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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗
DOE OSTI2021

Ca2+ Effects on Fe(II) Interactions with Mn-Binding Sites in Mn-Depleted Oxygen-Evolving Complexes of Photosystem II and on Fe Replacement of Mn in Mn-Containing, Ca-Depleted Complexes

Fe(II) cations bind with high efficiency and specificity at the high-affinity (HA), Mn-binding site (termed the “blocking effect” since Fe blocks further electron donation to the site) of the oxygen-evolving complex (OEC) in Mn-depleted, photosystem II (PSII) membrane fragments (Semin et al. in Biochemistry 41:5854, 2002). Furthermore, Fe(II) cations can substitute for 1 or 2Mn cations (pH dependent) in Ca-depleted PSII membranes (Semin et al. in Journal of Bioenergetics and Biomembranes 48:227, 2016; Semin et al. in Journal of Photochemistry and Photobiology B 178:192, 2018). In the current study, we examined the effect of Ca2+ cations on the interaction of Fe(II) ions with Mn-depleted [PSII(-Mn)] and Ca-depleted [PSII(-Ca)] photosystem II membranes. We found that Ca2+ cations (about 50 mM) inhibit the light-dependent oxidation of Fe(II) (5 µM) by about 25% in PSII(-Mn) membranes, whereas inhibition of the blocking process is greater at about 40%. Blocking of the HA site by Fe cations also decreases the rate of charge recombination between QA- and YZ•+ from t1/2?=?30 ms to 46 ms. However, Ca2+ does not affect the rate during the blocking process. An Fe(II) cation (20 µM) replaces 1Mn cation in the Mn4CaO5 catalytic cluster of PSII(-Ca) membranes at pH 5.7 but 2 Mn cations at pH 6.5. In the presence of Ca2+ (10 mM) during the substitution process, Fe(II) is not able to extract Mn at pH 5.7 and extracts only 1Mn at pH 6.5 (instead of two without Ca2+). Measurements of fluorescence induction kinetics support these observations. Inhibition of Mn substitution with Fe(II) cations in the OEC only occurs with Ca2+ and Sr2+ cations, which are also able to restore oxygen evolution in PSII(-Ca) samples. Nonactive cations like La3+, Ni2+, Cd2+, and Mg2+ have no influence on the replacement of Mn with Fe. These results show that the location and/or ligand composition of one Mn cation in the Mn4CaO5 cluster is strongly affected by calcium depletion or rebinding and that bound calcium affects the redox potential of the extractable Mn4 cation in the OEC, making it resistant to reduction.

calcium↗
DOE OSTI2023

Techno-Economic Analysis and Market Potential of Geological Thermal Energy Storage (GeoTES) Charged With Solar Thermal and Heat Pumps into Depleted Oil/Gas Reservoirs and Shallow Reservoirs: A Technology Overview: Preprint

Depleted oil/gas reservoirs represent a waste of underground resources and investments of drilling, and also a potential risk to the earth's environment. Geologic thermal energy storage (GeoTES) is proposed as a solution to convert depleted oil/gas reservoirs into long-term seasonal energy storage. GeoTES can be hybridized with other techniques for viable commercial deployment, such as 1) concentrating solar power (CSP) collectors and 2) heat pumps with excess renewable energy. Here, a technology overview is given on the two GeoTES technologies, which includes system overview, techno-economic models, and case study. Both GeoTES technologies show great potential in the economics of individual project deployment and applicability across the US.

concentrating solar power↗
DOE OSTI2018

Hop/STIP1 depletion alters nuclear structure via depletion of nuclear structural protein emerin

Highlights: • The link between the co-chaperone Hop/STIP1 and nuclear protein emerin is studied. • Hop overexpression or depletion targets emerin for degradation. • Hop and emerin interact in complexes that do not require Hsp90, but accommodate Hsp70. • Nuclear structure is altered in Hop and emerin depleted cells. Hop/STIP1 is a co-chaperone of Hsp70 and Hsp90 that regulates a number of cell biology processes via interactions with cellular proteins. Here we report a new relationship between Hop and the nuclear structural protein emerin in maintenance of nuclear morphology. Depletion or overexpression of Hop resulted in the reduction of emerin protein levels via proteasomal and lysosomal pathways. Co-immunoprecipitation assays confirmed that Hop and emerin are in a common complex, which could accommodate Hsp70 but not Hsp90, and that TPR2AB is required for the association. Loss of Hop or emerin led to a deformation of nuclear structure, a statistically significant decrease in nuclear size, and was associated with changes in the levels of nuclear proteins, lamin A-C and fibrillarin. The nuclear defects upon Hop loss could be rescued by emerin overexpression. Taken together, these data suggest that Hop stabilises emerin and that loss of Hop alters nuclear structure via emerin degradation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle: Mo depletion by Fe/Al precipitation at ORR

Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO 4 2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. In this paper, we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. Lastly, the depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Rapid depletion analysis of flowing-pebble reactor systems at equilibrium using SCALE

Several high-temperature gas-cooled reactor concepts (and more recently, salt-cooled designs such as the fluoride salt-cooled high-temperature reactor) feature core designs employing continuously circulating fuel pebbles. These reactor designs permit both continuous online refueling of fuel elements as well as higher overall achievable discharge burnups. However, rapid calculation of time-dependent fuel isotopic inventories proves challenging for this class of dynamic systems with current analysis tools. While iterative approaches employing coupled neutron transport have been developed to solve this issue, rapid depletion analysis techniques are needed to calculate time-dependent inventories for individual pebbles and batches (and thus the construction of full- core inventory at equilibrium). We propose a depletion analysis strategy for this type of system for cores at equilibrium. Drawing upon previous neutronic analysis of the PBMR-400 equilibrium core, we demonstrate the viability of developing collapsed one-group cross section libraries suitable for performing rapid depletion analyses with SCALE. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software for Depletion and Fuel Management

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the software release referred to as ADDER v1.1.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Deployment of the HFIRCON transport and depletion tool for plutonium-238 production studies

Irradiation of {sup 237}Np-bearing targets in Oak Ridge National Laboratory's (ORNL) High Flux Isotope Reactor (HFIR) results in the efficient production of {sup 238}Pu, which, in the form of heat source PuO{sub 2}, is used as a reliable power source for deep-space and planetary NASA missions. A technology demonstration subproject was initiated at ORNL in 2011 to develop and implement the technology required to establish a {sup 238}Pu supply chain. A systematic progression of NpO{sub 2}/Al cermet (20 vol.% NpO{sub 2}) activities to date has successfully demonstrated target fabrication, irradiation, and chemical recovery processes. Recent program tasks have included the development of the HFIRCON transport and depletion tool for efficient reactor physics analyses and the evaluation of increased NpO{sub 2} loadings (i.e., beyond 20 vol.%) and NpN-based targets. This paper documents the deployment of the HFIRCON code to assess various Np concentrations in NpO{sub 2}- and NpN-based targets in HFIR's inner small vertical experiment facilities. Results indicate that {sup 238}Pu production and quality can be enhanced with increased Np loadings; however, target conversion rates are reduced. The results recorded in this paper, thermal and material balance evaluations, and testing requirement planning will be used to determine whether increased NpO{sub 2} loadings or NpN-based targets will be further considered. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2019

The multiple depleted mantle components in the Hawaiian-Emperor chain

Oceanic island basalts are targeted for geochemical study because they provide a direct window into mantle composition and a wealth of information on the dynamics and timescales associated with Earth mixing. Previous studies mainly focused on the shield volcanic stage of oceanic islands and the more fusible, enriched mantle components that are easily distinguished in those basalts. Mantle depleted compositions are typically more difficult to resolve unless large amounts of this material participated in mantle melting (e.g., mid-ocean ridges), or unique processes allow for their compositions to be erupted undiluted, such as very small degrees of melting of a source with minimal fusible enriched components (e.g., rejuvenated basalts) or as xenoliths (e.g., abyssal peridotites). Mantle depleted components, defined here as material with low time-integrated Rb/Sr (low 87 Sr/ 86 Sr) and high time-integrated Sm/Nd and Lu/Hf ratios (high 143 Nd/ 144 Nd and 176 Hf/ 177 Hf) relative to primitive mantle, derive from a potentially very large volume reservoir (up to 80% of the mantle), and therefore need adequate characterization in order estimate the composition of the Earth and mantle-derived melts. Here, this review focuses on mantle depleted compositions in oceanic island basalts using the Hawaiian-Emperor chain as a case study. The Hawaiian-Emperor chain is the ~6000 km long geological record of the deeply sourced Hawaiian mantle plume, active for >81 Myr. Hawaiian volcanism evolves through four volcanic stages as a volcano traverses the Hawaiian plume: alkalic preshield, tholeiitic shield (80–90% volcano volume), alkalic postshield (~1%), and silica undersaturated rejuvenated (<0.1%). We report Pb-Sr-Nd-Hf isotope compositions and trace element concentrations of three rejuvenated Northwest Hawaiian Ridge basalts and compare them to an exhaustive compiled dataset of basalts from the Hawaiian Islands to the Emperor Seamounts. The Northwest Hawaiian Ridge (NWHR) includes 51 volcanoes spanning ~42 m.y. between the bend in the Hawaiian-Emperor chain and the Hawaiian Islands where there is no high-precision isotopic data published on the rejuvenated-stage over ~47% of the chain. NWHR and Hawaiian Island rejuvenated basalts are geochemically similar, indicating a consistent source for rejuvenated volcanism over ~12.5 million years. In contrast, shield-stage basalts from the oldest Emperor Seamounts are more depleted in isotopic composition (i.e., higher 176 Hf/ 177 Hf, and 143 Nd/ 144 Nd with lower 87 Sr/ 86 Sr and 208 Pb*/ 206 Pb*) and trace element concentrations (i.e., much lower concentrations of highly incompatible elements) than all other depleted Hawaiian basalts younger than the bend, including NWHR rejuvenated basalts. The strongly depleted source for the oldest Emperor Seamounts (>70 Ma) was likely related to interaction with the Kula-Pacific-Izanagi mid-ocean ridge spreading system active near the Hawaiian plume in the Late Cretaceous. In contrast, the incompatible trace element ratios of NWHR rejuvenated basalts require a distinct source in the Hawaiian mantle plume that was imprinted by ancient (>1 Ga) partial melting, likely ancient recycled oceanic lithosphere. This review of the geochemistry of Hawaiian depleted components documents the need for the sampling of multiple distinctive depleted compositions, each preferentially melted during specific periods of Hawaiian plume activity. This suggests that the composition of depleted components can evolve during the lifetime of the mantle plume, as observed for enriched components in the Hawaiian mantle plume. Changes in the composition of depleted components are dominantly controlled by the upper mantle tectonic configurations at the time of eruption (i.e., proximity to a mid-ocean ridge), as this effect overwhelms the signal imparted by potentially sampling different lower mantle components through time.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2022

Depletion-Driven Assembly of Polymer-Coated Nanocrystals

Depletion-driven assembly has been widely studied for micron-sized colloids, but questions remain at the nanoscale where the governing physics are impacted by stabilizing surface ligands or wrapping polymers, whose dimensions are similar to those of the colloidal core and the depletant. Here, we probe how wrapping colloidal tin-doped indium oxide nanocrystals with polymers affects their depletion-induced interactions and assembly in solutions of polyethylene glycol. Copolymers of polyacrylic acid grafted with polyethylene oxide provide nanocrystal wrappings with different effective polymer graft densities and molecular weights. (Ultra) small angle X-ray scattering, coarse-grained molecular dynamics simulation, and molecular thermodynamic theory were combined to analyze how depletant size and polymer wrapping characteristics affect depletion interactions, structure, and phase behavior. The results show how depletant molecular weight, as well as surface density and molecular weight of polymer grafts, set thresholds for assembly. These signatures are unique to depletion-driven assembly of nanoscale colloids and mirror phase behaviors of grafted nanoparticle–polymer composites. Optical and rheological responses of depletion-driven assemblies of nanocrystals with different polymer shell architectures were probed to learn how their structural differences impact properties. Finally, we discuss how these wrinkles for depletion-driven assembly at the nanoscale may provide fresh opportunities for designing responsive depletion interactions and dynamically reconfigurable materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Efficient continuous Energy-Multigroup hybrid depletion scheme using the Shift Monte Carlo code. Part I: Energy condensation sensitivity analysis

Monte Carlo (MC) codes coupled to depletion solvers are increasingly used to provide high fidelity fuel cycle modeling capabilities. Here, these coupled depletion-MC tools produce accurate results in general but can experience nonphysical spatial oscillations when time steps are large or when a system’s dominance ratio approaches unity. Two substepping techniques have been developed previously to remedy and dampen these spatial oscillations without needing to reduce step sizes. The first approach relied on higher-order techniques to account for spectral changes within steps (extrapolation and interpolation techniques). The second approach used the first order perturbation (FOP) theory to account for the change in the one-group spatial flux distribution within steps. This paper develops a hybrid depletion methodology which, in a way, combines how the flux is handled in both substepping techniques. Specifically, the multigroup (MG) MC Shift code is used to update the flux distribution within steps rather than a one-group FOP solver. A fully reflected pincell is investigated, which is not spatially dependent in the MG representation. Thus, the analysis in this paper is an initial demonstration of hybrid depletion. An upcoming companion paper will focus on how the hybrid depletion dampens spatial oscillations. The hybrid depletion approach is verified to be consistent with previous constant extrapolation depletion (CED) methods. This paper finds that the hybrid CED exhibits some error in the eigenvalue and one group constants within macro steps. To address this discrepancy, a simple interpolation scheme (CELI) is investigated. This work found that CELI sufficiently addresses the discrepancy in spectrum for macro steps up to 100 days. Overall, this work demonstrates that the hybrid depletion method can significantly reduce the number of high fidelity MC executions in a MC-coupled depletion with an acceptable eigenvalue error.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Identifying hydrologic signatures associated with streamflow depletion caused by groundwater pumping

Abstract Groundwater pumping can reduce streamflow in nearby waterways (‘streamflow depletion’), a process which must be accounted for in integrated management of surface and groundwater resources. However, causal identification of streamflow depletion from hydrographs alone is challenging because pumping impacts are masked by other drivers of hydrologic variability. To identify potential indicators of streamflow depletion, we used synthetic hydrographs and an analytical streamflow depletion model to assess potential pumping impacts on specific hydrograph characteristics (‘hydrologic signatures’) for 215 streamgages spanning the conterminous United States (CONUS). We found that streamflow depletion commonly impacts signatures associated with seasonal and annual low flows and low flow recessions. The largest impacts occurred during dry years, suggesting streamflow depletion may be evident in dry years even where impacts are unmeasurable in wet years. Random forest models indicated that streamflow depletion could significantly impact Annual, Summer, and Fall signatures in most streams. Our finding that multiple hydrologic signatures are consistently responsive to streamflow depletion across CONUS suggests that the underlying hydrological processes linking pumping to streamflow reductions are consistent across diverse settings, information that will aid in identifying indicators of streamflow depletion from streamflow hydrographs.

Lapides, Dana A.↗
DOE OSTI2021

CD8 Lymphocyte Depletion Enhances the Latency Reversal Activity of the SMAC Mimetic AZD5582 in ART-Suppressed Simian Immunodeficiency Virus-Infected Rhesus Macaques

ABSTRACT Inducing latency reversal to reveal infected cells to the host immune system represents a potential strategy to cure human immunodeficiency virus (HIV) infection. In separate studies, we have shown previously that CD8 + T cells may contribute to the maintenance of viral latency and have identified a novel SMAC (second mitochondrial activator of caspases) mimetic/IAP (inhibitor of apoptosis protein) inhibitor (AZD5582) capable of reversing HIV/simian immunodeficiency virus (SIV) latency in vivo by activating the noncanonical (nc) NF-κB pathway. Here, we use AZD5582 in combination with antibody (Ab)-mediated depletion of CD8α + cells to further evaluate the role of CD8 + T cells in the maintenance of viral latency. Six rhesus macaques (RMs) were infected with SIV mac239 and treated with antiretroviral therapy (ART) starting at week 8 postinfection. After 84 to 85 weeks of ART, all animals received a single dose of the anti-CD8α depleting Ab MT807R1 (50 mg/kg of body weight, administered subcutaneously [s.c.]), followed by five weekly doses of AZD5582 (0.1 mg/kg, administered intravenously [i.v.]). Following combined treatment with CD8α depletion and AZD5582, 100% of RMs experienced on-ART viremia levels above 60 copies per ml of plasma. In comparator groups of SIV-infected, ART-suppressed RMs treated with AZD5582 only or CD8α depletion only, on-ART viremia was experienced by 56% and 57% of the animals, respectively. Furthermore, the increased frequency of viremic episodes during the treatment period was greater in the group treated with CD8α depletion plus AZD5582 than in the other groups. Mathematical modeling of virus reactivation suggested that in addition to viral dynamics during acute infection, CD8α depletion influenced the response to AZD5582. This work suggests that the latency reversal induced by activation of the ncNF-κB signaling pathway with AZD5582 can be enhanced by CD8α + cell depletion. IMPORTANCE A favored approach to curing HIV infection aims at inducing viral expression using latency-reversing agents (LRAs) to allow the elimination of infected cells. Here, we tested a combination of two recently identified LRAs, the SMAC mimetic/IAP inhibitor AZD5582, which activates the noncanonical NF-κB pathway, and the antibody (Ab) MT807R1, which depletes CD8α + cells, in SIV-infected rhesus macaques (RMs) on ART. Latency reversal, as defined by increased on-ART viremia, was observed in all six SIV-infected, ART-treated RMs that received this combined treatment. Furthermore, comparison of viral reactivation between these animals and groups of SIV-infected, ART-treated RMs treated with AZD5582 only or CD8α + cell depletion only showed more frequent increases in viremic episodes when the two treatments were combined. This study provides additional evidence that CD8 + T cells may contribute to the maintenance of HIV/SIV latency on ART and potentially inhibit latency reversal during HIV cure approaches.

59 BASIC BIOLOGICAL SCIENCES↗