1 .

47 OTHER INSTRUMENTATION↗

Process Failure Detection via Recurrence Quantification Analysis in a Slot-Rectangular Spouted Bed

A study was conducted to explore the applicability of recurrence and recurrence quantification analysis (RQA) to the detection of process failures in spouted bed reactor systems. Here, three different potential failure modes were examined in a transparent, cold flow slot-rectangular spouted bed. These being, a simulated air leak from a side wall of the reactor, a simulated gas leak from the top wall of the reactor, and simulated agglomeration of solids via introduction of larger “klinker” particles. Bed pressure drop time history data were collected and analyzed via generation of recurrence plots (RPs) and RQA parameters. In general, the simulated agglomeration case was quite easily detected via ever RQA Parameter examined, whereas the simulated air leaks were detected by only a single RQA parameter.

30 DIRECT ENERGY CONVERSION↗

New Perspectives on the Exoplanet Radius Gap from a Mathematica Tool and Visualized Water Equation of State

Recent astronomical observations obtained with the Kepler and TESS missions and their related ground-based follow-ups revealed an abundance of exoplanets with a size intermediate between Earth and Neptune (1 R ⊕ ≤ R ≤ 4 R ⊕ ). A low occurrence rate of planets has been identified at around twice the size of Earth (2 × R ⊕ ), known as the exoplanet radius gap or radius valley. We explore the geometry of this gap in the mass–radius diagram, with the help of a Mathematica plotting tool developed with the capability of manipulating exoplanet data in multidimensional parameter space, and with the help of visualized water equations of state in the temperature–density (T–ρ) graph and the entropy–pressure (s–P) graph. We show that the radius valley can be explained by a compositional difference between smaller, predominantly rocky planets (<2 × R ⊕ ) and larger planets (>2 × R ⊕ ) that exhibit greater compositional diversity including cosmic ices (water, ammonia, methane, etc.) and gaseous envelopes. In particular, among the larger planets (>2 × R ⊕ ), when viewed from the perspective of planet equilibrium temperature (T eq ), the hot ones (T eq ≳ 900 K) are consistent with ice-dominated composition without significant gaseous envelopes, while the cold ones (T eq ≲ 900 K) have more diverse compositions, including various amounts of gaseous envelopes.

79 ASTRONOMY AND ASTROPHYSICS↗

Thermal Stimulation and Injectivity Testing at Raft River, ID EGS Site

The Raft River geothermal field is the site of an innovative Department of Energy Enhanced Geothermal System (EGS) project to determine the viability of using combined thermal and hydraulic stimulation techniques to improve energy production. Well RRG-9 is currently undergoing a stimulation program using injectate from the US Geothermal Raft River Power Plant and cold water from a cooling tower make-up water well. The stimulation began on 13 June 2013 with injection from the power plant at a temperature of about 39 °C and a pressure of 275 psig. Next, two positive displacement plunger type pumps were used to increase the injection pressure and flow rate for about one month. The highest rate achieved was 258 gpm at a pressure of 741 psig. During this time, fluid from the cooler water well was injected for about 2 weeks at various pressures. Then, the pumps were removed and plant injection resumed on 25 September. Plant injection will continue until the spring of 2014, when a high pressure hydraulic stimulation will be conducted. A series of seismic monitoring stations deployed around the well are providing data on seismic events occurring at the site. Over the past year, 51 microseismic events have been recorded, all less than Magnitude 1. During injection, several diagnostic tests were conducted to gain a better understanding of the well and reservoir. A step-rate test was performed on 22 August to measure the in-situ stress and aid in modeling in-situ fractures. A tracer was injected into the well on 9 September. No tracer was detected in adjacent production wells after several months. A second borehole televiewer survey was conducted for comparison to pre-stimulation images. Here, a third borehole televiewer survey is planned after the high pressure stimulation. Injection test data is evaluated in real time. A modified Hall plot analysis indicates the effective permeability is increasing. The injectivity index supports the results of the modified Hall plot analysis. As the thermal stimulation has continued, the injectivity index has consistently followed an upward trend from 0.1 gpm/psi to 0.53 gpm/psi.

enhanced geothermal systems↗

Inputs, Outputs and Plotting Scripts for paper Extending near-axis equilibria in DESC

Python scripts and outputs from the DESC and pyQSC/pyQIC codes used to create the results in the paper "Extending near-axis equilibria in DESC". The contained README file has the details of which scripts create which figures, as well as on what versions of the codes were used. The repo also contains python pickle (.p) files and .txt files with the data used to create each figure (which are used by the plotting scripts).

DESC↗

PRESSURE-FILM OPEN SOURCE SCANNING AND MAPPING

SF-22-099 Pressure-film Open Source Scanning and Mapping (POSSM) is software that analyses images of pressure-film (scans or photographs). POSSM collects data from that analysis in order to produce a number of visual aides, including pressure maps, histograms, and 3d surface plots. POSSM is designed to be able to analyze an entire folder full of images, exporting numeric data as .csv files and visual graphics as .png files.

Grider, Patrick↗

Ring Pull Strain Analysis Version 1.1

This report details an analysis package, Ring Pull Strain Analysis (RPSA), that can be used to present and quantify digital image correlation (DIC) data as it relates to a gaugeless ring pull test. Gaugeless ring pull is a testing technique for mechanical testing of small annular samples, usually cut from a thin-walled tube. DIC data is often necessary for this kind of test because bending moments present on the ring cause a non-uniform strain distribution and localized measurements are necessary. In addition, the annular geometry of a ring lends itself to a polar representation, which is not present with typical DIC analysis methods. RPSA was made to calculate and plot the polar representation of strain from standard pre-processed DIC data of a gaugeless ring pull test. Further analysis can be done on ring pull including a quasi-uniaxial tensile analysis and coating analysis, which are also performed by RPSA. In addition, due to the universality of DIC plotting and ring pull test analysis, RPSA can accommodate a wide variety of tests, though it is tailored for ring pull testing. This report details how RPSA works, including the theory, assumptions, and logic behind the calculations and the structure of the program.

36 MATERIALS SCIENCE↗

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗

Surface soil temperature and water content from warming experiment located at the Rocky Mountain Biological Laboratory, Colorado, 2015 to 2019

This data package consists of soil temperature and soil water content sensor data from the warming experiment near the Rocky Mountain Biological Laboratory. Data range is from summer 2015 to summer 2019, when the warming manipulation was terminated. The location of the warming experiment is in the upper montane life zone and consists of meadow vegetation with a mixture of sagebrush (Artemisia tridentata), forb species (Erigeron speciosus, Helianthella quinquenervis, Lathyrus lanszwertii), and graminoid species (Festuca thurberi, Carex spps). Early studies showed that the heating treatment led to earlier snowmelt as well as warmer and drier surface soils, and changes in the functional composition of aboveground biomass favoring sagebrush over forb species (Harte and Shaw, 1995). These changes were mainly observed in the upper, naturally drier zone for the experimental plots. More recent observations of aboveground biomass, soil carbon, and microbial composition require concurrent information about the abiotic environment for interpretation and extrapolation to process-based models. This data package provides the plot- and zone-level abiotic context for the final years of the experiment and consists of csv files with hourly soil temperature (WM_ST.csv) and soil water content (WM_SWC.csv).

54 ENVIRONMENTAL SCIENCES↗

CORRIGENDUM to Figures S3-S4 of "Quasi-stationary Planetary Scale Waves in Modern Climate Models"

In addition to fixing the color-coding legend, the new figures plot Fourier phase in a more easily recognizable format: polar coordinates rather than Cartesian coordinates. The same phase data is displayed—indicating the position of the first ridge to the east of the prime meridian—but the new plots avoid unphysical jumps, e.g. from +180° to -180° as longitude increases across the International Dateline. A slight disadvantage of the new format is that each hemisphere requires a separate plot. The wavenumber-1 Northern Hemisphere phase plots give, in effect, a view from above the North Pole, with Eurasia at the top and North America at the bottom. Wavenumber-1 Southern Hemisphere plots give an analogous view from the South Pole. Plots for higher wavenumbers, however, wrap around at fractions of 360° (180°, 120°, ...) and cannot be interpreted as a geographical view.

54 ENVIRONMENTAL SCIENCES↗

Dataset for First Full Dalitz Plot Measurement in Neutron β-Decay using the Nab Spectrometer and Implications for New Physics

The Nab apparatus at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source was designed to measure key observations in neutron beta decay, test the Standard Model's description of the weak interaction, and search for new physics. This data was collected using the Nab apparatus and are presented in the article "First Full Dalitz Plot Measurement in Neutron β-Decay using the Nab Spectrometer and Implications for New Physics." This data publication includes CSV (comma-separated values) files which are used to generate Figures 3 - 11 in the linked journal article.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗