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DOE OSTI2021

Quantification of Type I Interferon Inhibition by Viral Proteins: Ebola Virus as a Case Study

Type I interferons (IFNs) are cytokines with both antiviral properties and protective roles in innate immune responses to viral infection. They induce an antiviral cellular state and link innate and adaptive immune responses. Yet, viruses have evolved different strategies to inhibit such host responses. One of them is the existence of viral proteins which subvert type I IFN responses to allow quick and successful viral replication, thus, sustaining the infection within a host. We propose mathematical models to characterise the intra-cellular mechanisms involved in viral protein antagonism of type I IFN responses, and compare three different molecular inhibition strategies. We study the Ebola viral protein, VP35, with this mathematical approach. Approximate Bayesian computation sequential Monte Carlo, together with experimental data and the mathematical models proposed, are used to perform model calibration, as well as model selection of the different hypotheses considered. Finally, we assess if model parameters are identifiable and discuss how such identifiability can be improved with new experimental data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Data from: Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land-use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N2O emissions and potential environmental drivers of these fluxes from a three-year establishment-phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures (switchgrass, miscanthus, and poplar), and perennial polycultures (native grass mixture, early successional community, and restored prairie) all grown using best management practices specific to the system. Cumulative three-year N2O emissions from annuals were 142% higher than from perennials, with fertilized perennials 190% higher than unfertilized perennials. Emissions ranged from 3.1 to 19.1 kg N2O-N ha−1 yr−1 for the annuals with continuous corn > corn–soybean–canola rotation and 1.1 to 6.3 kg N2O-N ha−1 yr−1 for perennials. Nitrous oxide peak fluxes typically were associated with precipitation events that closely followed fertilization. Bayesian modeling of N2O fluxes based on measured environmental factors explained 33% of variability across all systems. Models trained on single systems performed well in most monocultures (e.g., R2 = 0.52 for poplar) but notably worse in polycultures (e.g., R2 = 0.17 for early successional, R2 = 0.06 for restored prairie), indicating that simulation models that include N2O emissions should be parameterized specific to particular plant communities. Our results indicate that perennial bioenergy crops in their establishment phase emit less N2O than annual crops, especially when not fertilized. These findings should be considered further alongside yield and other metrics contributing to important ecosystem services.

09 BIOMASS FUELS↗

DOE OSTI2014

Complex matrix multiplication operations with data pre-conditioning in a high performance computing architecture

Mechanisms for performing a complex matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the complex matrix multiplication operation to a first target vector register. The first vector operand comprises a real and imaginary part of a first complex vector value. A complex load and splat operation is performed to load a second complex vector value of a second vector operand and replicate the second complex vector value within a second target vector register. The second complex vector value has a real and imaginary part. A cross multiply add operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the complex matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored in a result vector register.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Simulating Pliocene warmth and a permanent El Niño-like state: The role of cloud albedo

We present that available evidence suggests that during the early Pliocene (4–5 Ma) the mean east-west sea surface temperature (SST) gradient in the equatorial Pacific Ocean was significantly smaller than today, possibly reaching only 1–2°C. The meridional SST gradients were also substantially weaker, implying an expanded ocean warm pool in low latitudes. Subsequent global cooling led to the establishment of the stronger, modern temperature gradients. Given our understanding of the physical processes that maintain the present-day cold tongue in the east, warm pool in the west and hence sharp temperature contrasts, determining the key factors that maintained early Pliocene climate still presents a challenge for climate theories and models. This study demonstrates how different cloud properties could provide a solution. We show that a reduction in the meridional gradient in cloud albedo can sustain reduced meridional and zonal SST gradients, an expanded warm pool and warmer thermal stratification in the ocean, and weaker Hadley and Walker circulations in the atmosphere. Having conducted a range of hypothetical modified cloud albedo experiments, we arrive at our Pliocene simulation, which shows good agreement with proxy SST data from major equatorial and coastal upwelling regions, the tropical warm pool, middle and high latitudes, and available subsurface temperature data. As suggested by the observations, the simulated Pliocene-like climate sustains a robust El Niño-Southern Oscillation despite the reduced mean east-west SST gradient. In conclusion, our results demonstrate that cloud albedo changes may be a critical element of Pliocene climate and that simulating the meridional SST gradient correctly is central to replicating the geographical patterns of Pliocene warmth.

58 GEOSCIENCES↗

DOE OSTI2013

Death-domain associated protein-6 (DAXX) mediated apoptosis in hantavirus infection is counter-balanced by activation of interferon-stimulated nuclear transcription factors

Hantaviruses are negative strand RNA species that replicate predominantly in the cytoplasm. They also activate numerous cellular responses, but their involvement in nuclear processes is yet to be established. Using human umbilical vein endothelial cells (HUVECs), this study investigates the molecular finger-print of nuclear transcription factors during hantavirus infection. The viral-replication-dependent activation of pro-myelocytic leukemia protein (PML) was followed by subsequent localization in nuclear bodies (NBs). PML was also found in close proximity to activated Sp100 nuclear antigen and interferon-stimulated gene 20 kDa protein (ISG-20), but co-localization with death-domain associated protein-6 (DAXX) was not observed. These data demonstrate that hantavirus triggers PML activation and localization in NBs in the absence of DAXX-PLM-NB co-localization. The results suggest that viral infection interferes with DAXX-mediated apoptosis, and expression of interferon-activated Sp100 and ISG-20 proteins may indicate intracellular intrinsic antiviral attempts.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations and splice variants identified in cancer cells are translated. Herein we therefore describe a proteogenomic data integration tool (QUILTS) and illustrate its application to whole genome, transcriptome and global MS peptide sequence datasets generated from a pair of luminal and basal-like breast cancer patient derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS process replicates. Despite over thirty sample replicates, only about 10% of all SNV (somatic and germline) were detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNV without a detectable mRNA transcript were also observed demonstrating the transcriptome coverage was also incomplete (~80%). In contrast to germ-line variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than the luminal tumor raising the possibility of differential translation or protein degradation effects. In conclusion, the QUILTS program integrates DNA, RNA and peptide sequencing to assess the degree to which somatic mutations are translated and therefore biologically active. By identifying gaps in sequence coverage QUILTS benchmarks current technology and assesses progress towards whole cancer proteome and transcriptome analysis.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2024

New results in the CTEQ-TEA global analysis of parton distributions in the nucleon

This report summarizes the latest developments in the CTEQ-TEA global analysis of parton distribution functions (PDFs) in the nucleon. The focus is on recent NNLO fits to high-precision LHC data at 8 and 13 TeV, including Drell–Yan, jet, and top-quark pair production, pursued on the way toward the release of the new generation of CTEQ-TEA general-purpose PDFs. The report also discusses advancements in statistical and numerical methods for PDF determination and uncertainty quantification, highlighting the importance of robust and replicable uncertainties for high-stakes observables. Additionally, it covers phenomenological studies related to PDF determination, such as the interplay of experimental constraints, exploration of correlations between high-x nucleon sea and low-energy parity-violating measurements, fitted charm in the nucleon, the photon PDF in the neutron, and simultaneous SMEFT-PDF analyses.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2013

Nebivolol stimulates mitochondrial biogenesis in 3T3-L1 adipocytes

Highlights: •Nebivolol may act as a partial agonist of β3-adrenergic receptor (AR). •Nebivolol stimulates mitochondrial DNA replication and protein expression. •Nebivolol promotes mitochondrial synthesis via activation of eNOS by β3-AR. -- Abstract: Nebivolol is a third-generation β-adrenergic receptor (β-AR) blocker with additional beneficial effects, including the improvement of lipid and glucose metabolism in obese individuals. However, the underlying mechanism of nebivolol’s role in regulating the lipid profile remains largely unknown. In this study, we investigated the role of nebivolol in mitochondrial biogenesis in 3T3-L1 adipocytes. Exposure of 3T3-L1 cells to nebivolol for 24 h increased mitochondrial DNA copy number, mitochondrial protein levels and the expression of transcription factors involved in mitochondrial biogenesis, including PPAR-γ coactivator-1α (PGC-1α), Sirtuin 3 (Sirt3), mitochondrial transcription factor A (Tfam) and nuclear related factor 1 (Nrf1). These changes were accompanied by an increase in oxygen consumption and in the expression of genes involved in fatty acid oxidation and antioxidant enzymes in 3T3-L1 adipocytes, including nebivolol-induced endothelial nitric oxide synthase (eNOS), as well as an increase in the formation of cyclic guanosine monophosphate (cGMP). Pretreatment with NG-nitro-L-arginine methyl ester (l-NAME) attenuated nebivolol-induced mitochondrial biogenesis, as did the soluble guanylate cyclase inhibitor, ODQ. Treatment with nebivolol and β3-AR blocker SR59230A markedly attenuated PGC-1α, Sirt3 and manganese superoxide dismutase (MnSOD) protein levels in comparison to treatment with nebivolol alone. These data indicate that the mitochondrial synthesis and metabolism in adipocytes that is promoted by nebivolol is primarily mediated through the eNOS/cGMP-dependent pathway and is initiated by the activation of β3-AR receptors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Elemental mercury neurotoxicity and clinical recovery of function: A review of findings, and implications for occupational health

Highlights: • Substantial human studies, both acute and chronic, are available for evaluation. • Elemental mercury induced toxicity often displays substantial recovery. • Numerous examples fail to show full recovery from elemental mercury toxicity. • Recovery from elemental mercury toxicity is affected by age and endpoint. • Few animal studies have been directed to elemental mercury toxicity recovery. This paper assessed approximately 30 studies, mostly involving occupationally exposed subjects, concerning the extent to which those who developed elemental mercury (Hg)-induced central and/or peripheral neurotoxicities from chronic or acute exposures recover functionality and/or performance. While some recovery occurred in the vast majority of cases, the extent of such recoveries varied considerably by individual and endpoint. Factors accounting for the extensive inter-individual variation in toxicity and recovery were not specifically assessed such as age, gender, diet, environmental enrichment, chelation strategies and dose-rate. While the data indicate that psychomotor endpoints often show substantial and relatively rapid (i.e., 2–6 months) recovery and that neuropsychological endpoints display slower and less complete recovery, generalizations are difficult due to highly variable study designs, use of different endpoints measured between studies, different Hg exposures based on blood/urine concentrations and Hg dose-rates, the poor capacity for replicating findings due to the unpredictable/episodic nature of harmful exposures to elemental Hg, and the inconsistency of the initiation of studies after induced toxicities and the differing periods of follow up during recovery periods. Finally, there is strikingly limited animal model literature on the topic of recovery/reversibility of elemental Hg toxicity, a factor which significantly contributes to the overall marked uncertainties for predicting the rate and magnitude of recovery and the factors that affect it.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed analysis and relative quantification, and provides 3×higher throughput than iTRAQ (isobaric tags for absolute and relative quantification)-4-based methods with high intraand inter-laboratory reproducibility. The workflow was systematically characterized and benchmarked across three independent laboratories using two distinct breast cancer subtypes from patient-derived xenograft models to enable assessment of proteome and phosphoproteome depth and quantitative reproducibility. Each plex consisted of ten samples, each being 300 µg of peptide derived from <50 mg of wet-weight tissue. Of the 10,000 proteins quantified per sample, we could distinguish 7,700 human proteins derived from tumor cells and 3100 mouse proteins derived from the surrounding stroma and blood. The maximum deviation across replicates and laboratories was <7%, and the interlaboratory correlation for TMT ratio–based comparison of the two breast cancer subtypes was r > 0.88. The maximum deviation for the phosphoproteome coverage was <24% across laboratories, with an average of >37,000 quantified phosphosites per sample and differential quantification correlations of r > 0.72. The full procedure, including sample processing and data generation, can be completed within 10 d for ten tissue samples, and 100 samples can be analyzed in ~4 months using a single LC-MS/MS instrument. The high quality, depth, and reproducibility of the data obtained both within and across laboratories should enable new biological insights to be obtained from mass spectrometry-based proteomics analyses of cells and tissues together with proteogenomic data integration.

Mertins, Philipp↗

DOE OSTI2017

Should the Standard Count Be Excluded from Neutron Probe Calibration?

About 6 decades after its introduction, the neutron probe remains one of the most accurate methods for indirect measurement of soil moisture content. Traditionally, the calibration of a neutron probe involves the ratio of the neutron count in the soil to a standard count, which is the neutron count in the fixed environment such as the probe shield or a specially-designed calibration tank. The drawback of this count-ratio-based calibration is that the error in the standard count is carried through to all the measurements. An alternative calibration is to use the neutron counts only, not the ratio, with proper correction for radioactive decay and counting time. To evaluate both approaches, the shield counts of a neutron probe used for three decades were analyzed. The results show that the surrounding conditions have a substantial effect on the standard count. The error in the standard count also impacts the calculation of water storage and could indicate false consistency among replicates. The analysis of the shield counts indicates negligible aging effect of the instrument over a period of 26 years. It is concluded that, by excluding the standard count, the use of the count-based calibration is appropriate and sometimes even better than ratio-based calibration. The count-based calibration is especially useful for historical data when the standard count was questionable or absent

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Savannah River Site HB-Line Plutonium Oxide Production Process Simulation Model - 17458

The AFS II/Plutonium Oxide Production process is in its initial operational phase at the Savannah River Site's (SRS) HB-Line. The process is new for the facility where it is being performed, but the facility itself has been in use on and off for over 50 years. Beginning this process inside the facility has resulted in multiple process delays, due to both equipment issues and process restrictions. In order to better understand the process and to identify ways to improve facility performance, Savannah River Nuclear Solutions (SRNS), in conjuncture with Newport News Shipbuilding (NNS), developed the HB-Line Process Simulation Model. This tool completely replicates the operations that comprise the HB-Line process and simulates all of the constraints associated with the process. The model realistically accounts for the number of personnel required for a process step, the time required for a process step to occur, rules related to the parallel operation of process steps, and realistic equipment and operational delay data. The result is a tool that allows SRNS to test different scenarios for improving the process throughput, while realistically accounting for potential process delays and restrictions. The tool is currently in use and has allowed SRNS to present to their customer, the National Nuclear Security Administration (NNSA), estimated production capabilities over wide-ranging timetables and assumptions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Molecular and biochemical characterization of rice developed through conventional integration of nDart1-0 transposon gene

Mutations, the genetic variations in genomic sequences, play an important role in molecular biology and biotechnology. During DNA replication or meiosis, one of the mutations is transposons or jumping genes. An indigenous transposon nDart1-0 was successfully introduced into local indica cultivar Basmati-370 from transposon-tagged line viz., GR-7895 (japonica genotype) through conventional breeding technique, successive backcrossing. Plants from segregating populationsshowed variegated phenotypes were tagged as BM-37 mutants. Blast analysis of the sequence data revealed that the GTP-binding protein, located on the BAC clone OJ1781_H11 of chromosome 5, contained an insertion of DNA transposon nDart1-0. The nDart1-0 has “A” at position 254 bp, whereas nDart1 homologs have “G”, which efficiently distinguishes nDart1-0 from its homologs. The histological analysis revealed that the chloroplast of mesophyll cells in BM-37 was disrupted with reduction in size of starch granules and higher number of osmophillic plastoglobuli, which resulted in decreased chlorophyll contents and carotenoids, gas exchange parameters (Pn, g, E, Ci), and reduced expression level of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development. Along with the rise of GTP protein, the salicylic acid (SA) and gibberellic acid (GA) and antioxidant contents(SOD) and MDA levels significantly enhanced, while, the cytokinins (CK), ascorbate peroxidase (APX), catalase (CAT), total flavanoid contents (TFC) and total phenolic contents (TPC) significantly reduced in BM-37 mutant plants as compared with WT plants. These results support the notion that GTP-binding proteins influence the process underlying chloroplast formation. Therefore, it is anticipated that to combat biotic or abiotic stress conditions, the nDart1-0 tagged mutant (BM-37) of Basmati-370 would be beneficial.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Advanced Reactor Control and Operations (ARCO): A University Research Facility for Developing Optimized Digital Control Rooms

The Advanced Reactor Control and Operations (ARCO) facility was constructed in January 2018 to serve as a test bed for advanced reactor control rooms and operator support systems. Since then, it has supported human-machine interface user experience research, fault detection and mitigation technology development, control room concept of operations development, and remote operations research. ARCO serves as the control room for the Compact Integral Effects Test (CIET) facility, which replicates the primary-side flow paths and thermal-hydraulic behavior of a fluoride-salt-cooled high-temperature reactor (FHR) using simulant fluids and scaling principles. New reactor designs feature different operating conditions and scenarios than those in existing reactors. ARCO supports the research and development of digital tools for operator communications, intuitive real-time data analysis, online health monitoring and prognostics, and control room cybersecurity. By integrating these different technologies, ARCO acts as a prototypical control system to iteratively develop methods and tools of operation in advanced small modular nuclear reactors. This paper describes the features of and challenges to operating advanced small modular reactors underlying the design basis for ARCO and its operator support systems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Evolving Metrics for Resource Adequacy Assessment

Resource adequacy analysis quantifies the likelihood of capacity shortfall on a power system in a probabilistic manner. Using a combination of statistical techniques and power system fundamentals, the analysis typically evaluates hundreds or thousands of stochastic random samples (replications) of varying load, generator outages, variable renewable energy availability, and other aspects of power system uncertainty. In this range of uncertainty, there are - at times - periods where the power system's available resources are insufficient to meet system demand, referred to as a shortfall event. Today's power systems' rapidly evolving generation mix is changing the types of data needed by system planners and regulators, which can often render traditional resource adequacy metrics insufficient for ensuring resource adequacy for tomorrow's grid. In this paper we provide a critical assessment of traditional measures of shortfall risk in power systems, discussing their shortcomings and how they compare to metrics used in other domains. From this analysis we propose four steps forward for improving power system resource adequacy risk metrics in the future.

ENERGY PLANNING, POLICY, AND ECONOMY,POWER TRANSMI↗

DOE OSTI2023

Beyond Expected Values Evolving Metrics for Resource Adequacy Assessment

ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2014

A molecular thermodynamic model for the stability of hepatitis B capsids

Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Data for Approximately 15% of Miscanthus Yield is Lost at Current Commercial Cutting Heights in Iowa

Various works have quantitatively characterized the effects of environmental and management factors on Miscanthus x giganteus Greef et Deu ( mxg ) yield and, therefore, anticipated land requirement per unit production. However, little work has addressed the effects of cutting height, which may significantly contribute to the difference between the standing aboveground biomass at harvest (i.e., biological yield) and harvested yield. This study quantitatively characterized the effect of cutting height using a replicated nitrogen trial of a 5-year-old mxg stand in southeast Iowa and related this information to observations of cutting height in nearby commercial fields. Nitrogen fertilizer did not significantly change the relationship of the stem segment mass to length, and overall, a 1-cm stem segment contributes 0.5% of the total stem biomass within the bottom 44 cm of the stem. This results in an average harvest loss of 15% of the aboveground standing biomass when cutting at 30 cm, typically seen in commercial mxg fields in eastern Iowa. Cutting height should be considered when accurately predicting commercial mxg harvest yields and changes in soil organic carbon in a commercial mxg agroecosystem.

Biomass Analytics↗