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DOE OSTI2023

CRISPR/Cas9-based gene activation and base editing in Populus

The genus Populus has long been used for environmental, agroforestry and industrial applications worldwide. Today Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological research. As such, various modern biotechnologies, including CRISPR/Cas9-based techniques, have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin composition. However, CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone “717-1B4” (P. tremula x P. alba clone INRA 717-1B4). Alternative CRISPR/Cas9-based technologies, e.g. those involving modified Cas9 for gene activation and base editing, have not been evaluated in most Populus species for their efficacy. Here we employed a deactivated Cas9 (dCas9)-based CRISPR activation (CRISPRa) technique to fine-tune the expression of two target genes, TPX2 and LecRLK-G which play important roles in plant growth and defense response, in hybrid poplar clone “717-1B4” and poplar clone “WV94” (P. deltoides “WV94”), respectively. We observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation, demonstrating the effectiveness of dCas9-based CRISPRa system in Populus. In addition, we applied Cas9 nickase (nCas9)-based cytosine base editor (CBE) to precisely introduce premature stop codons via C-to-T conversion, with an efficiency of 13%–14%, in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone “717-1B4”. Overall, we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species, facilitating the adoption of emerging genome editing tools in woody species.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2005

The NASA Bed Rest Project

NASA s National Vision for Space Exploration includes human travel beyond low earth orbit and the ultimate safe return of the crews. Crucial to fulfilling the vision is the successful and timely development of countermeasures for the adverse physiological effects on human systems caused by long term exposure to the microgravity environment. Limited access to in-flight resources for the foreseeable future increases NASA s reliance on ground-based analogs to simulate these effects of microgravity. The primary analog for human based research will be head-down bed rest. By this approach NASA will be able to evaluate countermeasures in large sample sizes, perform preliminary evaluations of proposed in-flight protocols and assess the utility of individual or combined strategies before flight resources are requested. In response to this critical need, NASA has created the Bed Rest Project at the Johnson Space Center. The Project establishes the infrastructure and processes to provide a long term capability for standardized domestic bed rest studies and countermeasure development. The Bed Rest Project design takes a comprehensive, interdisciplinary, integrated approach that reduces the resource overhead of one investigator for one campaign. In addition to integrating studies operationally relevant for exploration, the Project addresses other new Vision objectives, namely: 1) interagency cooperation with the NIH allows for Clinical Research Center (CRC) facility sharing to the benefit of both agencies, 2) collaboration with our International Partners expands countermeasure development opportunities for foreign and domestic investigators as well as promotes consistency in approach and results, 3) to the greatest degree possible, the Project also advances research by clinicians and academia alike to encourage return to earth benefits. This paper will describe the Project s top level goals, organization and relationship to other Exploration Vision Projects, implementation strategy, address Project deliverables, schedules and provide a status of bed rest campaigns presently underway.

Rhodes, Bradley↗

NASA NTRS1961

The Effect of Lateral-Directional Control Coupling on Pilot Control of an Airplane as Determined in Flight and in a Fixed-Base Flight Simulator

A flight and fixed-base simulator study was made of the effects of aileron-induced yaw on pilot opinion of aircraft lateral-directional controllability characteristics. A wide range of adverse and favorable aileron-induced yaw was investigated in flight at several levels of Dutch-roll damping. The flight results indicated that the optimum values of aileron- induced yaw differed only slightly from zero for Dutch-roll damping from satisfactory to marginally controllable levels. It was also shown that each range of values of aileron-induced yawing moment considered satisfactory, acceptable, or controllable increased with an increase in the Dutch- roll damping. The increase was most marked for marginally controllable configurations exhibiting favorable aileron-induced yaw. Comparison of fixed-base flight simulator results with flight results showed agreement, indicating that absence of kinesthetic motion cues did not markedly affect the pilots' evaluation of the type of control problem considered in this study. The results of the flight study were recast in terms of several parameters which were considered to have an important effect on pilot opinion of lateral-directional handling qualities, including the effects of control coupling. Results of brief tests with a three-axis side-arm controller indicated that for control coupling problems associated with highly favorable yaw and cross-control techniques, use of the three-axis controller resulted in a deterioration of control relative to results obtained with the conventional center stick and rudder pedals.

Vomaske, Richard F.↗

NASA NTRSDate not supplied

Material Response Modeling of Ablative Thermal Protection Systems using PATO

Developing thermal protection systems (TPS) for future space vehicles involves an extensive design and test cycle. A key component of the cycle is determining margins for a safe design that rely on confidence in the performance of the TPS. Predicting the complicated multiphysics phenomena that occur during atmospheric entry requires high-fidelity modeling tools. To this end, the Porous-material Analysis Toolbox based on OpenFOAM (PATO) has been developed. PATO is an open-source software for computing material response of reactive porous materials submitted to high-temperature environments. Recent applications of PATO include computation of the full heatshield 3D material response from the Mars Science Laboratory atmospheric entry and ablation during arc jet testing. Current efforts are underway to loosely couple PATO with other discipline specialized codes including hypersonic computational fluid dynamics (CFD) to assess the effects of pyrolysis-gas blowing into the boundary layer and computational solid mechanics to address modeling of mechanical erosion. Surface phenomena modeling capabilities to address the effects of silicone-based coatings applied to the TPS during flight preparation are also being added.

Thermal Protection Systems↗

NASA NTRSDate not supplied

Material Response Modeling of Ablative Thermal Protection Systems using PATO

Thermal Protection Systems↗

DOE OSTI2022

Global Dust Cycle and Direct Radiative Effect in E3SM Version 1: Impact of Increasing Model Resolution

Quantification of dust aerosols in Earth System Models (ESMs) has important implications for water cycle and biogeochemistry studies. This study examines the global life cycle and direct radiative effects (DREs) of dust in the U.S. Department of Energy's Energy Exascale Earth System Model version 1 (E3SMv1), and the impact of increasing model resolution both horizontally and vertically. The default 1° E3SMv1 captures the spatial and temporal variability in the observed dust aerosol optical depth (DAOD) reasonably well, but overpredicts dust absorption in the shortwave (SW). Simulations underestimate the dust vertical and long-range transport, compared with the satellite dust extinction profiles. After updating dust refractive indices and correcting for a bias in partitioning size-segregated emissions, both SW cooling and longwave (LW) warming of dust simulated by E3SMv1 are increased and agree better with other recent studies. The estimated net dust DRE of –0.42 Wm –2 represents a stronger cooling effect than the observationally based estimate –0.2 Wm –2 (–0.48 to +0.2), due to a smaller LW warming. Constrained by a global mean DAOD, model sensitivity studies of increasing horizontal and vertical resolution show strong influences on the simulated global dust burden and lifetime primarily through the change of dust dry deposition rate; there are also remarkable differences in simulated spatial distributions of DAOD, DRE, and deposition fluxes. Thus, constraining the global DAOD is insufficient for accurate representation of dust climate effects, especially in transitioning to higher- or variable-resolution ESMs. Better observational constraints of dust vertical profiles, dry deposition, size, and LW properties are needed.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1972

Development of thermally stable phosphonitrile elastomers for advanced aerospace structures

Attempts to prepare low molecular weight, curable poly-(fluoroalkoxyphosphazenes) have been successful. Derivatization of /Cl2PN/n polymer with alkoxides gave functionally reactive terpolymers. These terpolymers could be crosslinked with polyisocyanates at room temperature. Attempts to control molecular weight have not been as successful. The effects of (Cl2PN)3 monomer purity, use of (Cl2PN)3,4 mixture, and early termination of the bulk polymerization of (Cl2PN)3 were studied briefly. Both low and high molecular weight polymers were obtained. Reaction of NH4Cl with PCl5 with subsequent heating to give chain extension gave either gels of oils with molecular weights of several thousand. The stabilization of poly-(fluoroalkoxyphosphazene) was investigated. The results generally were inconclusive, but acids were found to be deleterious while bases had little discernible effect. Improvements in stability by modification of end groups was inconclusive.

Reynard, K. A.↗

NASA NTRS2022

Global Dust Cycle and Direct Radiative Effect in E3SM Version 1: Impact of Increasing Model Resolution

Quantification of dust aerosols in Earth System Models (ESMs) has important implications for water cycle and biogeochemistry studies. This study examines the global life cycle and direct radiative effects (DREs) of dust in the U.S. Department of Energy's Energy Exascale Earth System Model version 1 (E3SMv1), and the impact of increasing model resolution both horizontally and vertically. The default 1° E3SMv1 captures the spatial and temporal variability in the observed dust aerosol optical depth (DAOD) reasonably well, but overpredicts dust absorption in the shortwave (SW). Simulations underestimate the dust vertical and long-range transport, compared with the satellite dust extinction profiles. After updating dust refractive indices and correcting for a bias in partitioning size-segregated emissions, both SW cooling and longwave (LW) warming of dust simulated by E3SMv1 are increased and agree better with other recent studies. The estimated net dust DRE of −0.42 Wm−2 represents a stronger cooling effect than the observationally based estimate −0.2 Wm−2 (−0.48 to +0.2), due to a smaller LW warming. Constrained by a global mean DAOD, model sensitivity studies of increasing horizontal and vertical resolution show strong influences on the simulated global dust burden and lifetime primarily through the change of dust dry deposition rate; there are also remarkable differences in simulated spatial distributions of DAOD, DRE, and deposition fluxes. Thus, constraining the global DAOD is insufficient for accurate representation of dust climate effects, especially in transitioning to higher- or variable-resolution ESMs. Better observational constraints of dust vertical profiles, dry deposition, size, and LW properties are needed.

dust aerosol↗

DOE OSTI2025

When to vaccinate for seasonal influenza: check the peak forecast

Background Seasonal influenza infects 5-20% of people every year in the United States, resulting in hospitalizations, deaths, and adverse economic impacts. To mitigate these impacts, influenza vaccines are developed and distributed annually; however, growing evidence suggests that vaccine effectiveness (VE) wanes over the course of a flu season. Delaying influenza vaccination for older adults has attracted attention as a potential public health strategy. However, given the uncertainties in seasonal peak, vaccine effectiveness, and waning rates, postponing vaccination could also lead to increased morbidity, motivating an evaluation of a range of potential scenarios. The aim of this study was to investigate favorable age group-specific vaccination schedules that could lead to the greatest disease burden reduction. Methods We systematically investigated a broad range of vaccination start times for five age groups under six combinations of initial effectiveness and waning rates, based on influenza cases and vaccine uptake data from 10 influenza seasons. We defined the most favorable vaccination schedule as the one that resulted in the greatest reduction in disease burden. Results In scenarios with fast waning, all age groups benefit from delaying vaccination regardless of initial VE and peak timing. In scenarios with slower waning, results are mixed. For the ≥65 group, high initial VE and slow waning suggests that in early-peaking seasons, early vaccination most effectively reduces disease burden, while in late-peaking seasons delaying vaccination is most effective. For the ≥65 group in medium and low initial VE, and slow waning scenarios, delaying vaccination appears to prevent the greatest number of cases, regardless of whether the season peaks early or late. Conclusion The most favorable vaccination schedule is sensitive to changes in initial VE, waning rate, and peak timing. Given estimates of these quantities from statistical and immunological models and observations, our methods can inform vaccination recommendations in order to most effectively reduce the annual disease burden caused by seasonal influenza. Specifically, accurate peak timing forecasts for the upcoming season have the potential to guide decisions on when to vaccinate.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2002

SEE and TID extension testing of the Xilinx XQR18V04 4Mbit radiation hardened configuration PROM

The XQR18V04 was evaluated for single event upset rates using proton and heavy ions. The PROM was demonstrated to be immune to latch-up, as well as to static upset in the flash memory cells, to an LET > 125 MeV/mg/cmz (effective). The PROM was also tested in a dynamic mode, which revealed three distinct error modes: Read Bit Errors, Address Errors, and a Single Event Functional Interrupt (SEW which affected the data output drivers. Saturation cross-sections, and onset thresholds, for these errorinodes were measured at the heavy ion facility at Texas A&M University, and the proton facility at UC Davis. Additional testing was performed at UC Davis and the Cobalt 60 source at McClellan Air Force Base to examine the effect to TID life as a function of power biasing. The PROM demonstrated a 100% improvement in total TID life with an 84% percent decrease in device usage.

FPGA Virtex II SEU↗

DOE OSTI2023

Machine learning-based jet and event classification at the Electron-Ion Collider with applications to hadron structure and spin physics

We explore machine learning-based jet and event identification at the future Electron-Ion Collider (EIC). We study the effectiveness of machine learning-based classifiers at relatively low EIC energies, focusing on (i) identifying the flavor of the jet and (ii) identifying the underlying hard process of the event. We propose applications of our machine learning-based jet identification in the key research areas at the future EIC and current Relativistic Heavy Ion Collider program, including enhancing constraints on (transverse momentum dependent) parton distribution functions, improving experimental access to transverse spin asymmetries, studying photon structure, and quantifying the modification of hadrons and jets in the cold nuclear matter environment in electron-nucleus collisions. We establish first benchmarks and contrast the estimated performance of flavor tagging at the EIC with that at the Large Hadron Collider. We perform studies relevant to aspects of detector design including particle identification, charge information, and minimum transverse momentum capabilities. Additionally, we study the impact of using full event information instead of using only information associated with the identified jet. These methods can be deployed either on suitably accurate Monte Carlo event generators, or, for several applications, directly on experimental data. We provide an outlook for ultimately connecting these machine learning-based methods with first principles calculations in quantum chromodynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

A numerical examination of the effect of sulfide dissolution on silicate weathering

Silicate weathering regulates climate on geological time scales as a net, climate-sensitive sink of atmospheric CO 2 . On the other hand, sulfuric acid produced through sulfide dissolution affects silicate weathering, diminishing its effectiveness as a climate regulator based on evidence from river chemistry. This study takes a theoretical approach to quantitatively examine the effect of sulfide dissolution, coupling a one-dimensional model of pyrite weathering to that of albite transformation to kaolinite. The coupled model reveals that when the reaction front of sulfide is deeper than that of silicates reacting with CO 2 , the silicate-weathering feedback on climate is not directly affected by sulfide dissolution, but only indirectly through oceanic processes such as reverse weathering and carbonate deposition. In turn, when sulfide dissolution occurs within zones of CO 2 -silicate reactions close to the surface, the feedback between climate and silicate weathering can be significantly weakened because sulfuric acid competes effectively with carbonic acid in mineral dissolution. As the depth of the sulfide reaction front can be changed by variations in water table depth, the latter feedback weakening could have occurred in concert with climate-change-driven water table fluctuations, amplifying atmospheric CO 2 variations during the Phanerozoic.

58 GEOSCIENCES↗

DOE OSTI2023

Annihilation-gamma-based diagnostic techniques for magnetically confined electron–positron pair plasma

Efforts are underway to magnetically confine electron–positron pair plasmas to study their unique behaviour, which is characterized by significant changes in plasma time and length scales, supported waves and unstable modes. However, use of conventional plasma diagnostics presents challenges with these low-density and annihilating matter–antimatter plasmas. To address this problem, we propose to develop techniques based on the distinct emission provided by annihilation. This emission exhibits two spatial correlations: the distance attenuation of isotropic sources and the back-to-back propagation of momentum-preserving 2 $\gamma$ annihilation. We present the results of our analysis of the $\gamma$ emission rate and the spatial profile of the annihilation in a magnetized pair plasma from direct pair collisions, from the formation and decay of positronium as well as from transport processes. In order to demonstrate the effectiveness of annihilation-based techniques, we tested them on annular $\gamma$ emission profiles produced by a $\beta ^+$ radioisotope on a rotating turntable. Direct and positronium-mediated annihilation result in overlapping volumetric $\gamma$ sources, and the 2 $\gamma$ emission from these volumetric sources can be tomographically reconstructed from coincident counts in multiple detectors. Transport processes result in localized annihilation where field lines intersect walls, limiters or internal magnets. These localized sources can be identified by the fractional $\gamma$ counts on spatially distributed detectors.

Physics↗

NASA NTRS1989

Mixed finite element formulation for frictionless contact problems

Simple mixed finite element models and a computational procedure are presented for the solution of frictionless contact problems. The analytical formulation is based on a form of Reissner's large-rotation theory of the structure with the effect of transverse shear deformation included. The contact conditions are incorporated into the formulation by using a perturbed Lagrangian approach with the fundamental unknowns consisting of the internal forces (or stress resultants), the generalized displacements, and the Lagrange multipliers associated with the contact conditions. Numerical examples of axisymmetric deformations of a hemispherical shell and planar deformations of a circular ring are presented. Both structures are pressed against a rigid plate. Detailed information about the response of the structures is presented. The numerical studies demonstrate the high accuracy of the mixed models and the effectiveness of the computational procedure based on combining the geometrically nonlinear terms and the contact conditions in one iteration loop.

Noor, Ahmed K.↗

DOE OSTI2024

Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action

It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO 4 ) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2005

Deposition and Characterization of Thin Films on Metallic Substrates

A CVD method was successfully developed to produce conversion coatings on aluminum alloys surfaces with reproducible results with a variety of precursors. A well defined protocol to prepare the precursor solutions formulated in a previous research was extended to other additives. It was demonstrated that solutions prepared following such a protocol could be used to systematically generate protective coatings onto aluminum surfaces. Experiments with a variety of formulations revealed that a refined deposition protocol yields reproducible conversion coatings of controlled composition. A preliminary correlation between solution formulations and successful precursors was derived. Coatings were tested for adhesion properties enhancement for commercial paints. A standard testing method was followed and clear trends were identified. Only one precursors was tested systematically. Anticipated work on other precursors should allow a better characterization of the effect of intermetallics on the production of conversion/protective coatings on metals and ceramics. The significance of this work was the practical demonstration that chemical vapor deposition (CVD) techniques can be used to systematically generate protective/conversion coating on non-ferrous surfaces. In order to become an effective approach to replace chromate-based pre- treatment processes, namely in the aerospace or automobile industry, the process parameters must be defined more precisely. Moreover, the feasibility of scale-up designs necessitates a more comprehensive characterization of the fluid flow, transport phenomena, and chemical kinetics interacting in the process. Kinetic characterization showed a significantly different effect of magnesium-based precursors when compared to iron-based precursors. Future work will concentrate on refining the process through computer simulations and further experimental studies on the effect of other transition metals to induce deposition of conversion/protective films on aluminum and other metallic substrates.

Gatica, Jorge E.↗

NASA NTRS1993

Modeling and managing risk early in software development

In order to improve the quality of the software development process, we need to be able to build empirical multivariate models based on data collectable early in the software process. These models need to be both useful for prediction and easy to interpret, so that remedial actions may be taken in order to control and optimize the development process. We present an automated modeling technique which can be used as an alternative to regression techniques. We show how it can be used to facilitate the identification and aid the interpretation of the significant trends which characterize 'high risk' components in several Ada systems. Finally, we evaluate the effectiveness of our technique based on a comparison with logistic regression based models.

Briand, Lionel C.↗

NASA NTRSDate not supplied

Interlaminar R-Curve Effects in Thermoplastic Composites: Experiments and Model Correlations

The interlaminar fracture behavior of thermoplastic composites under Mode-I and Mode-II static loading is investigated in this research. The material system under consideration is a carbon fiber reinforced low melt semi-crystalline resin TC1225 LMPAEK T700G (T700/LMPAEK)†. Characterization experiments were conducted to measure the load-displacement response, peak load, and propagation of delamination from a pre-implanted Kapton® insert. The Mode-I response was characterized using a double cantilever beam (DCB) test according to the ASTM D5528-22 standard. It was observed that the propagation exhibited significant resistance to delamination growth, i.e., an R-Curve effect. The test data indicated that the steady-state fracture toughness, G SS I , was approximately twice the mean initiation fracture toughness, G Ic . The Mode-II response of an end notch flexure (ENF) specimen tested according to the ASTM D7905-19 standard exhibited an unexpected stable behavior upon attaining peak load. Prior to attaining peak load, the Mode-II response exhibited some non-linearity, which may be attributed to nonlinear bulk material response, e.g., hyper-elasticity, viscoelasticity, plasticity, etc., and potentially friction at the load/support rollers and R-Curve effects. Finite element models based on the Cohesive Zone Method (CZM) and the Virtual Crack Closure Technique (VCCT) were used to predict the DCB and ENF specimen responses. DCB analysis results obtained using G SS I predicted propagation consistent with experimental data. However, results obtained with the as characterized G Ic were inaccurate in predicting delamination growth onset and peak load. ENF analysis results obtained with the as-characterized Mode-II fracture toughness, G IIc , were inaccurate in predicting the peak load and propagation. Hence, R-Curve effects were included in both DCB and ENF simulations, which enabled improved predictions. The experimentally determined Mode-I R-Curve was used for the DCB simulations, whereas an R-Curve was derived for Mode-II assuming that the change in compliance of the specimen was associated with crack growth only.

Prabhakar M Rao↗