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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Multi-Model and Multi-Scale Global Sensitivity Analysis for Identifying Controlling Processes of Complex Systems

An environmental model consists of multiple process level sub-models, and each sub-model represents a process that is key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing hypotheses about one or more processes. To address this problem, this project develops a new method to probe model output sensitivity to competing process models by integrating model averaging methods with variance-based global sensitivity analysis to address uncertainty in process models and parameters. The new method yields three process sensitivity indices. The first one is called first-order process sensitivity index, and it is derived as a single summary measure of relative process importance. Evaluating the index is computationally expensive, because it relies in a Monte Carlo scheme that requires thousands and even millions of model executions. To reduce computational cost, this project develops a computationally efficient, quasi Monte Carlo method, and this method is presented in Chapter 2 of this report with and a numerical example for demonstration. The numerical example shows that the results of the quasi Monte Carlo method are substantially close to those of the full Monte Carlo method, but the computational cost of the quasi Monte Carlo method is only 0.7% of that of the full Monte Carlo method. The second index is called total-effect process sensitivity index, and it measures interactions between different processes. Therefore, this sensitivity index includes the first-order process sensitivity index, and can be used to identify influential processes. On the other hand, the total-effect process sensitivity index can also be used to screen non-influential processes. This is demonstrated by two numerical examples using the Sobol-G* functions and groundwater flow models that consider recharge process, geological process, and snowmelt process. The numerical examples shows that the total-effect process sensitivity index is more informative than the first-order process sensitivity. The derivation of the process sensitivity index and the numerical examples are discussed in Chapter 3. Chapter 4 presents two computationally efficient methods for screening non-influential processes to exclude them from further investigation. The two methods are the multi-model difference-based sensitivity (MMDS) analysis method, which can be implemented using the Latin Hypercube Sampling. The second one is the implementation of MMDS method using a binning method. The numerical example for the Sobol-G* function indicates the two methods are capable of identifying non-influential models, and the numerical examples for the groundwater flow and reactive transport show that the two methods are effective for groundwater problems. However, it should be noted that the two methods are numerical approximations, and they can only be used for screening non-influential processes, not for ranking importance of system processes. All the sensitivity analysis methods are implemented by developing python codes, and the codes are in a software called SAMMPY: a python package for process sensitivity analysis under multiple models. The SAMMPY design and structure are discussed in Chapter 5, and the package is released to the public for free download.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Evaluating Barcode Size and Metal Surface Treatment Options for a Global UF 6 Cylinder Identifier

A team at Oak Ridge National Laboratory tested various barcode sizes, materials, surface finishes, and marking techniques to determine suitable direct part marking techniques and barcode specifications for a new uranium hexafluoride (UF 6 ) cylinder global identifier. This paper describes testing those variables at different read distances and angles with several commercial off-the-shelf direct part mark or barcode readers. This research concluded that a 1.4 in. 2D Data Matrix barcode with a 0.1 in. quiet zone would be appropriate for the machine-readable feature on the proposed UF 6 cylinder global identifier. Testing suggests that this size barcode could be read from an angle of up to 30° over the range of 10–100 cm using multiple commercial off-the-shelf handheld direct part mark or barcode readers. Testing also suggested that barcodes marked on ball-blasted stainless steel with CerMark laser marking ink may be a good choice for the proposed UF 6 cylinder global identifier because they exhibited high contrast and were readable from a desirable range of distances and angles.

42 ENGINEERING↗
DOE OSTI2021

Application of Machine Learning Algorithms to Identify Problematic Nuclear Data

In this work we aim to show that Machine learning algorithms are promising tools for the identification of nuclear data that contribute to increased errors in transport simulations. We demonstrate this through an application of a machine learning algorithm (Random Forest) to the Whisper/MCNP6 criticality validation library to identify nuclear data that are associated with an increase of the bias (simulated - experimental $k_{eff}$) in the calculations. Specifically, the $k_{eff}$ sensitivity profiles (w.r.t. nuclear data) of 233 U solution benchmarks are used to predict the bias and Shapley Additive Explanations (SHAP) are used to explain how the sensitivities are related to the predicted bias. The SHAP values can be interpreted as sensitivity coefficients of the machine learning model to the $k_{eff}$ sensitivities which are used to make predictions of bias. Using the SHAP values we can identify specific subsets of nuclear data which have the highest probability of influencing bias. We demonstrate the utility of this method by showing how SHAP values were used to identify an inconsistency in the 19 F inelastic scattering nuclear data. The methodology presented here is not limited to transport problems and can be applied to other simulations if there are experimental measurements to compare against, simulations of those experimental measurements, and the ability to calculate sensitivities of the model output with respect to the data inputs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules (Final Report)

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

EvoNet: A phylogenomic and systems biology approach to identify genes underlying plant survival in marginal, low‐N soils

The DOE‐BER “EvoNet” project investigates the genetic and molecular basis of plant resilience in extreme environments. We do this by identifying key genes that enable “extreme survivor” species to thrive in the nitrogen-poor soils of Chile’s hyper-arid Atacama Desert. Our collections focus on 32 Atacama extremophile species, including seven grass species with potential biofuel applications. To identify genes-of-importance to survival we compared genomic and transcriptomic profiles of extremophile species that thrive in the Atacama to those of closely related “sister” species from nitrogen-rich arid and mesic regions of California. Deep RNA sequencing and de novo transcriptome assembly across these triplet species sets supported a phylogenomic framework for identifying positively selected genes associated with adaptive divergence. Our integrative analysis combined ecological and environmental data, metagenomics, evolutionary and systems biology, and metabolomics. This enabled us to create an unprecedented framework for systematically understanding how non-model plants have adapted to survive in extreme conditions. Our resulting database of positively selected ortholog groups in the extremophile plants offers promising targets for engineering crop and biofuel species with enhanced resilience to drought and extreme weather. Additionally, our newest dataset explores and exploits a complementary metabolomic approach. This new aspect provides innovative strategies to manipulate plant cell metabolism, further supporting efforts to improve agricultural productivity in the face of extreme climates. Importantly, our combined evolutionary- and metabolomic-based strategies focused on convergent patterns of adaptation, providing a genetic and metabolomic toolkit for improving crop and biofuel resilience across diverse plant species. Finally, our novel exploration of ecological and evolutionary dynamics delivered to the community a phylogenomic computational pipeline called “PhyloGeneious.” Our continued adaptations of this pipeline are publicly available to expedite evolutionary genomic research for future scientific discoveries. In total, our DOE-BER has provided genomic, metabolomic, and computational strategies to understand how extremophile plants provide evolutionary and physiological targets for improving agricultural and biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Combining genome-wide association studies and expression quantitative trait nucleotide mapping with molecular and genetic validations to identify transcriptional networks regulating drought tolerance in Populus

Objectives: (i). To deploy a large-scale experimental drought trial for up to 1000 unique genotypes of Populus equipping the sites with controlled irrigation and drought treatments that are fully automated and monitored. FULLY COMPLETED (ii) To test the hypothesis that a suite of traits identified for drought tolerance in P. nigra can be measured in drought and control treatments in the wide germplasm collection of P. trichocarpa. FULLY COMPLETED (iii) To use established and novel GWAS model approaches to identify gene loci linked to drought tolerance traits on interest in P. trichocarpa. FULLY COMPLETED (iv) To undertake comparative analysis of GWAS results for drought tolerance traits in P. nigra and P. trichocarpa. PARTIALLY COMPLETED – remains active (v) Using RNAseq in P. trichocarpa, in droughted and control treatments to identify cis- and trans-regulated eQTN. FULLY COMPLETED (vi) Validate up to 50 cis-QTNs, from network hubs using transient protoplast assays. FULLY COMPLETED (vii) To establish Agrobacterium-based gene editing protocols in Populus. FULLY COMPLETED (viii) To utilize early leads from previous research to investigate at least 6 candidate genes for drought tolerance in Populus. FULLY COMPLETED (ix) To validate up to 20 candidate genes for drought tolerance in P. trichocarpa refined from the long-list tested in the transient assays for cis-acting hub gene targets. PARTIALLY COMPLETED- remains active.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.

3’ RNA-seq↗
DOE OSTI2021

Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma

Three clinically relevant ebolaviruses – Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo ® ) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb ® [atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga ® (ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP – glycan cap and base – play a principal role in plasma-antibody-mediated protective immunity against EVD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9™

Ultra-high performance liquid chromatography–high-resolution mass spectrometry (UPHLC–HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect 1000’s of molecules (i.e., metabolites) in a single instrument run and provide a measurement of the global metabolome, which could be a fingerprint of activity. Despite the power of this approach, technical challenges have hindered the effective use of metabolomics to interrogate microbial communities implicated in the removal of priority contaminants. Herein, our efforts to circumvent these challenges and apply this emerging systems biology technique to microbiomes relevant for contaminant biodegradation will be discussed. Chlorinated ethenes impact many contaminated sites, and detoxification can be achieved by organohalide-respiring bacteria, a process currently assessed by quantitative gene-centric tools (e.g., quantitative PCR). This laboratory study monitored the metabolome of the SDC-9™ bioaugmentation consortium during cis-1,2-dichloroethene (cDCE) conversion to vinyl chloride (VC) and nontoxic ethene. Untargeted metabolomics using an UHPLC-Orbitrap mass spectrometer and performed on SDC-9™ cultures at different stages of the reductive dechlorination process detected ~10,000 spectral features per sample arising from water-soluble molecules with both known and unknown structures. Multivariate statistical techniques including partial least squares-discriminate analysis (PLSDA) identified patterns of measurable spectral features (peak patterns) that correlated with dechlorination (in)activity, and ANOVA analyses identified 18 potential biomarkers for this process. Statistical clustering of samples with these 18 features identified dechlorination activity more reliably than clustering of samples based only on chlorinated ethene concentration and Dhc 16S rRNA gene abundance data, highlighting the potential value of metabolomic workflows as an innovative site assessment and bioremediation monitoring tool.

environmental monitoring↗
DOE OSTI2023

Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Identifying Candidate Biomarkers of Ionizing Radiation in Human Pulmonary Microvascular Lumens Using Microfluidics—A Pilot Study

The microvasculature system is critical for the delivery and removal of key nutrients and waste products and is significantly damaged by ionizing radiation. Single-cell capillaries and microvasculature structures are the primary cause of circulatory dysfunction, one that results in morbidities leading to progressive tissue and organ failure and premature death. Identifying tissue-specific biomarkers that are predictive of the extent of tissue and organ damage will aid in developing medical countermeasures for treating individuals exposed to ionizing radiation. In this pilot study, we developed and tested a 17 µL human-derived microvascular microfluidic lumen for identifying candidate biomarkers of ionizing radiation exposure. Through mass-spectrometry-based proteomics, we detected 35 proteins that may be candidate early biomarkers of ionizing radiation exposure. This pilot study demonstrates the feasibility of using humanized microfluidic and organ-on-a-chip systems for biomarker discovery studies. A more elaborate study of sufficient statistical power is needed to identify candidate biomarkers and test medical countermeasures of ionizing radiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Possibilities and Limitations of Kinematically Identifying Stars from Accreted Ultra-faint Dwarf Galaxies

Abstract The Milky Way has accreted many ultra-faint dwarf galaxies (UFDs), and stars from these galaxies can be found throughout our Galaxy today. Studying these stars provides insight into galaxy formation and early chemical enrichment, but identifying them is difficult. Clustering stellar dynamics in 4D phase space ( E , L z , J r , J z ) is one method of identifying accreted structure that is currently being utilized in the search for accreted UFDs. We produce 32 simulated stellar halos using particle tagging with the Caterpillar simulation suite and thoroughly test the abilities of different clustering algorithms to recover tidally disrupted UFD remnants. We perform over 10,000 clustering runs, testing seven clustering algorithms, roughly twenty hyperparameter choices per algorithm, and six different types of data sets each with up to 32 simulated samples. Of the seven algorithms, HDBSCAN most consistently balances UFD recovery rates and cluster realness rates. We find that, even in highly idealized cases, the vast majority of clusters found by clustering algorithms do not correspond to real accreted UFD remnants and we can generally only recover 6% of UFDs remnants at best. These results focus exclusively on groups of stars from UFDs, which have weak dynamic signatures compared to the background of other stars. The recoverable UFD remnants are those that accreted recently, z accretion ≲ 0.5. Based on these results, we make recommendations to help guide the search for dynamically linked clusters of UFD stars in observational data. We find that real clusters generally have higher median energy and J r , providing a way to help identify real versus fake clusters. We also recommend incorporating chemical tagging as a way to improve clustering results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Identifying a regional aerosol baseline in the eastern North Atlantic using collocated measurements and a mathematical algorithm to mask high-submicron-number-concentration aerosol events

Abstract. High-time-resolution measurements of in situ aerosol and cloud properties provide the ability to study regional atmospheric processes that occur on timescales of minutes to hours. However, one limitation to this approach is that continuous measurements often include periods when the data collected are not representative of the regional aerosol. Even at remote locations, submicron aerosols are pervasive in the ambient atmosphere with many sources. Therefore, periods dominated by local aerosol should be identified before conducting subsequent analyses to understand aerosol regional processes and aerosol–cloud interactions. Here, we present a novel method to validate the identification of regional baseline aerosol data by applying a mathematical algorithm to the data collected at the U.S. Department of Energy's (DOE) Atmospheric Radiation Measurement (ARM) user facility in the eastern North Atlantic (ENA). The ENA central facility (C1) includes an aerosol observing system (AOS) for the measurement of aerosol physical, optical, and chemical properties at time resolutions from seconds to minutes. A second temporary supplementary facility (S1), located ∼0.75 km from C1, was deployed for ∼1 year during the Aerosol and Cloud Experiments (ACE-ENA) campaign in 2017. First, we investigate the local aerosol at both locations. We associate periods of high submicron number concentration (Ntot) in the fine-mode condensation particle counter (CPC) and size distributions from the Ultra-High Sensitivity Aerosol Spectrometer (UHSAS) as a function of wind direction using a meteorology sensor with local sources. Elevated concentrations of Aitken-mode (< 100 nm diameter) particles were observed in correspondence with the wind directions associated with airport operations. At ENA, the Graciosa Airport and its associated activities were found to be the main sources of high-concentration aerosol events at ENA, causing peaks in 1 min Ntot that exceeded 8000 and 10 000 cm−3 at C1, in summer and winter, respectively, and 5000 cm−3 at S1 in summer. Periods with high Ntot not associated with these wind directions were also observed. As a result, the diverse local sources at ENA yielded a poor relationship between Ntot measurements collected at C1 and S1 (R2=0.03 with a slope =0.05±0.001). As a first approach to mask these events, the time periods when the wind direction was associated with the airport operations (west to northwest and southeast to south at C1 and east to south at S1) were applied. The meteorological masks removed 38.9 % of the data at C1 and 43.4 % at S1, and they did not significantly improve the relationship between the two sites (R2=0.18 with a slope =0.06±0.001). Due to the complexity of high-Ntot events observed at ENA, we develop and validate a mathematical ENA Aerosol Mask (ENA-AM) to identify high-Ntot events using 1 min resolution data from the AOS CPC at C1 and S1. After its parameterization and application, ENA-AM generated a high correlation between Ntot in the summer at C1 and S1 (R2=0.87 with a slope =0.84±0.001). We identified the regional baseline at ENA to be 428±228 cm−3 in the summer and 346±223 cm−3 in the winter. Lastly, we compared masked measurements from the AOS with the ARM Aerial Facility (AAF) during flights over C1 in the summer to understand submicron aerosol vertical mixing over C1. The high correlation (R2=0.71 with a slope of 1.04±0.01) observed between C1 and the AAF Ntot collected within an area of 10 km surrounding ENA and at altitudes < 500 m indicated that the submicron aerosol at ENA was well mixed within the first 500 m of the marine boundary layer during the month of July during ACE-ENA. Our novel method for determining a regional aerosol baseline at ENA can be applied to other time periods and at other locations with validation by a secondary site or additional collocated measurements.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves

Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops.

3D reconstruction↗
DOE OSTI2020

DISCo-microbe: design of an identifiable synthetic community of microbes

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).

16S rRNA↗
DOE OSTI2021

A Commercial Building Plug Load Management System that Uses Internet of Things Technology to Automatically Identify Plugged-In Devices and Their Locations

Plug and process loads (PPLs) account for a large portion of U.S. commercial building energy use. There is a huge potential to reduce whole building consumption by targeting PPLs for energy savings measures or implementing some form of plug load management (PLM). Despite this potential, there has yet to be a widely adopted commercial PLM technology. This paper describes the Automatic Type and Location Identification System (ATLIS), a PLM system framework with automatic and dynamic load detection (ADLD). ADLD gives PLM systems the ability to automatically identify devices as they are plugged into the outlets of a building. The ATLIS framework takes advantage of smart, connected devices to identify device locations in a building, meter and control their power, and communicate this information to a central database. ATLIS includes five primary capabilities: location identification, communication, control, energy metering, and data storage. A laboratory proof of concept (PoC) demonstrated all but the energy metering capability, and these capabilities were validated using a series of system tests. The PoC was able to identify when a device was plugged into an outlet and the location of the device in the building. When a device was moved, the PoC's dashboard and database were automatically updated with the new location. The PoC implemented controls to devices from the system dashboard so that devices maintained correct schedules regardless of where they were plugged in within the building. ATLIS's primary technology application is improved PLM, but other applications include asset management, energy audits, and interoperability for grid-interactive efficient buildings. An ATLIS-based system could also be used to direct power to critical devices, such as ventilators, during a brownout or blackout. Such a framework is an opportunity to make PLM more widespread and reduce the amount of energy consumed by PPLs in current and future commercial buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗