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DOE OSTI2022

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines ( Triticum aestivum , CDC Stanley x CDC Landmark), wheat-barley ( T . aestivum x Hordeum vulgare ) and wheat-wheatgrass ( Triticum durum x Thinopyrum intermedium ) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

How Wrong Can the Operational AEP Uncertainty Estimate Be When We Ignore the Correlations Between the Uncertainty Components?

Calculations of wind farm annual energy production (AEP) on operational data are essential for a variety of financial transactions during the life of wind plants. The AEP estimate is associated with an uncertainty value, which is calculated by combining contributions connected to on-site measurements, long-term reference measurements, losses, regression, windiness adjustment, and wind resource interannual variability. Although very limited documentation on the topic exists, the conventional approach currently used by the wind energy community to assess the uncertainty connected to the operational AEP estimate assume that the different uncertainty components are uncorrelated and therefore calculates the overall uncertainty with a sum of squares approach. In this analysis, we contrast the traditional technique to estimate the overall AEP uncertainty by ignoring the correlation between its different components with a novel Monte Carlo based approach, which can instead take into account the correlation between different uncertainty categories. We consider monthly operational data from 472 wind farms from the Energy Information Administration (EIA) 923 database to assess the difference between the two approaches. Long-term wind speed data needed for the AEP assessment are taken from three reanalysis products: the Modern-Era Retrospective analysis for Research and Applications v2 (MERRA-2), the European Reanalysis Interim (ERA-interim), and the National Centers for Environmental Prediction v2 (NCEP-2). The results of the Monte Carlo approach show that three pairs of AEP uncertainty components do show a statistically significant correlation: the uncertainty connected with wind resource inter-annual variability is positively correlated with the one related to the windiness correction and negatively correlated with the one due to the regression, and the wind measurement uncertainty is positively correlated with the regression uncertainty. All these correlations, which are found between uncertainty components which are not only part of an operational analysis, but also of a wind resource assessment, are currently ignored in the conventional techniques used as industry standard. We further investigate the causes of these correlations, in terms of common dependencies of different uncertainty components on wind resource variability, number of data points, and quality of the regression between wind speed and energy production data. Next, we quantify the error in the current industry standard technique, in terms of the percentage difference in total uncertainty calculated with the two considered approaches, for all the analyzed wind farms. We find a mean absolute percentage difference of about 6%, with the largest differences being greater than 20%. The data clearly confirm that ignoring the actual correlation between the uncertainty components can lead to large errors in the assessment of the operational AEP uncertainty, and the proposed Monte Carlo approach should be preferred.

Monte Carlo↗

DOE OSTI2025

Lessons Learned from AskGDR: Usage and Impact Analysis of the Geothermal Data Repository's AI Research Assistant: Preprint

In October of 2024, the Department of Energy's (DOE) Geothermal Data Repository (GDR) team officially launched AskGDR, an AI research assistant resulting from the integration of a Large Language Model (LLM) with the metadata and supporting documents associated with GDR datasets. AskGDR allows GDR users to ask deeper questions about the origin of datasets, the methods used to collect them, and the findings they help support. Using Retrieval Augmented Generation (RAG), AskGDR can be used to summarize findings spread across dozens of papers and technical reports or to extract relevant information describing a single data field. However, generative AI is experimental. The National Renewable Energy Laboratory (NREL) has been collecting metrics on AskGDR and documenting lessons learned during its deployment. This paper will outline the efficacy and impact of AskGDR through analysis of its use, operating costs, number and types of questions asked, and the quality of answers provided.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

A robust synthetic data generation framework for machine learning in high-resolution transmission electron microscopy (HRTEM)

Machine learning techniques are attractive options for developing highly-accurate analysis tools for nanomaterials characterization, including high-resolution transmission electron microscopy (HRTEM). However, successfully implementing such machine learning tools can be difficult due to the challenges in procuring sufficiently large, high-quality training datasets from experiments. In this work, we introduce Construction Zone, a Python package for rapid generation of complex nanoscale atomic structures which enables fast, systematic sampling of realistic nanomaterial structures and can be used as a random structure generator for large, diverse synthetic datasets. Using Construction Zone, we develop an end-to-end machine learning workflow for training neural network models to analyze experimental atomic resolution HRTEM images on the task of nanoparticle image segmentation purely with simulated databases. Further, we study the data curation process to understand how various aspects of the curated simulated data—including simulation fidelity, the distribution of atomic structures, and the distribution of imaging conditions—affect model performance across three benchmark experimental HRTEM image datasets. Using our workflow, we are able to achieve state-of-the-art segmentation performance on these experimental benchmarks and, further, we discuss robust strategies for consistently achieving high performance with machine learning in experimental settings using purely synthetic data. Construction Zone and its documentation are available at https://github.com/lerandc/construction_zone.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Producing Evaluation-quality 239 Pu Average Prompt Fission Neutron Multiplicities using a Correlated Fission Model

An evaluation of the average prompt fission neutron multiplicity, $\bar{ν}_p$, of 239 Pu(n,f) is shown. This evaluation includes (a) the correlated fission model CGMF, and (b) a detailed analysis of past and recently published experimental data. Using CGMF-calculated $\bar{ν}_p$ as prior enables to link, through the use of evaluated model input parameters, $\bar{ν}_p$ to other fission observables such as the prompt fission neutron spectrum (PFNS), preneutron emission fission yields as a function of mass, and the average total kinetic energy of the fragments. These evaluated parameters produce realistic predictions of many fission observables, while the evaluated $\bar{ν}_p$ agrees well (χ 2 ≈ 1) with data. Moreover, with the new evaluated $\bar{ν}_p$, the effective neutron multiplication factor of fast Pu ICSBEP critical assemblies are predicted with a mean bias of 58 pcm compared to 18 pcm with ENDF/B-VIII.0, when paired with a new 239 Pu PFNS and fission cross section. Due to these encouraging validation results, the evaluated $\bar{ν}_p$ is currently part of a release candidate for the 239 Pu ENDF/B-VIII.1 file. Hence, a correlated fission model was used for the first time for evaluating $\bar{ν}_p$ that is of evaluation quality. This is an important step towards consistent evaluations of prompt fission observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The R -process Alliance: A Nearly Complete R -process Abundance Template Derived from Ultraviolet Spectroscopy of the R -process-enhanced Metal-poor Star HD 222925 *

We present a nearly complete rapid neutron-capture process (r-process) chemical inventory of the metal-poor ([Fe/H] = -1.46 ± 0.10) r-process-enhanced ([Eu/Fe] = +1.32 ± 0.08) halo star HD 222925. This abundance set is the most complete for any object beyond the solar system, with a total of 63 metals detected and seven with upper limits. It comprises 42 elements from 31 ≤ Z ≤ 90, including elements rarely detected in r-process-enhanced stars, such as Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, W, Re, Os, Ir, Pt, and Au. We derive these abundances from an analysis of 404 absorption lines in ultraviolet spectra collected using the Space Telescope Imaging Spectrograph on the Hubble Space Telescope and previously analyzed optical spectra. A series of appendices discusses the atomic data and quality of fits for these lines. The r-process elements from Ba to Pb, including all elements at the third r-process peak, exhibit remarkable agreement with the solar r-process residuals, with a standard deviation of the differences of only 0.08 dex (17%). In contrast, deviations among the lighter elements from Ga to Te span nearly 1.4 dex, and they show distinct trends from Ga to Se, Nb through Cd, and In through Te. The r-process contribution to Ga, Ge, and As is small, and Se is the lightest element whose production is dominated by the r-process. The lanthanide fraction, log X La = -1.39 ± 0.09, is typical for r-process-enhanced stars and higher than that of the kilonova from the GW170817 neutron-star merger event. We advocate adopting this pattern as an alternative to the solar r-process-element residuals when confronting future theoretical models of heavy-element nucleosynthesis with observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

3-D Radiological Data Acquisition, Visualization and Modeling - 20211

The U.S. Army Corps of Engineers (USACE) was tasked to investigate and remediate low activity radiological contamination from research and production of the nation's first nuclear weapons at the former DuPont Chambers Works Formerly Utilized Sites Remedial Action Program (FUSRAP) site (DuPont). The DuPont site had several buildings used for the Manhattan project that were demolished in the 1940's and 1950's apparently using heavy earthmoving equipment. Some of the contaminated rubble from the demolition appears to have been spread out by this equipment resulting in somewhat random scattering of radiologically contaminated soil and debris along with aqueous spills. Traditional investigative methods such as soil borings, test pits and 2-dimensional gamma walkovers were only partially successful in delineating the radiological contamination at the site. It was feared that even 'chasing' the contamination during remediation would miss contamination if the demolition resulted in discontinuous trails of radiologically contaminated soils. In evaluating the data generated over the interceding decades, the USACE determined that a better method to collect and process the remedial action radiological data was needed to enable the project team to optimize predictive planning and meet documentation expectations. The purpose of this paper is to provide an overview of the effort and progress to combine and organize radiological survey methods into a highly flexible sampling, modeling, and decision analysis approach that emphasizes the quality of decision-making during remediation. This innovative system blends multiple tools to develop a methodology that can extend MARRSIM [1] into the subsurface and provide tools that can be applied to other sites. (authors)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Blazar variability power spectra from radio up to TeV photon energies: Mrk 421 and PKS 2155−304

ABSTRACT We present the results of the power spectral density (PSD) analysis for the blazars Mrk 421 and PKS 2155−304, using good-quality, densely sampled light curves at multiple frequencies, covering 17 decades of the electromagnetic spectrum, and variability time-scales from weeks up to a decade. The data were collected from publicly available archives of observatories at radio from Owens Valley Radio Observatory, optical and infrared (B, V, R, I, J, H, and Kbands), X-rays from the Swift and the Rossi X-ray Timing Explorer, high and very high energy (VHE) γ-rays from the Fermi and Very Energetic Radiation Imaging Telescope Array System as well as the High Energy Stereoscopic System. Our results are: (1) the power-law form of the variability power spectra at radio, infrared, and optical frequencies have slopes ∼1.8, indicative of random-walk-type noise processes; (2) the power-law form of the variability power spectra at higher frequencies, from X-rays to VHE γ-rays, however, have slopes ∼1.2, suggesting a flicker noise-type process; and (3) there is significantly more variability power at X-rays, high and VHE γ-rays on time-scales ≲ 100 d, as compared to lower energies. Our results do not easily fit into a simple model, in which a single compact emission zone is dominating the radiative output of the blazars across all the time-scales probed in our analysis. Instead, we argue that the frequency-dependent shape of the variability power spectra points out a more complex picture, with highly inhomogeneous outflow producing non-thermal emission over an extended, stratified volume.

Goyal, Arti↗

DOE OSTI2020

Performance Understanding and Analysis for Exascale Data Management Workflows (Collaboration)

The general approach of the MONA project is depicted in Figure 1. The figure shows performance monitoring applied to an I/O workflow associated with a scientific simulation, with online measurements captured from this workflow informing methods for workflow reconfiguration and dynamic adjustment. The goal is to maintain suitable levels of Quality of Service for workflow execution, by understanding the underlying causes of workflow performance and behavior. One outcome will be workflow performance models able to characterize realistic workflows. Another outcome will be performance ‘mini-apps’ implementing such workflow behavior. Out of scope for this project are advanced methods for online workflow control.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Dynamically Downscaled Hourly Future Weather Data with 12-km Resolution Covering Most of North America

This is an hourly future weather dataset for energy modeling applications. The dataset is primarily based on the output of a regional climate model (RCM), i.e., the Weather Research and Forecasting (WRF) model version 3.3.1. The WRF simulations are driven by the output of a general circulation model (GCM), i.e., the Community Climate System Model version 4 (CCSM4). This dataset is in the EPW format, which can be read or translated by more than 25 building energy modeling programs (e.g., EnergyPlus, ESP-r, and IESVE), energy system modeling programs (e.g., System Advisor Model (SAM)), indoor air quality analysis programs (e.g., CONTAM), and hygrothermal analysis programs (e.g., WUFI). It contains 13 weather variables, which are the Dry-Bulb Temperature, Dew Point Temperature, Relative Humidity, Atmospheric Pressure, Horizontal Infrared Radiation Intensity from Sky, Global Horizontal Irradiation, Direct Normal Irradiation, Diffuse Horizontal Irradiation, Wind Speed, Wind Direction, Sky Cover, Albedo, and Liquid Precipitation Depth. The weather data is created for two emissions scenarios: RCP4.5 and RCP8.5 and spans two 10-year time slices in the future: 2045 - 2054 and 2085 - 2094. It offers a spatial resolution of 12 km by 12 km with extensive coverage across most of North America. Due to the enormous size of the entire dataset, in the first stage of its distribution, we provide 20 years of future weather data for the centroid of each Public Use Microdata Area (PUMA), excluding Hawaii. PUMAs are non-overlapping, statistical geographic areas that partition each state or equivalent entity into geographic areas containing no fewer than 100,000 people each. The 2,378 PUMAs as a whole cover the entirety of the U.S. The weather data can be utilized alongside the large-scale energy analysis tools, ResStock and ComStock, developed by National Renewable Energy Laboratory, whose smallest resolution is at the PUMA scale. The data for RCP4.5 is still being processed and will be published soon.

Array↗

DOE OSTI2024

Analysis and Grading of the Test Performance of PS Modules for the CMS Phase-2 Outer Tracker Upgrade

The Outer Tracker of the CMS experiment provides information about the trajectory of charged particles produced in proton-proton collisions at the LHC. During the High Luminosity LHC upgrade, scheduled for the late 2020s, the Outer Tracker will be replaced with new modules capable of transmitting data to the L1 Trigger. These modules are being assembled at several facilities around the world, including Fermilab, necessitating coordinated standards of module quality. Here I discuss the development of POTATO (Phase-2 Outer Tracker Analyzer of Test Outputs), a C++ software which provides a standardized procedure for analyzing and grading test results of the Outer Tracker modules. The particular focus of this poster is on the analysis and grading of the PS (pixel-strip) modules in POTATO.

Riggall, Caroline↗

DOE OSTI2023

Clustering High-dimensional Toxicogenomics Data with Rare Signals

Toxicogenomics studies the gene and protein activities to drug treatments or toxic exposures. As the drugs and genes are numerous, toxicogenomics data are naturally high dimensional, with dimension sizes up to millions. In addition, the distribution of toxicogenomics data is oftentimes skewed, and they contain rare but important signals representing a cell or organism’s response to toxicity. The combination of high dimension and extremely skewed distribution of toxicogenomics data makes clustering analysis extremely challenging.We present our study of clustering toxicogenomics data using classical approaches such as principal component analysis as well as deep learning approaches such as auto-encoders. Our experiments show that these approaches fail to preserve rare signals and produce high-quality clusters. We then explore augmenting matrix factorization with deep learning techniques such as attention mechanism to produce latent representations for clustering. Our technique is able to better preserve rare signals after dimensionality reduction than prior approaches. Furthermore, we combine our augmented matrix factorization with a mechanism similar to autoencoder to balance separable clusters and low regeneration errors. Our experiments demonstrate better clustering with our proposed approach.

Cong, Guojing↗

DOE OSTI2022

Network Models of Active Degradation Mechanisms and Pathways for Service Life Prediction of Indoor and Outdoor PV Modules

ct: PV service lifetime prediction (SLP) enables accurate calculation of levelized cost of energy (LCOE), which is crucial to rationalizing PV investment and installation. However, SLP is challeging since PV reliability in the field is affected by many combined factors, including various environmental stresses and module quality. In order to map out the active degradation mechanisms and pathways that best resemble real world conditions, we introduce the framework of a study protocol and use network models fitted to data, to enable analysis and SLP of complex PV systems with multiple active degradation mechanisms. The study protocol is the experimental design, including module variants and different exposure conditions, selection of evaluation methods, time-series data acquisition and training of network models to these data. We present SLP of minimodules in the lab and PV systems in the field. For lab SLP, minimodules with 8 variants based on manufacturer, architecture, and encapsulation were prepared and aged in modified damp heat with or without full spectrum light exposure. Stepwise I-V and Suns-Voc data acquisition tracks changes in electrical properties including Rs,IV, Isc,IV, Vmp,PIV providing insights into power loss of minimodules. Network structural equation modeling (netSEM) was utilized to construct degradation pathway models that identify active degradation mechanisms and predict power loss over time. For field SLP, datastreams of Pmp values and I-V curve datastreams of two types of modules installed in three distinctly different Köppen-Geiger climate zones for 9 years were acquired. With power loss modes corresponding to uniform current loss (ΔPIsc), recombination (ΔPVoc), series resistance (ΔPRs), and current mismatch (ΔPImis) determined, the performance loss rates (PLR) were determined using PVplr. We show how to establish a study protocol framework to ensure appropriate parametric variations and valid data collection from the variants of your complex systems. Then the data-driven netSEM model fitting provides a comprehensive mapping of multiple active degradation mechanisms, and accurate service life prediction.

network model, degradation, photovoltaic, solar↗

DOE OSTI2022

EDD Basic Stats and Graphs Notebook analysis (EDD BSG Notebook) v1.0

This jupyter notebook calculates basic statistics (e.g., mean, standard deviation, coefficient of variation) and simple graphs (e.g., bar graphs, line plots) for data from the Experiment Data Depot (EDD) to provide rapid and reproducible assessment of data quality to aid research efforts across the JBEI and ABF projects. It rapidly and reproducibly calculates basic statistical values for data stored in the EDD which aids researchers and strengthens comparisons across different experiments and projects.

Petzold, ChristopherJ↗

DOE OSTI2023

Thermal Hydraulic Experimental Test Article - Fiscal Year 2023 (Final Report)

The Thermal Hydraulic Experimental Test Article (THETA) is a facility that is used to develop sodium components and instrumentation as well as acquire experimental data for validation of reactor thermal hydraulic and safety analysis codes. The facility simulates nominal conditions as well as protected/unprotected loss of flow accidents in a sodium-cooled fast reactor (SFR). High fidelity distributed temperature profiles of the developed flow field may be acquired with Rayleigh backscatter based optical fiber temperature sensors. The facility was designed in partnership with systems code experts to tailor the experiment to ensure the most relevant and highest quality data for code validation. THETA is comprised of a traditional primary coolant and secondary coolant system. The primary system is submerged in the pool of sodium and consists of a pump, electrically heated core, intermediate heat exchanger, and connected piping and thermal barriers (redan). The secondary system, located outside of the sodium pool, consists of a pump, sodium to air heat exchanger, and connected piping and valves. To date a test matrix has been completed utilizing the primary system of THETA. These tests, along with computational fluid dynamics and systems code models, determined the heat transfer across the core barrel and intermediate heat exchanger outlet was too great to effectively represent scaled thermal hydraulic phenomena of a liquid metal cooled reactor. Therefore, a significant effort was made to remove the primary system from the METL 28” test vessel #4 and clean the residual sodium from the primary system to facilitate upgrades. Thermal insulation was then incorporated in the core barrel and intermediate heat exchanger outlets. The primary system was then replaced, and a series of tests were performed to assess the performance of the thermal insulation. With primary system testing and upgrades complete, the secondary system could then be brought online. The tube side of the shell-and-tube intermediate heat exchanger was installed onto the primary system flange to begin installing the secondary system. The support structure for the secondary system was then erected on the METL mezzanine alongside the THETA primary system to facilitate installation of the secondary system components (sodium-to-air heat exchanger, flowmeter and pump). The piping and expansion tank were welded into the secondary system. Non-destructive examination of the secondary system welds was completed in order to satisfy ASME B31.3 pipe code for class M process fluids. The heating system and insulation were then added to prepare the system to be filled with sodium. The ancillary electrical equipment was installed which included the pump control box, blower VFD, pipe heater control system, etc. The secondary system will be filled, and a test matrix will be completed in early FY2024.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2021

Dark Energy Survey Year 3 results: galaxy sample for BAO measurement

Here, we present and validate the galaxy sample used for the analysis of the baryon acoustic oscillation (BAO) signal in the Dark Energy Survey (DES) Y3 data. The definition is based on a colour and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.5, while ensuring a high-quality determination. The sample covers ~ 4100 square degrees to a depth of i = 22.3 (AB) at 10σ. It contains 7,031,993 galaxies in the redshift range from z = 0.6 to 1.1, with a mean effective redshift of 0.835. Redshifts are estimated with the machine learning algorithm DNF, and are validated using the VIPERS PDR2 sample. We find a mean redshift bias of z bias ~ 0.01 and a mean uncertainty, in units of 1 + z, of σ 68 ~ 0.03$. We evaluate the galaxy population of the sample, showing it is mostly built upon Elliptical to Sbc types. Furthermore, we find a low level of stellar contamination of ≲ 4 %. We present the method used to mitigate the effect of spurious clustering coming from observing conditions and other large-scale systematics. We apply it to the BAO sample and calculate weights that are used to get a robust estimate of the galaxy clustering signal. This paper is one of a series dedicated to the analysis of the BAO signal in DES Y3. In the companion papers, we present the galaxy mock catalogues used to calibrate the analysis and the angular diameter distance constraints obtained through the fitting to the BAO scale.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

A next-generation toolset for the life-cycle analysis of electricity use

This works presents an overview--including background, data flow, and case study--of a tool for analyzing impacts utilizing the electricity baseline provided by ElectricityLCI and the impact-modeling techniques of Grid Mix Explorer (along with air and water quality) as a part of a next-generation LCA analytical framework.

Davis, Tyler↗