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DOE OSTI2014

Effects of Wind Energy Development on Nesting Ecology of Greater Prairie-Chickens in Fragmented Grasslands: Wind Power and Prairie-Chickens

Wind energy is targeted to meet 20% of U.S. energy needs by 2030, but new sites for development of renewable energy may overlap with important habitats of declining populations of grassland birds. Greater Prairie-Chickens (Tympanuchus cupido) are an obligate grassland bird species predicted to respond negatively to energy development. We used a modified before–after control–impact design to test for impacts of a wind energy development on the reproductive ecology of prairie-chickens in a 5-year study. We located 59 and 185 nests before and after development, respectively, of a 201 MW wind energy facility in Greater Prairie-Chicken nesting habitat and assessed nest site selection and nest survival relative to proximity to wind energy infrastructure and habitat conditions. Proximity to turbines did not negatively affect nest site selection (β = 0.03, 95% CI = -1.2–1.3) or nest survival (β = -0.3, 95% CI = -0.1). Instead, nest site selection and survival were strongly related to vegetative cover and other local conditions determined by management for cattle production. Integration of our project results with previous reports of behavioral avoidance of oil and gas facilities by other species of prairie grouse suggests new avenues for research to mitigate impacts of energy development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

A partition of the combined impacts of socioeconomic development and climate variation on economic risks of riverine floods

Nonstationarities in both climate and socioeconomic systems play a role in flood risk. Based on a data-driven case study in an urbanized watershed subjected to nonstationary factors in climate (rain, snow, and rain on snow) and socioeconomic conditions (e.g., built environment market changes), a multi-scale, multi-model approach was adopted to develop local-scale flood hazard predictions and an analytical framework was developed to quantify the associated flood risk. The case study shows that socioeconomic development can have a comparable contribution as climate variability when evaluating the expected annual damage. Here, the relative contributions from socioeconomic development, in some cases, do not necessarily compound the risk, but can, in fact, act as a mitigating factor in annualized risk. Timelines of risk management planning are an important factor to consider. Socioeconomic factors such as market value can produce non-linear and reversed trends in flood impact assessments within the 10-year time frame. Further, the nonstationarity of climate and development conditions together was shown to cause up to 43% of the variation in risk estimates and up to 70% of the variation in the benefit-cost effectiveness.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

DEVELOPMENT OF A HYBRID LAGRANGIAN-EULERIAN MODEL TO DESCRIBE SPARK-IGNITION PROCESSES AT ENGINE-LIKE TURBULENT FLOW CONDITIONS

With the engine technology moving towards more challenging (highly dilute and boosted) operation, spark-ignition processes play a key role in determining flame propagation and completeness of the combustion process. On the computational side, there is plenty of spark-ignition models available in literature and validated under conventional, stoichiometric SI operation. Nevertheless, these models need to be expanded and developed on more physical grounds since at challenging operation they are not truly predictive. This paper reports on the development of a dedicated model for the spark-ignition event at non-quiescent, engine-like conditions, performed in the commercial CFD code CONVERGE. The developed methodology leverages previous findings that have expanded the use and improved the accuracy of Eulerian-type energy deposition models. In this work, the Eulerian energy deposition is coupled at every computational time-step with a Lagrangian-type evolution of the spark channel. Typical features such as spark channel elongation, stretch, attachment to the electrodes are properly described to deliver realistic energy deposition along the channel during the entire ignition process. The numerical results are validated against schlieren images from an optical constant volume chamber and show the improvement in the simulation of the spark channel during the entire ignition event, with respect to the most commonly used energy deposition approach. Further development pathways are discussed to provide more physics-based features from the developed ignition model in the future.

Scarcelli, Riccardo↗

DOE OSTI2016

A Methodology for the Development of a Reliability Database for an Advanced Reactor Probabilistic Risk Assessment

GE Hitachi Nuclear Energy (GEH) and Argonne National Laboratory are currently engaged in a joint effort to modernize and develop probabilistic risk assessment (PRA) techniques for advanced non-light water reactors. At a high level the primary outcome of this project will be the development of next-generation PRA methodologies that will enable risk-informed prioritization of safety- and reliability-focused research and development, while also identifying gaps that may be resolved through additional research. A subset of this effort is the development of a reliability database (RDB) methodology to determine applicable reliability data for inclusion in the quantification of the PRA. The RDB method developed during this project seeks to satisfy the requirements of the Data Analysis element of the ASME/ANS Non-LWR PRA standard. The RDB methodology utilizes a relevancy test to examine reliability data and determine whether it is appropriate to include as part of the reliability database for the PRA. The relevancy test compares three component properties to establish the level of similarity to components examined as part of the PRA. These properties include the component function, the component failure modes, and the environment/boundary conditions of the component. The relevancy test is used to gauge the quality of data found in a variety of sources, such as advanced reactor-specific databases, non-advanced reactor nuclear databases, and non-nuclear databases. The RDB also establishes the integration of expert judgment or separate reliability analysis with past reliability data. This paper provides details on the RDB methodology, and includes an example application of the RDB methodology for determining the reliability of the intermediate heat exchanger of a sodium fast reactor. The example explores a variety of reliability data sources, and assesses their applicability for the PRA of interest through the use of the relevancy test.

Grabaskas, Dave↗

DOE OSTI2024

DEVELOPMENT AND DEMONSTRATION TESTBED FOR THE REMOTE OPERATIONS AND MONITORING OF MICROREACTORS

The nuclear industry is rapidly developing many advanced-reactor concepts for near-term deployment in both traditional and non-traditional nuclear-powered applications. One such category of advanced reactor is the microreactor, a class of reactor with less than 20MWth power output, intended for applications where the economics or logistics of traditional power sources are difficult. This includes applications such as remote communities, mining sites, defense installations, or humanitarian and disaster-relief missions. One key enabling feature for the successful deployment of microreactors is a remote operations capability. Remote operations provide monitoring and control capabilities which can significantly reduce staffing costs by eliminating the need for licensed operators at each reactor facility and improve the economic viability for microreactor deployment. A remote concept of operations is not currently an established capability in the nuclear industry. In addition, no demonstration microreactor is expected to complete construction or go critical until at least 2026. This leaves two major capability gaps: the successful demonstration of a remote concept of operations for microreactors and a test bed suitable for said demonstration. Both gaps must be addressed in order to advance the remote concepts of nuclear operation and, more broadly, microreactors themselves from paper to reality. This paper aims to fill these gaps and describes a test bed that would support development and deployment of a remote concept of nuclear operations, initial experimental results from that test bed, and the application of the test bed and experimental results for a digital-twin-based remote concept of operations underdevelopment at Idaho National Laboratory (INL). The platform chosen as a remote concept of nuclear operations test bed is the Single Primary Heat Extraction and Removal Emulator, known as SPHERE, located at INL. SPHERE is a small-scale non-nuclear test bed that emulates thermal behavior of a microreactor. The small-scale and non-nuclear nature of SHPERE limit safety concerns associated with remote operations while still providing the physical response representative of a microreactor. A network connection was added to SPHERE that enables remote-monitoring capability. This allows for real-time data streaming to networked workstations, data historians, and human-machine interfaces (HMIs). These are all critical components in a remote concept of operations, thus providing a robust development and demonstration platform. An initial experiment was performed using the SPHERE remote operations testbed. This included running a comprehensively instrumented SPHERE through a series of steady-state and transient operating scenarios in both normal and abnormal operating conditions, all while streaming live test data to a remote HMI and data warehouse. This initial experiment served three purposes: (1) characterizing the response of SPHERE, (2) demonstrating the remote connection to SPHERE, and (3) providing a baseline data set for development of a digital-twin-based remote concept of operations that is under development at INL.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2018

Numerical Model Development and Validation for the WECCCOMP Control Competition

This paper details the development and validation of a numerical model of the Wavestar wave energy converter (WEC) developed in WEC-Sim. This numerical model was developed in support of the WEC Control Competition (WECCCOMP), a competition with the objective of maximizing WEC performance over costs through innovative control strategies. WECCCOMP has two stages: numerical implementation of control strategies, and experimental implementation. The work presented in this paper is for support of the numerical implementation, where contestants are provided a WEC-Sim model of the 1:20 scale Wavestar device to develop their control algorithms. This paper details the development of the numerical model in WEC-Sim and of its validation through comparison to experimental data.

16 TIDAL AND WAVE POWER↗

DOE OSTI2014

Toward the development of intrafraction tumor deformation tracking using a dynamic multi-leaf collimator

Purpose: Intrafraction deformation limits targeting accuracy in radiotherapy. Studies show tumor deformation of over 10 mm for both single tumor deformation and system deformation (due to differential motion between primary tumors and involved lymph nodes). Such deformation cannot be adapted to with current radiotherapy methods. The objective of this study was to develop and experimentally investigate the ability of a dynamic multi-leaf collimator (DMLC) tracking system to account for tumor deformation. Methods: To compensate for tumor deformation, the DMLC tracking strategy is to warp the planned beam aperture directly to conform to the new tumor shape based on real time tumor deformation input. Two deformable phantoms that correspond to a single tumor and a tumor system were developed. The planar deformations derived from the phantom images in beam's eye view were used to guide the aperture warping. An in-house deformable image registration software was developed to automatically trigger the registration once new target image was acquired and send the computed deformation to the DMLC tracking software. Because the registration speed is not fast enough to implement the experiment in real-time manner, the phantom deformation only proceeded to the next position until registration of the current deformation position was completed. The deformation tracking accuracy was evaluated by a geometric target coverage metric defined as the sum of the area incorrectly outside and inside the ideal aperture. The individual contributions from the deformable registration algorithm and the finite leaf width to the tracking uncertainty were analyzed. Clinical proof-of-principle experiment of deformation tracking using previously acquired MR images of a lung cancer patient was implemented to represent the MRI-Linac environment. Intensity-modulated radiation therapy (IMRT) treatment delivered with enabled deformation tracking was simulated and demonstrated. Results: The first experimental investigation of adapting to tumor deformation has been performed using simple deformable phantoms. For the single tumor deformation, the A{sub u}+A{sub o} was reduced over 56% when deformation was larger than 2 mm. Overall, the total improvement was 82%. For the tumor system deformation, the A{sub u}+A{sub o} reductions were all above 75% and the total A{sub u}+A{sub o} improvement was 86%. Similar coverage improvement was also found in simulating deformation tracking during IMRT delivery. The deformable image registration algorithm was identified as the dominant contributor to the tracking error rather than the finite leaf width. The discrepancy between the warped beam shape and the ideal beam shape due to the deformable registration was observed to be partially compensated during leaf fitting due to the finite leaf width. The clinical proof-of-principle experiment demonstrated the feasibility of intrafraction deformable tracking for clinical scenarios. Conclusions: For the first time, we developed and demonstrated an experimental system that is capable of adapting the MLC aperture to account for tumor deformation. This work provides a potentially widely available management method to effectively account for intrafractional tumor deformation. This proof-of-principle study is the first experimental step toward the development of an image-guided radiotherapy system to treat deforming tumors in real-time.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2014

SU-E-E-03: Developing Solutions to Critical Radiation Oncology Challenges in Tanzania

Purpose: Develop solutions to critical medical physics challenges in Tanzania. Methods: In September of 2013 we began working with Jumaa Bin Dachi, a Therapy Physicist at the Ocean Road Cancer Institute in Dar es Salaam, Tanzania. We developed a bi-lateral learning partnership over the course of eight qualitative Skype meetings with Jumaa. From these meetings we have ascertained that there is a gap between the installation of new equipment and treating patients. This gap has often been overlooked by international partners attempting to improve radiation therapy access. Relationships with academic institutions abroad can fill these gaps, and lead to sustained care of patients needing radiation. Results: Our efforts are best given in a supporting role to help develop solutions and new technology that can reduce the burden on the Medical Physicist. Solutions may include: training material, support for radiation therapy classes, development of appropriate local protocols, and peer-review on documents being produced. New technology needs to focus around simple and easy field shaping, improved patient imaging systems, and systems for patient set-up. We believe our work can help alleviate some of the burdens faced by this institute. Conclusion: While we are just in the beginning stage of this partnership, we believe there is great potential for success between both parties. We hope that the Ocean Road Cancer Institute will benefit from potential funding and resources by partnering with a High Income Country to develop affordable solutions to clinical problems in Tanzania.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-C-17A-02: Sirius MRI Markers for Prostate Post-Implant Assessment: MR Protocol Development

Purpose: Currently, CT is used to visualize prostate brachytherapy sources, at the expense of accurate structure contouring. MRI is superior to CT for anatomical delineation, but the sources appear as voids on MRI images. Previously we have developed Sirius MRI markers (C4 Imaging) to replace spacers to assist source localization on MRI images. Here we develop an MRI pulse sequence protocol that enhances the signal of these markers to enable MRI-only post-implant prostate dosimetric analysis. Methods: To simulate a clinical scenario, a CIRS multi-modality prostate phantom was implanted with 66 markers and 86 sources. The implanted phantom was imaged on both 1.5T and 3.0T GE scanners under various conditions, different pulse sequences (2D fast spin echo [FSE], 3D balanced steadystate free precession [bSSFP] and 3D fast spoiled gradient echo [FSPGR]), as well as varying amount of padding to simulate various patient sizes and associated signal fall-off from the surface coil elements. Standard FSE sequences from the current clinical protocols were also evaluated. Marker visibility, marker size, intra-marker distance, total scan time and artifacts were evaluated for various combinations of echo time, repetition time, flip angle, number of excitations, bandwidth, slice thickness and spacing, fieldof- view, frequency/phase encoding steps and frequency direction. Results: We have developed a 3D FSPGR pulse sequence that enhances marker signal and ensures the integrity of the marker shape while maintaining reasonable scan time. For patients contraindicated for 3.0T, we have also developed a similar sequence for 1.5T scanners. Signal fall-off with distance from prostate to coil can be compensated mainly by decreasing bandwidth. The markers are not visible using standard FSE sequences. FSPGR sequences are more robust for consistent marker visualization as compared to bSSFP sequences. Conclusion: The developed MRI pulse sequence protocol for Sirius MRI markers assists source localization to enable MRIonly post-implant prostate dosimetric analysis. S.J. Frank is a co-founder of C4 Imaging (manufactures the MRI markers)

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-CD-207B-01: BEST IN PHYSICS (IMAGING): Development of High Brightness Multiple-Pixel X-Ray Source Using Oxide Coated Cathodes

Purpose: To develop and characterize a high brightness multiple-pixel thermionic emission x-ray (MPTEX) source. Methods: Multiple-pixel x-ray sources allow for designs of novel x-ray imaging techniques, such as fixed gantry CT, digital tomosynthesis, tetrahedron beam computed tomography, etc. We are developing a high-brightness multiple-pixel thermionic emission x-ray (MPTEX) source based on oxide coated cathodes. Oxide cathode is chosen as the electron source due to its high emission current density and low operating temperature. A MPTEX prototype has been developed which may contain up to 41 micro-rectangular oxide cathodes in 4 mm pixel spacing. Electronics hardware was developed for source control and switching. The cathode emission current was evaluated and x-ray measurements were performed to estimate the focal spot size. Results: The oxide cathodes were able to produce ∼110 mA cathode current in pulse mode which corresponds to an emission current density of 0.55 A/cm{sup 2}. The maximum kVp of the MPTEX prototype currently is limited to 100 kV due to the rating of high voltage feedthrough. Preliminary x-ray measurements estimated the focal spot size as 1.5 × 1.3 mm{sup 2}. Conclusion: A MPTEX source was developed with thermionic oxide coated cathodes and preliminary source characterization was successfully performed. The MPTEX source is able to produce an array of high brightness x-ray beams with a fast switching speed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Development of Distributed Microgrid Controllers Using HELICS [SWR-21-94]

Development of Distributed Microgrid Controllers Using HELICS uses HELICS framework develop distributed microgrid controllers (DMCs) for coordinated grid service. Development of Distributed Microgrid Controllers Using HELICS includes thirteen agents, including OpenDSS agent, data manager agent, and eleven DMC agents. Development of Distributed Microgrid Controllers Using HELICS can be used as a standard framework to develop fully distributed control solutions that dispatches simulated DERs in simulation platform.

Wang, Jing↗

DOE OSTI2022

Sex Determination and Ovarian Development in Reptiles and Amphibians: From Genetic Pathways to Environmental Influences

Background: Reptiles and amphibians provide untapped potential for discovering how a diversity of genetic pathways and environmental conditions are incorporated into developmental processes that can lead to similar functional outcomes. These groups display a multitude of reproductive strategies, and whereas many attributes are conserved within groups and even across vertebrates, several aspects of sexual development show considerable variation. Summary: Here, in this review, we focus our attention on the development of the reptilian and amphibian ovary. First, we review and describe the events leading to ovarian development, including sex determination and ovarian maturation, through a comparative lens. We then describe how these events are influenced by environmental factors, focusing on temperature and exposure to anthropogenic chemicals. Lastly, we identify critical knowledge gaps and future research directions that will be crucial to moving forward in our understanding of ovarian development and the influences of the environment in reptiles and amphibians. Key Messages: Reptiles and amphibians provide excellent models for understanding the diversity of sex determination strategies and reproductive development. However, a greater understanding of the basic biology of these systems is necessary for deciphering the adaptive and potentially disruptive implications of embryo-by-environment interactions in a rapidly changing world.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Development of Community, Capabilities and Understanding Through Unmanned Aircraft-Based Atmospheric Research: The LAPSE-RATE Campaign

Members of the international community developing unmanned aircraft for atmospheric research conducted a highly-successful coordinated flight week in Colorado during summer 2018 to collect measurements, develop capabilities, and enhance community in the field. Because unmanned aircraft systems (UAS) offer new perspectives on the atmosphere, their use in atmospheric science is expanding rapidly. In support of this growth, the International Society for Atmospheric Research using Remotely-piloted Aircraft (ISARRA) has been developed and have convened annual meetings and 'flight weeks'. The 2018 flight week, dubbed the Lower Atmospheric Profiling Studies at Elevation - a Remotely-piloted Aircraft Team Experiment (LAPSE-RATE), involved a one-week deployment to Colorado's San Luis Valley. Between 14-20 July 2018 over 100 students, scientists, engineers, pilots and outreach coordinators conducted an intensive field operation using unmanned aircraft and ground-based assets to develop datasets, community, and capabilities. In addition to a coordinated 'community day' which offered a chance for groups to share their aircraft and science with the San Luis Valley community, LAPSE-RATE participants conducted nearly 1300 research flights totaling over 250 flight hours. The measurements collected have been used to advance capabilities (instrumentation, platforms, sampling techniques and modeling tools), conduct a detailed system intercomparison study, develop new collaborations, and foster community support for the use of UAS in atmospheric science.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Process-Oriented Diagnostics: Principles, Practice, Community Development, and Common Standards

Process-oriented diagnostics (PODs) aim to provide feedback for model developers through model analysis based on physical hypotheses. However, the step from a diagnostic based on relationships among variables, even when hypothesis driven, to specific guidance for revising model formulation or parameterizations can be substantial. The POD may provide more information than a purely performance-based metric, but a gap between POD principles and providing actionable information for specific model revisions can remain. Furthermore, in coordinating diagnostics development, there is a trade-off between freedom for the developer, aiming to capture innovation, and near-term utility to the modeling center. Best practices that allow for the former, while conforming to specifications that aid the latter, are important for community diagnostics development that leads to tangible model improvements. Promising directions to close the gap between principles and practice include the interaction of PODs with perturbed physics experiments and with more quantitative process models as well as the inclusion of personnel from modeling centers in diagnostics development groups for immediate feedback during climate model revisions. Examples are provided, along with best-practice recommendations, based on practical experience from the NOAA Model Diagnostics Task Force (MDTF). Common standards for metrics and diagnostics that have arisen from a collaboration between the MDTF and the Department of Energy’s Coordinated Model Evaluation Capability are advocated as a means of uniting community diagnostics efforts.

58 GEOSCIENCES↗

DOE OSTI2022

Cloud Radiative Effects on MJO Development in DYNAMO

Observed Madden-Julian Oscillation (MJO) events are examined with the aid of regional model simulations to understand the role of cloud radiative effects in the MJO development. The importance of this role is demonstrated by the absence of MJO in the model simulations that contain no cloud radiative effects. Comparisons of model simulations with and without the cloud radiative effects and observation help identify the major processes arising from those effects. Those processes develop essentially from heating in the upper-troposphere due to shortwave absorption within anvil clouds in the upper troposphere and the convergence of longwave radiation in the middle-upper troposphere, with a peak at 300-hPa, during deep convection. First, that heating adds extra buoyancy and accelerates the rising motion in the upper troposphere in deep convection. The vertical acceleration in the upper troposphere creates a vacuum effect and demands for more deep convection to develop. Second, in response to that demand and required by mass balance arises the large-scale horizontal and vertical mass, moisture, and energy convergence. It strengthens deep convection and, with the feedback from continuing cloud radiative effect, creates conditions that can perpetuate deep convection and MJO development. That perpetuation does not occur however because those processes arising from the cloud radiative heating in the upper troposphere stabilize the troposphere till it supports no further deep convection. Weakening deep convection reduces cloud radiative effects. The subsequent reduction of the vacuum effect in the upper troposphere diminishes deep convection completing an MJO cycle. These results advance our understanding of the development of the MJO in the radiative-convective system over warm waters in the tropics. They show that while the embryo of intraseasonal oscillation may exist in the system its growth/development is largely dependent on cloud radiative effects and feedbacks.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens

Background: The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota. Results: Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M. Conclusions: These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

16S↗

DOE OSTI2015

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

Background: Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Results: Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. Conclusions: In this first genome-wide analysis of a modified histone in a woody tissue, we optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Development and validation of a 30-day mortality index based on pre-existing medical administrative data from 13,323 COVID-19 patients: The Veterans Health Administration COVID-19 (VACO) Index

Background Available COVID-19 mortality indices are limited to acute inpatient data. Using nationwide medical administrative data available prior to SARS-CoV-2 infection from the US Veterans Health Administration (VA), we developed the VA COVID-19 (VACO) 30-day mortality index and validated the index in two independent, prospective samples. Methods and findings We reviewed SARS-CoV-2 testing results within the VA between February 8 and August 18, 2020. The sample was split into a development cohort (test positive between March 2 and April 15, 2020), an early validation cohort (test positive between April 16 and May 18, 2020), and a late validation cohort (test positive between May 19 and July 19, 2020). Our logistic regression model in the development cohort considered demographics (age, sex, race/ethnicity), and pre-existing medical conditions and the Charlson Comorbidity Index (CCI) derived from ICD-10 diagnosis codes. Weights were fixed to create the VACO Index that was then validated by comparing area under receiver operating characteristic curves (AUC) in the early and late validation cohorts and among important validation cohort subgroups defined by sex, race/ethnicity, and geographic region. We also evaluated calibration curves and the range of predictions generated within age categories. 13,323 individuals tested positive for SARS-CoV-2 (median age: 63 years; 91% male; 42% non-Hispanic Black). We observed 480/3,681 (13%) deaths in development, 253/2,151 (12%) deaths in the early validation cohort, and 403/7,491 (5%) deaths in the late validation cohort. Age, multimorbidity described with CCI, and a history of myocardial infarction or peripheral vascular disease were independently associated with mortality–no other individual comorbid diagnosis provided additional information. The VACO Index discriminated mortality in development (AUC = 0.79, 95% CI: 0.77–0.81), and in early (AUC = 0.81 95% CI: 0.78–0.83) and late (AUC = 0.84, 95% CI: 0.78–0.86) validation. The VACO Index allows personalized estimates of 30-day mortality after COVID-19 infection. For example, among those aged 60–64 years, overall mortality was estimated at 9% (95% CI: 6–11%). The Index further discriminated risk in this age stratum from 4% (95% CI: 3–7%) to 21% (95% CI: 12–31%), depending on sex and comorbid disease. Conclusion Prior to infection, demographics and comorbid conditions can discriminate COVID-19 mortality risk overall and within age strata. The VACO Index reproducibly identified individuals at substantial risk of COVID-19 mortality who might consider continuing social distancing, despite relaxed state and local guidelines.

60 APPLIED LIFE SCIENCES↗