Search NASA⌕ Search

SEARCH · Search NASA

Results for “Association study”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Physical Structure of Four Symbiotic Binaries

Disk accretion powers many astronomical objects, including pre-main sequence stars, interacting binary systems, and active galactic nuclei. Unfortunately, models developed to explain the behavior of disks and their surroundings - boundary layers, jets, and winds - lack much predictive power, because the physical mechanism driving disk evolution - the viscosity - is not understood. Observations of many types of accreting systems are needed to constrain the basic physics of disks and provide input for improved models. Symbiotic stars are an attractive laboratory for studying physical phenomena associated with disk accretion. These long period binaries (P(sub orb) approx. 2-3 yr) contain an evolved red giant star, a hot companion, and an ionized nebula. The secondary star usually is a white dwarf accreting material from the wind of its red giant companion. A good example of this type of symbiotic is BF Cygni: our analysis shows that disk accretion powers the nuclear burning shell of the hot white dwarf and also manages to eject material perpendicular to the orbital plane (Mikolajewska, Kenyon, and Mikolajewski 1989). The hot components in other symbiotic binaries appear powered by tidal overflow from a very evolved red giant companion. We recently completed a study of CI Cygni and demonstrated that the accreting secondary is a solar-type main sequence star, rather than a white dwarf (Kenyon et aL 1991). This project continued our study of symbiotic binary systems. Our general plan was to combine archival ultraviolet and optical spectrophotometry with high quality optical radial velocity observations to determine the variation of line and continuum sources as functions of orbital phase. We were very successful in generating orbital solutions and phasing UV+optical spectra for five systems: AG Dra, V443 Her, RW Hya, AG Peg, and AX Per. Summaries of our main results for these systems appear below. A second goal of our project was to consider general models for the outbursts of symbiotic stars, with an emphasis on understanding the differences between disk-driven and nuclear-powered eruptions.

Kenyon, Scott J.↗
DOE OSTI2023

Interface models for three-dimensional Rayleigh–Taylor instability

We derive interface models for three-dimensional Rayleigh–Taylor instability (RTI), making use of a novel asymptotic expansion in the non-locality of the fluid flow. These interface models are derived for the purpose of studying universal features associated with RTI such as the Froude number in single-mode RTI, the predicted quadratic growth of the interface amplitude under multi-mode random perturbations, the optimal (viscous) mixing rates induced by the RTI and the self-similarity of horizontally averaged density profiles and the remarkable stabilization of the mixing layer growth rate which arises for the three-fluid two-interface heavy–light–heavy configuration, in which the addition of a third fluid bulk slows the growth of the mixing layer to a linear rate. Our interface models can capture the formation of small-scale structures induced by severe interface roll-up, reproduce experimental data in a number of different regimes and study the effects of multiple interface interactions even as the interface separation distance becomes exceedingly small. Compared with traditional numerical schemes used to study such phenomena, our models provide a computational speed-up of at least two orders of magnitude.

Mechanics↗
DOE OSTI2021

Non-Thermal Plasma as a Novel Strategy for Treating or Preventing Viral Infection and Associated Disease

Pathogenic viruses cause many human, animal, and plant diseases that are associated with substantial morbidity, mortality and socio-economic impact. Although effective strategies for combatting virus transmission and associated disease are available, global outbreaks of viral pathogens such as the virus responsible for the COVID-19 pandemic demonstrate that there is still a critical need for new approaches that can be used to interrupt the chain of viral infection and mitigate virus-associated pathogenesis. Recent studies point to non-thermal plasma (NTP), a partly ionized gas comprised of a complex mixture of reactive oxygen and nitrogen species along with physical effectors, as the potential foundation for new antiviral approaches. A more thorough understanding of the antiviral properties and safety of NTP has stimulated explorations of NTP as the basis for treatments of viral diseases. The recently described immunomodulatory properties of NTP are also being evaluated for potential use in immunotherapies of viral diseases as well as in antiviral vaccination strategies. In this review, we present the current state-of-the-art in addition to compelling arguments that NTP merits further exploration for use in the prevention and management of viral infections and associated diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Aggregation and analysis of indication-symptom relationships for drugs approved in the USA

Abstract Purpose Drug indications and disease symptoms often confound adverse event reports in real-world datasets, including electronic health records and reports in the FDA Adverse Event Reporting System (FAERS). A thorough, standardized set of indications and symptoms is needed to identify these confounders in such datasets for drug research and safety assessment. The aim of this study is to create a comprehensive list of drug-indication associations and disease-symptom associations using multiple resources, including existing databases and natural language processing. Methods Drug indications for drugs approved in the USA were extracted from two databases, RxNorm and Side Effect Resource (SIDER). Symptoms for these indications were extracted from MedlinePlus and using natural language processing from PubMed abstracts. Results A total of 1361 unique drugs, 1656 unique indications, and 2201 unique symptoms were extracted from a wide variety of MedDRA System Organ Classes. Text-mining precision was maximized at 0.65 by examining Term Frequency Inverse Document Frequency (TF-IDF) scores of the disease-symptom associations. Conclusion The drug-indication associations and disease-symptom associations collected in this study may be useful in identifying confounders in other datasets, such as safety reports. With further refinement and additional drugs, indications, and symptoms, this dataset may become a quality resource for disease symptoms.

Punyala, Ananth↗
DOE OSTI2020

Theoretical study of the reaction mechanism and kinetics of the phenyl + propargyl association

Potential energy surface for the phenyl + propargyl radical recombination reaction has been studied at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G** level of theory for the closed-shell singlet species and at the triplet–singlet gap CASPT2/cc-pVTZ-CCSD(T)-F12/cc-pVTZ-f12//CASSCF/cc-pVTZ level of theory for the diradical species. High-pressure limit rate constants for the barrierless channels were evaluated with variable reaction coordinate transition state theory (VRC-TST). Rice–Ramsperger–Kassel–Marcus Master Equation (RRKM-ME) calculations have been performed to assess temperature- and pressure-dependent phenomenological rate constants and product branching ratios. Here, the entrance channels of the radical association reaction produce 3-phenyl-1-propyne and phenylallene which can further dissociate/isomerize into a variety of unimolecular and bimolecular products. Theoretical evidence is presented that, at combustion relevant conditions, the phenyl + propargyl recombination provides a feasible mechanism for the addition of a second five-member ring to the first six-member aromatic ring producing the prototype two-ring species indene and indenyl. Rate expressions for all important reaction channels in a broad range of temperatures and pressures have been generated for kinetic modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1998

Physics of Interplanetary Dust Collection with Aerogel

This report presents the results of research undertaken to study various problems associated with hypervelocity capture of dust particles in aerogel. The primary topics investigated were the properties of shocked aerogel and the requirements for reliable capture of particles on the STARDUST mission. In particular, the viscosity of shocked aerogel has been an open question. The results presented here suggest that the viscosity of aerogel at high impact velocities is negligible, although there remains some uncertainty about lower velocities. The model adopted for viscosity treats the mixture of polymeric silica and decomposition products and finds that, for particle velocities of 6-7 km/s, the viscosity is similar to that typical of light gasses at STP. Expressions for the Hugoniot of aerogel as a function of density were also obtained from the available data. All aerogels of interest for cosmic dust collectors have very similar shock velocity-particle velocity Hugoniot curves. The strength behavior of aerogel for low-speed penetration was measured, but further work is needed to study the proper way to apply this to the issue of terminal deceleration of a dust particle. Preliminary calculations designed to maximize the penetration depths were performed to determine the required density of aerogel to reliably stop a particle in a 3 cm thickness of aerogel (the path length expected for a normal impact into the STARDUST collector). In order to stop a particle of density rho(sub p) and diameter d(sub p), the mean density of the aerogel collector should be no less than that given by the expression bar rho(sub 0) = 1.085 X 10(exp -4 )rho(sub p)d(sub p), for densities measured in g/ cu cm and the particle diameter measured in micrometers.

Anderson, William W.↗
DOE OSTI2023

Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics

In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Theoretical and computational study of rotating isotropic turbulence

The various flow regimes that occur in rotating isotropic turbulence and their associated turbulence structure are studied. Direct numerical simulations are conducted for moderate and rapid rotation rates and comparisons are made with the predictions of generalized Eddy Damped Quasi-Normal Markovian (EDQNM) approximations. It is shown that at high rotation rates the nonlinear transfer terms remain small and that the development of the spectrum is through pure viscous decay. This shows that the effect of rapid rotation on the turbulence kinetic energy is through the shutting off of the production term in the dissipation rate equation. At moderate and relatively rapid rates, the rotation causes a discernible anisotropy to develop in the integral length scale with a mild trend toward a two-dimensionalization of the flow. As the flow decays, the Rossby number decreases, leading again to the shutting off of the nonlinear transfer terms. For extremely rapid rotation rates, the anisotropies in the integral length scales are small and direct numerical simulation results are in good agreement with rapid distortion theory.

Mansour, N. N.↗
DOE OSTI2022

Large-Area (Ag,Cu)(In,Ga)Se 2 Thin-Film Solar Cells with Increased Bandgap and Reduced Voltage Losses Realized with Bulk Defect Reduction and Front-Grading of the Absorber Bandgap

The 1.24 eV bandgap, 18.8% power conversion efficiency Ag-alloyed chalcopyrite (Ag,Cu)(In,Ga)Se 2 (ACIGS) solar cells are characterized to relate voltage and efficiency improvements to electro-optical (EO) characteristics. Shockley-Read-Hall recombination center defect density, identified and characterized through deep level transient spectroscopy and time-resolved photoluminescence (TRPL), is reduced through potassium and copper treatment optimization. Concomitantly, longer minority carrier lifetimes are achieved, which increases open-circuit voltage (V OC ). Near-conduction band defects associated in earlier studies with light-induced current instability are also mitigated. Analysis of charge-carrier dynamics after single- and two-photon excitation is used to separate recombination at the front interface and in the absorber bulk. From TRPL decay simulations, the authors estimate ranges of key solar cell material characteristics: bulk carrier lifetime T bulk = 110-210 ns, charge-carrier mobility u = 110-160 cm 2 V -1 s -1 , and front interface recombination velocity S front = 700-1050 cm s -1 . This lowest-reported S front for ACIGS absorbers originates from the notched conduction band grading, which also makes the impact of the back interface recombination negligible. It is suggested in the results that solar cell performance enhancements can be made most readily with two distinct strategies: improving device architecture and reducing semiconductor defect densities. Using these approaches, power conversion efficiency in large-area solar cells is improved by 1.1% absolute.

14 SOLAR ENERGY↗
DOE OSTI2022

Challenges for unsupervised anomaly detection in particle physics

Anomaly detection relies on designing a score to determine whether a particular event is uncharacteristic of a given background distribution. One way to define a score is to use autoencoders, which rely on the ability to reconstruct certain types of data (background) but not others (signals). In this paper, we study some challenges associated with variational autoencoders, such as the dependence on hyperparameters and the metric used, in the context of anomalous signal (top and W) jets in a QCD background. We find that the hyperparameter choices strongly affect the network performance and that the optimal parameters for one signal are non-optimal for another. In exploring the networks, we uncover a connection between the latent space of a variational autoencoder trained using mean-squared-error and the optimal transport distances within the dataset. We then show that optimal transport distances to representative events in the background dataset can be used directly for anomaly detection, with performance comparable to the autoencoders. Whether using autoencoders or optimal transport distances for anomaly detection, we find that the choices that best represent the background are not necessarily best for signal identification. These challenges with unsupervised anomaly detection bolster the case for additional exploration of semi-supervised or alternative approaches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Dark Matter searches with photons at the LHC

We unveil blind spot regions in dark matter (DM) direct detection (DMDD), for weakly interacting massive particles with a mass around a few hundred GeV that may reveal interesting photon signals at the LHC. We explore a scenario where the DM primarily originates from the singlet sector within the Z 3 -symmetric Next-to-Minimal Supersymmetric Standard Model (NMSSM). A novel DMDD spin-independent blind spot condition is revealed for singlino-dominated DM, in cases where the mass parameters of the higgsino and the singlino-dominated lightest supersymmetric particle (LSP) exhibit opposite relative signs (i.e., κ < 0), emphasizing the role of nearby bino and higgsino-like states in tempering the singlino-dominated LSP. Additionally, proximate bino and/or higgsino states can act as co-annihilation partner(s) for singlino-dominated DM, ensuring agreement with the observed relic abundance of DM. Remarkably, in scenarios involving singlino-higgsino co-annihilation, higgsino-like neutralinos can distinctly favor radiative decay modes into the singlino-dominated LSP and a photon, as opposed to decays into leptons/hadrons. In exploring this region of parameter space within the singlino-higgsino compressed scenario, we study the signal associated with at least one relatively soft photon alongside a lepton, accompanied by substantial missing transverse energy (E T ) and a hard initial state radiation jet at the LHC. In the context of singlino-bino co-annihilation, the bino state, as the next-to-LSP, exhibits significant radiative decay into a soft photon and the LSP, enabling the possible exploration at the LHC through the triggering of this soft photon alongside large E T and relatively hard leptons/jets resulting from the decay of heavier higgsino-like states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

A comparison of neural network architectures for data-driven reduced-order modeling

The popularity of deep convolutional autoencoders (CAEs) has engendered new and effective reduced-order models (ROMs) for the simulation of large-scale dynamical systems. Despite this, it is still unknown whether deep CAEs provide superior performance over established linear techniques or other network-based methods in all modeling scenarios. To elucidate this, the effect of autoencoder architecture on its associated ROM is studied through the comparison of deep CAEs against two alternatives: a simple fully connected autoencoder, and a novel graph convolutional autoencoder. Through benchmark experiments, it is shown that the superior autoencoder architecture for a given ROM application is highly dependent on the size of the latent space and the structure of the snapshot data, with the proposed architecture demonstrating benefits on data with irregular connectivity when the latent space is sufficiently large.

42 ENGINEERING↗
DOE OSTI2021

Dolomites in hydrated fine-grained Antarctic micrometeorites: Effective tools for analyzing secondary processes

We report detailed transmission electron microscope (TEM) observations of carbonates from one hydrated fine-grained Antarctic micrometeorite (H-FgMM). These carbonates show the occurrence of complex chemical variations and microstructures that provide important evidence regarding the formation and evolution of rarely analyzed H-FgMMs. The chemical variations were identified at both micrometer and nanometer scales, indicating that these carbonates formed under localized fluid conditions that suggest a variable chemical microenvironment. Individual carbonates grew from isolated reservoirs of fluid. Moreover, these carbonates contain manganese amounts almost twice as high as those measured in CM chondrites but similar to those identified in CI chondrites. Their particular compositions indicate reducing and progressively evolving conditions in the fluid from which these carbonates precipitated, probably due to water consumption during phyllosilicates formation. In addition to the compositional variability, microstructural features are pervasive in these carbonates, similar to those described in heavily shocked meteorites indicating that these carbonates were probably modified during shock processes after their formation. Since carbonates are highly susceptible to shock metamorphism, we suggest that it is essential to investigate their structure in detail before interpreting the isotopic measurements related to the time of their formation. Additionally, associated with carbonates, ubiquitous phosphates were identified in the micrometeorite analyzed. Future studies of these mineral associations will provide us further insight into the formation and evolution of asteroids, especially since they were both identified in the surface materials of Ryugu and Bennu.

58 GEOSCIENCES↗
DOE OSTI2020

Assessing the sensitivity and repeatability of permanganate oxidizable carbon as a soil health metric: An interlab comparison across soils

Soil organic matter is central to the soil health framework. Therefore, reliable indicators of Soil organic matter is central to the soil health framework. Therefore, reliable indicators of changes in soil organic matter are essential to inform land management decisions. Permanganate oxidizable carbon (PDXC), an emerging soil health indicator, has shown promise for being sensitive to soil management. However, strict standardization is required for widespread implementation in research and commercial contexts. Here, we used 36 soils-three from each of the 12 USDA soil orders-to determine the effects of sieve size and soil mass of analysis on PDXC results. Using replicated measurements across 12 labs in the US and the EU (n = 7951 samples), we quantified the relative importance of 1) variation between labs, 2) variation within labs, 3) effect soil mass, and 4) effect of soil sieve size on the repeatability of PDXC. We found a wide range of overall variability in PDXC values across labs (0.03 to 171.8%; mean = 13.4%), and much of this variability was attributable to within-lab variation (median = 6.5%) independently of soil mass or sieve size. Greater soil mass (2.5 g) decreased absolute PDXC values by a mean of 177 mg kg -1 soil and decreased analytical variability by 6.5%. For soils with organic carbon (SOC) >10%, greater soil mass (2.5 g) resulted in more frequent PDXC values above the limit of detection whereas the lower soil mass (0.75 g) resulted in PDXC values below the limit of detection for SOC contents <5%. A finer sieve size increased absolute values of PDXC by 124 mg kg -1 while decreasing the analytical variability by 1.8%. In general, soils with greater SOC contents had lower analytical variability. These results point to potential standardizations of the PDXC protocol that can decrease the variability of the metric. We recommend that the PDXC protocol be standardized to use 2.5 g for soils <10% SOC. Sieve size was a relatively small contributor to analytical variability and therefore we recommend that this decision be tailored to the study purpose. Tradeoffs associated with these standardizations can be mitigated, ultimately providing guidance on how to standardize PDXC for routine analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Impact of Diabetes and Insulin Use on Prognosis in Patients With Resected Pancreatic Cancer: An Ancillary Analysis of NRG Oncology RTOG 9704

Diabetes mellitus (DM) has been proposed to be tumorigenic; however, prior studies of the association between DM and survival are conflicting. The goal of this ancillary analysis of RTOG 9704, a randomized controlled trial of adjuvant chemotherapy in pancreatic cancer, was to determine the prognostic effects of DM and insulin use on survival.

62 RADIOLOGY AND NUCLEAR MEDICINE↗