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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 253 records · Page 14

MO-FG-CAMPUS-IeP3-01: Evaluation of Specific Absorption Rate and Temperature Increase Induced by Artificial Medical Implants During MRI Scan

Purpose: Heating of patients or burning of biological tissues around medical implants by RF power during MRI scan is a significant patient safety concern. The purpose of this study is to not only measure SAR values, but also RF-induced temperature elevation due to artificial hip joints during MRI scans. Methods: SAR measurement experiment was performed on three discrete manufacturers at 1.5 and 3T. Three MRI RF sequences (T1w TSE, T2w inversion recovery, and T2w TSE) with imaging parameters were selected. A gelled saline phantom mimicking human body tissue was made (Fig.1). FDTD method was utilized to calculate the SAR distribution using Sim4Life software. Based on the results of the simulation, 4 electrical field (E-field) sensors were located around two artificial hip joints inside the phantom. 56 Fiber Bragg Grating (FBG) temperature sensors (28 sensors on each artificial hip joint) were located on both left and right artificial hip joints to measure temperature change during MRI scan (Fig.1). Both E-field and FBG temperature sensors were calibrated with traceability at Korea Research Institute of Standards and Science (KRISS). Results: Simulation shows that high SAR values occur in the head and tail of the implanted artificial hip joints (Fig.1 lower right). 3T MRI scanner shows that the local averaged-SAR values measured by probe 1, 2, and 3 are 2.30, 2.77, and 1.68 W/kg, compared to MRI scanner-reported whole body SAR value (≤1.5 W/kg) for T1w TSE and T2w-IR (Table 1). The maximum temperature elevation measured by FBG sensors is 1.49°C at 1.5 T, 2.0°C at 3 T, and 2.56°C at 3 T for T1w TSE, respectively (Table 2). Conclusion: It is essential to assess the safety of MRI system for patient with medical implant by measuring not only accurate SAR deposited in the body, but also temperature elevation due to the deposited SAR during clinical MRI.

60 APPLIED LIFE SCIENCES↗

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures

Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis. We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Abstract Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

59 BASIC BIOLOGICAL SCIENCES↗

The DESI-Lensing Mock Challenge: large-scale cosmological analysis of 3x2-pt statistics

The current generation of large galaxy surveys will test the cosmological model by combining multiple types of observational probes. Realising the statistical promise of these new datasets requires rigorous attention to all aspects of analysis including cosmological measurements, modelling, covariance and parameter likelihood. In this paper we present the results of an end-to-end simulation study designed to test the analysis pipeline for the combination of the Dark Energy Spectroscopic Instrument (DESI) Year 1 galaxy redshift dataset and separate weak gravitational lensing information from the Kilo-Degree Survey, Dark Energy Survey and Hyper-Suprime-Cam Survey. Our analysis employs the 3x2-pt correlation functions including cosmic shear and galaxy-galaxy lensing, together with the projected correlation function of the spectroscopic DESI lenses. We build realistic simulations of these datasets including galaxy halo occupation distributions, photometric redshift errors, weights, multiplicative shear calibration biases and magnification. We calculate the analytical covariance of these correlation functions including the Gaussian, noise and super-sample contributions, and show that our covariance determination agrees with estimates based on the ensemble of simulations. We use a Bayesian inference platform to demonstrate that we can recover the fiducial cosmological parameters of the simulation within the statistical error margin of the experiment, investigating the sensitivity to scale cuts. This study is the first in a sequence of papers in which we present and validate the large-scale 3x2-pt cosmological analysis of DESI-Y1.

79 ASTRONOMY AND ASTROPHYSICS↗

A theoretical approach for transient shock strengthening in high-energy-density laser compression experiments

In high-energy-density shock compression experiments, the desired state of compression is typically achieved by passing shock waves through a sequence of different materials. Here, a theoretical approach for transiently strengthening such shocks passing through interfaces of experimentally relevant impedance ratios is examined. A semi-analytical method based on characteristics analysis is used to solve the problem of a shock passing from one material to another through an intermediate region of non-uniform impedance; by appropriately designing this region, a greater shock strength can be achieved in the second material for a finite duration than in the absence of this region. When a shock passes into a material of higher impedance, the shock strengthening increases to a maximum before decreasing to an asymptotic value as the strength of the incident shock is increased. For shocks passing into materials of decreasing impedance, the shock strengthening increases monotonically as the strength of the incident shock is increased when the impedance ratio is above a critical threshold. Incorporating multiple intermediate materials can further increase the strength of the transmitted shock, with an exponential discretization of intermediate material impedances being the most effective distribution for strengthening strong shocks. The results suggest that up to 25% and 9% increases in pressure behind the leading shock can be achieved for materials of increasing and decreasing impedance, respectively. The technique is applied to the design of laser-driven dynamic compression experiments, and the results of the analysis are verified via comparison to simulations performed with the HYADES hydrodynamics code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

GHOST (Grid Hardware Open Source Testbed) [SWR-18-32]

The software was developed for the purpose of Microgrid Controller Procurement where multiple Microgrid Controller vendors were competing to prove the best performance. Each microgrid controller was connected to Real-Time Simulator (Opal-RT) where the Real-Time model of microgrid was simulated. Microgrid controllers were able to control most of the assets in the model. To be able to fairly compare controller's performance each controller was evaluated using exactly the same model, with the same initial conditions and exactly the same test sequence. The microgrid evaluation test sequence lasted 100 minutes and consist of various grid disturbances to which a microgrid controller must respond. The microgrid and power system will experience multiple types of disturbances while performing dispatch functions. Many functions are tested in grid-connected and islanded modes such as unexpended failures of generators, energy storage trip events, and large load fluctuations. The test sequence focuses on fault scenarios that cause the highest short-circuit fault current contribution; force a swing bus or generator capable of being a swing bus offline; cause the most reconfigurations; and cause conflicting objectives for the microgrid controller. During the test sequence execution multiple datapoints are being recorded and stored. During data postprocessing key performance parameters are extracted allowing quantitative comparison of performance on multiple aspects including: resiliency, fuel utilization, grid interconnection, ancillary services and power quality and eventually after summing all key performance parameters by comparing the overall result. To be able to perform such testing multiple tools had to be developed included in this repository including: - Real time model of microgrid (Urban-Banshee, Remote-smaller model) - Test sequence configuration tools - Test execution real-time scripts - Post processing scripts - Human Machine Interface software

Koralewicz, Przemyslaw↗

Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA)

Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via EPR spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, one equivalent at a time. The step–by–step reduction of the hemes was then followed using UV–Vis and EPR spectroscopy. EPR–spectral simulations elucidate the sequence of heme reduction within the pentaheme scaffold, and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow +11 (Heme 5) to –212 mV (Heme 3) range (vs SHE). Based on quantitative analysis/simulation of the EPR data, we demonstrate that Hemes 4 and 5 are reduced first (before the active site Heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central Heme 3, a H108M NrfA variant was generated where the reduction potential of Heme 3 is shifted positively (from –212 mV to +29 mV). Here, the H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 3% compared to wild–type. We propose that this is due to Heme 3’s important role as an electron gateway in the wild–type enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Novel Δ J = 1 Sequence in Ge 78 : Possible Evidence for Triaxiality

Here, a sequence of low-energy levels in 78 32 Ge 46 has been identified with spins and parity of 2 + , 3 + , 4 + , 5 + , and 6 + . Decays within this band proceed strictly through ΔJ=1 transitions, unlike similar sequences in neighboring Ge and Se nuclei. Above the 2+ level, members of this sequence do not decay into the ground-state band. Moreover, the energy staggering of this sequence has the phase that would be expected for a γ-rigid structure. The energies and branching ratios of many of the levels are described well by shell-model calculations. However, the calculated reduced transition probabilities for the ΔJ=2 in-band transitions imply that they should have been observed, in contradiction with the experiment. Within the calculations of Davydov, Filippov, and Rostovsky for rigid-triaxial rotors with γ=30°, there are sequences of higher-spin levels connected by strong ΔJ=1 transitions which decay in the same manner as those observed experimentally, yet are calculated at too high an excitation energy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine

Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2")-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗

Collective modes of excitation in 64 Cu

Medium and high-spin level sequences in 64 Cu were investigated using the complex 26 Mg( 48 Ca, αp5nγ ) multinucleon transfer reaction. The experiment was performed at the ATLAS accelerator facility at the Argonne National Laboratory using the Gammasphere array and the fragment mass analyzer (FMA). Two high-spin, quasirotational bands consisting of stretched-E2 transitions were observed in coincidence with the known low-spin structure for the first time. These bands share remarkable similarities with highly deformed and/or superdeformed bands observed in the A ≈ 60–70 mass region. In addition, a regular dipole sequence with weak E2 crossover transitions was observed. A general discussion of the observed structures, complemented by theoretical calculations carried out within the framework of the adiabatic and configuration-fixed constrained covariant density functional theory and the quantum particle-rotor model, are presented. Furthermore, the results are interpreted in the context of shell-structure evolution and the collectivity in the mass region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental quantification of decoherence via the Loschmidt echo in a many spin system with scaled dipolar Hamiltonians

We performed Loschmidt echo nuclear magnetic resonance experiments to study decoherence under a scaled dipolar Hamiltonian by means of a symmetrical time-reversal pulse sequence denominated Proportionally Refocused Loschmidt (PRL) echo. The many-spin system represented by the protons in polycrystalline adamantane evolves through two steps of evolution characterized by the secular part of the dipolar Hamiltonian, scaled down with a factor |k| and opposite signs. The scaling factor can be varied continuously from 0 to 1/2, giving access to a range of complexity in the dynamics. The experimental results for the Loschmidt echoes showed a spreading of the decay rates that correlate directly to the scaling factors |k|, giving evidence that the decoherence is partially governed by the coherent dynamics. The average Hamiltonian theory was applied to give an insight into the spin dynamics during the pulse sequence. The calculations were performed for every single radio frequency block in contrast to the most widely used form. The first order of the average Hamiltonian numerically computed for an 8-spin system showed decay rates that progressively decrease as the secular dipolar Hamiltonian becomes weaker. Notably, the first order Hamiltonian term neglected by conventional calculations yielded an explanation for the ordering of the experimental decoherence rates. However, there is a strong overall decoherence observed in the experiments which is not reflected by the theoretical results. The fact that the non-inverted terms do not account for this effect is a challenging topic. A number of experiments to further explore the relation of the complete Hamiltonian with this dominant decoherence rate are proposed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Factors governing extracellular DNA degradation dynamics in soil

We examined the impacts of soil moisture, temperature, agricultural management and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high-throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39–80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End-point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no-till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time-points, it became inconsistently detectable with high-throughput gene sequencing in less than 1 week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.

59 BASIC BIOLOGICAL SCIENCES↗

Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP

DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R. Here, we also discuss key experimental parameters to consider when designing DNA-SIP experiments and how these parameters affect accuracy of analysis.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗

Suppressing 1 H Spin Diffusion in Fast MAS Proton Detected Heteronuclear Correlation Solid-State NMR Experiments

Fast magic angle spinning (MAS) and indirect detection by high gyromagnetic ratio (γ) nuclei such as proton or fluorine are increasingly utilized to obtain 2D heteronuclear correlation (HETCOR) solid-state NMR spectra of spin-1/2 nuclei by using cross polarization (CP) for coherence transfer. However, one major drawback of CP HETCOR pulse sequences is that 1 H spin diffusion during the back X→ 1 H CP transfer step results in relayed correlations. This problem is particularly pronounced for the indirect detection of very low-γ nuclei such as 89 Y, 103 Rh, 109 Ag and 183 W where long contact times on the order of 10 to 30 ms are necessary for optimal CP transfer. In this work, we propose two methods that eliminate relayed correlations and allow more reliable distance information to be obtained from 2D HETCOR NMR spectra. The first method uses Lee-Goldburg (LG) CP during the X→ 1 H back-transfer step to suppress 1 H spin diffusion. We determine LG conditions compatible with fast MAS frequencies (ν rot ) of 40- 95 kHz and show that 1 H spin diffusion can be efficiently suppressed at low effective radiofrequency (RF) fields (ν 1,eff << 0.5ν rot ) and also at high effective RF fields (ν 1,eff >> 2ν rot ). We describe modified Hartmann-Hahn LG-CP match conditions compatible with fast MAS and suitable for indirect detection of moderate-γ nuclei such as 13 C, and low-γ nuclei such as 89 Y. The second method uses D-RINEPT (dipolar refocused insensitive nuclei enhanced by polarization transfer) during the X→ 1 H back-transfer step of the HETCOR pulse sequence. The effectiveness of these methods for acquiring HETCOR spectra with reduced relayed signal intensities is demonstrated with 1 H{ 13 C} HETCOR NMR experiments on L-histidine•HCl•H 2 O and 1 H{ 89 Y} HETCOR NMR experiments on an organometallic yttrium complex.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Integration of Russian Tier-1 Grid Center with High Performance Computers at NRC-KI for LHC experiments and beyond HENP

The LHC experiments are preparing for the precision measurements and further discoveries that will be made possible by higher LHC energies from April 2015 (LHC Run2). The need for simulation, data processing and analysis would overwhelm the expected capacity of grid infrastructure computing facilities deployed by the Worldwide LHC Computing Grid (WLCG). To meet this challenge the integration of the opportunistic resources into LHC computing model is highly important. The Tier-1 facility at Kurchatov Institute (NRC-KI) in Moscow is a part of WLCG and it will process, simulate and store up to 10% of total data obtained from ALICE, ATLAS and LHCb experiments. In addition Kurchatov Institute has supercomputers with peak performance 0.12 PFLOPS. The delegation of even a fraction of supercomputing resources to the LHC Computing will notably increase total capacity. In 2014 the development a portal combining a Tier-1 and a supercomputer in Kurchatov Institute was started to provide common interfaces and storage. The portal will be used not only for HENP experiments, but also by other data- and compute-intensive sciences like biology with genome sequencing analysis; astrophysics with cosmic rays analysis, antimatter and dark matter search, etc.

97 MATHEMATICS AND COMPUTING↗