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NASA NTRS2000

Influence of Design Variations on Systems Performance

High-risk aerospace components have to meet very stringent quality, performance, and safety requirements. Any source of variation is a concern, as it may result in scrap or rework. poor performance, and potentially unsafe flying conditions. The sources of variation during product development, including design, manufacturing, and assembly, and during operation are shown. Sources of static and dynamic variation during development need to be detected accurately in order to prevent failure when the components are placed in operation. The Systems' Health and Safety (SHAS) research at the NASA Ames Research Center addresses the problem of detecting and evaluating the statistical variation in helicopter transmissions. In this work, we focus on the variations caused by design, manufacturing, and assembly of these components, prior to being placed in operation (DMV). In particular, we aim to understand and represent the failure and variation information, and their correlation to performance and safety and feed this information back into the development cycle at an early stage. The feedback of such critical information will assure the development of more reliable components with less rework and scrap. Variations during design and manufacturing are a common source of concern in the development and production of such components. Accounting for these variations, especially those that have the potential to affect performance, is accomplished in a variety ways, including Taguchi methods, FMEA, quality control, statistical process control, and variation risk management. In this work, we start with the assumption that any of these variations can be represented mathematically, and accounted for by using analytical tools incorporating these mathematical representations. In this paper, we concentrate on variations that are introduced during design. Variations introduced during manufacturing are investigated in parallel work.

Tumer, Irem Y.↗

NASA NTRS2017

Small-Scale Density Variations in the Lunar Crust Revealed by GRAIL

Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that approximately 98 percent of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2 percent of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10's of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by plus or minus 10 percent over scales ranging from centimeters to 100’s of kilometers.

J C Jansen↗

DOE OSTI2024

Induced and natural variation affect traits independently in hybrid Populus

Abstract The genetic control of many plant traits can be highly complex. Both allelic variation (sequence change) and dosage variation (copy number change) contribute to a plant's phenotype. While numerous studies have investigated the effect of allelic or dosage variation, very few have documented both within the same system, leaving their relative contribution to phenotypic effects unclear. The Populus genome is highly polymorphic, and poplars are fairly tolerant of gene dosage variation. Here, using a previously established Populus hybrid F1 population, we assessed and compared the effect of natural allelic variation and induced dosage variation on biomass, phenology, and leaf morphology traits. We identified QTLs for many of these traits, but our results indicate limited overlap between the QTLs associated with natural allelic variation and induced dosage variation. Additionally, the integration of data from both allelic and dosage variation identifies a larger set of QTLs that together explain a larger percentage of the phenotypic variance. Finally, our results suggest that the effect of the large indels might mask that of allelic QTLs. Our study helps clarify the relationship between allelic and dosage variation and their effects on quantitative traits.

Guo, Weier (ORCID:0000000251789334)↗

DOE OSTI2024

Daytime variation in the aerosol indirect effect for warm marine boundary layer clouds in the eastern North Atlantic

Abstract. Warm boundary layer clouds in the eastern North Atlantic region exhibit significant diurnal variations in cloud properties. However, the diurnal cycle of the aerosol indirect effect (AIE) for these clouds remains poorly understood. This study takes advantage of recent advancements in the spatial resolution of geostationary satellites to explore the daytime variation in the AIE by estimating the cloud susceptibilities to changes in cloud droplet number concentration (Nd). Cloud retrievals for the month of July over 4 years (2018–2021) from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) on Meteosat-11 over this region are analyzed. Our results reveal a significant “U-shaped” daytime cycle in susceptibilities of the cloud liquid water path (LWP), cloud albedo, and cloud fraction. Clouds are found to be more susceptible to Nd perturbations at noon and less susceptible in the morning and evening. The magnitude and sign of cloud susceptibilities depend heavily on the cloud state defined by cloud LWP and precipitation conditions. Non-precipitating thin clouds account for 44 % of all warm boundary layer clouds in July, and they contribute the most to the observed daytime variation. Non-precipitating thick clouds are the least frequent cloud state (10 %), and they exhibit more negative LWP and albedo susceptibilities compared to thin clouds. Precipitating clouds are the dominant cloud state (46 %), but their cloud susceptibilities show minimal variation throughout the day. We find evidence that the daytime variation in LWP and albedo susceptibilities for non-precipitating clouds is influenced by a combination of the diurnal transition between non-precipitating thick and thin clouds and the “lagged” cloud responses to Nd perturbations. The daytime variation in cloud fraction susceptibility for non-precipitating thick clouds can be attributed to the daytime variation in cloud morphology (e.g., overcast or broken). The dissipation and development of clouds do not adequately explain the observed variation in cloud susceptibilities. Additionally, daytime variation in cloud susceptibility is primarily driven by variation in the intensity of cloud response rather than the frequency of occurrence of cloud states. Our results imply that polar-orbiting satellites with an overpass time at 13:30 LT underestimate daytime mean values of cloud susceptibility, as they observe susceptibility daily minima in the study region.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Variation-Resilient FeFET-Based In-Memory Computing Leveraging Probabilistic Deep Learning

Reliability issues stemming from device level nonidealities of nonvolatile emerging technologies like ferroelectric field-effect transistors (FeFETs), especially at scaled dimensions, cause substantial degradation in the accuracy of in-memory crossbar-based AI systems. Here, in this work, we present a variation-aware design technique to characterize the device level variations and to mitigate their impact on hardware accuracy employing a Bayesian neural network (BNN) approach. An effective conductance variation model is derived from the experimental measurements of cycle-to-cycle (C2C) and device-to-device (D2D) variations performed on FeFET devices fabricated using 28 nm high-k metal gate technology. The variations were found to be a function of different conductance states within the given programming range, which sharply contrasts earlier efforts where a fixed variation dispersion was considered for all conductance values. Such variation characteristics formulated for three different device sizes at different read voltages were provided as prior variation information to the BNN to yield a more exact and reliable inference. Near-ideal accuracy for shallow networks (MLP5 and LeNet models) on the MNIST dataset and limited accuracy decline by ~3.8%–16.1% for deeper AlexNet models on CIFAR10 dataset under a wide range of variations corresponding to different device sizes and read voltages, demonstrates the efficacy of our proposed device-algorithm co-design technique.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Rubidium and potassium isotopic variations in chondrites and Mars: Accretion signatures and planetary overprints

As moderately volatile elements, isotopes of Rb and K can trace volatilization processes in planetary bodies. Rubidium isotopic data are however very scarce, especially for non-carbonaceous meteorites. Here, in this study, we report combined Rb and K isotopic data (δ 87/85 Rb and δ 41/39 Κ) for 7 ordinary, 6 enstatite, and 4 Martian meteorite falls to understand the causes for the variations in volatile abundances and isotopic compositions. Bulk Rb and K isotopic compositions of planetary bodies are estimated to be (Table 1): Mars +0.10 ± 0.03 ‰ for Rb and -0.26 ± 0.05 ‰ for K, bulk OCs $-0.12^{+0.15}_{-0.24}$ ‰ for Rb and $-0.72^{+0.28}_{-0.41}$ ‰ for K, bulk ECs $-0.02^{+0.29}_{-0.26}$ ‰ for Rb and $-0.33^{+0.37}_{-0.23}$ ‰ for K. The bulk K isotopic compositions of subgroup OCs are estimated to be $-0.72^{+0.26}_{-0.55}$ ‰ for H chondrites, $-0.71^{+0.23}_{-0.39}$ ‰ for L chondrites, and $-0.77^{+0.63}_{-0.30}$ ‰ for LL chondrites. A broad correlation between the Rb and K isotopic compositions of planetary bodies is observed. The correlation follows a slope that is consistent with kinetic evaporation and condensation processes, suggesting volatility-controlled mass-dependent isotope fractionation (as opposed to nucleosynthetic anomalies). Individual ordinary and enstatite chondrites show large Rb and K isotopic variations (-1.02 to +0.29 ‰ for Rb and -0.91 to -0.15 ‰ for K). Samples of lower metamorphic grades display correlated elemental and isotopic fractionations between Rb and K, while samples of higher metamorphic grades show great scatter, suggesting that chondrite parent-body processes have decoupled the two elements and their isotopes at the sample scale. Several processes could have contributed to the observed isotopic variations of Rb and K, including (i) chondrule “nugget effect”, (ii) volatilization during parent-body thermal metamorphism (heat-induced vaporization and gas transport within parent bodies), (iii) thermal diffusion during parent-body metamorphism, and (iv) impact/shock heating. Quantitative modeling of the first two processes suggests that neither of them could produce isotopic variations large enough to explain the observed isotopic variations. Volatilization during parent-body thermal metamorphism [the scenario (ii)], which has been commonly invoked to explain the isotopic variations of volatile elements, is gas transport-limited and its effect on isotopic fractionations of moderately volatile elements should be negligible. Modeling of diffusion processes suggests that (iii) could produce K isotopic variation comparable to the observed variation. The large isotopic variations in non-carbonaceous meteorites are thus most likely due to diffusive redistribution of K and Rb during metamorphism and/or shock-induced heating and vaporization.

58 GEOSCIENCES↗

DOE OSTI2023

Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure

Abstract The distribution of ecotypic variation in natural populations is influenced by neutral and adaptive evolutionary forces that are challenging to disentangle. This study provides a high‐resolution portrait of genomic variation in Chinook salmon ( Oncorhynchus tshawytscha ) with emphasis on a region of major effect for ecotypic variation in migration timing. With a filtered data set of ~13 million single nucleotide polymorphisms (SNPs) from low‐coverage whole genome resequencing of 53 populations (3566 barcoded individuals), we contrasted patterns of genomic structure within and among major lineages and examined the extent of a selective sweep at a major effect region underlying migration timing (GREB1L/ROCK1). Neutral variation provided support for fine‐scale structure of populations, while allele frequency variation in GREB1L/ROCK1 was highly correlated with mean return timing for early and late migrating populations within each of the lineages ( r 2 = .58–.95; p < .001). However, the extent of selection within the genomic region controlling migration timing was much narrower in one lineage (interior stream‐type) compared to the other two major lineages, which corresponded to the breadth of phenotypic variation in migration timing observed among lineages. Evidence of a duplicated block within GREB1L/ROCK1 may be responsible for reduced recombination in this portion of the genome and contributes to phenotypic variation within and across lineages. Lastly, SNP positions across GREB1L/ROCK1 were assessed for their utility in discriminating migration timing among lineages, and we recommend multiple markers nearest the duplication to provide highest accuracy in conservation applications such as those that aim to protect early migrating Chinook salmon. These results highlight the need to investigate variation throughout the genome and the effects of structural variants on ecologically relevant phenotypic variation in natural species.

Horn, Rebekah L.↗

NASA NTRS1994

Dynamical influences on the moment of inertia tensor from lateral viscosity variations inferred from seismic tomographic models

We have investigated the influences of lateral variations of viscosity on the moment of inertia tensor from viscous flows due to the density anomalies in the mantle inferred from seismic tomographic models. The scaling relations between the density and the seismic anomalies is taken as either a constant or a function increasing with depth in accord with the recent high-pressure experimental studies. The viscosity is taken as an exponential function of the 3D density anomaly. In models with an isoviscous background, the effects on the perturbed moment of inertia tensor from the lateral viscosity variations are smaller than those due to variations in the radial viscosity profiles. In mantle models with a background viscosity increasing with depth, the influences of the lateral viscosity variations are significant. The most striking feature in the latter case is that the two off-diagonal elements delta I(sub xz) and delta I(sub yz) in the inertia tensor exhibit greatest sensitivity to lateral variations of the viscosity. While the other elements of the inertia change by only about a few tens of percent in the range of lateral viscosity contrast considered (less than 300), delta I(sub xz) and delta I(sub yz) can vary up to 40 times even with a change in sign, depending on the radial viscosity stratification and the location of the strongest lateral variations. The increase in the velocity-density scaling relation with depth can reduce the influences of the lateral viscosity variations, but it does not change the overall sensitive nature of delta I(sub xz) and delta I(sub yz). This study demonstrates clearly that the lateral viscosity variations, especially in the upper mantle, must be considered in the determination of long-term polar wander, since the variations in the delta I(sub xz) and delta I(sub yz) terms are directly responsible for exciting rotational movements.

Zhang, Shuxia↗

NASA NTRS1994

Measurement of diurnal and semidiurnal rotational variations and tidal parameters of Earth

We discuss the determination of diurnal and semidiurnal variations in the rotation rate and the direction of rotation axis of Earth from the analysis of 8 years of very long baseline interferometry (VLBI) data. This analysis clearly show that these variations are largely periodic and tidally driven; that is, the periods of the variations correspond to the periods of the largest lunar and solar tides. For rotation rate variations, expressed in terms of changes in universal time (UT), the tidal lines with the largest observed signals are O1 (amplitude 23.5 microseconds in time (microseconds), period 25.82 solar hours); KL (18.9 microseconds, 23.93 hours); M2 (17.9 microseconds, 12.54 hours); and S2 (8.6 microseconds, 12.00 hours). For variations in the direction of the rotation axis (polar motion), significant signals exist in the retrograde semidiurnal band at the M2 and S2 tides (amplitudes 265 and 119 microarc seconds (microarc seconds, respectively); the prograde diurnal band at the O1, K1, and P1 tides (amplitudes 199, 152, and 60 microarc seconds, respectively); and the prograde semidiurnal band at the M2 and K2 tides (amplitudes 58 and 39 microarc seconds, respectively). Variations in the retrograde diurnal band are represented by corrections with previous estimates except that a previously noted discrepancy in the 13.66-day nutation (corresponding to the O1 tide) is largely removed in this new analysis. We estimate that the standard deviations of these estimates are 1.0 microseconds for the UT1 variations and 14-16 microarc seconds for the polar motion terms. These uncertainties correspond to surface displacements of approximately 0.5 mm. From the analysis of atmospheric angular momentum data we conclude that variations in UT1 excited by the atmosphere with subdaily periods are small (approximately 1 microsecond). We find that the average radial tidal displacements of the VLBI sites in the diurnal band are largely consistent with known deficiencies in current tidal models, i.e., deficiencies of up to 0.9 mm in the treatment of the free core nutation resonance. In the semidiurnal band, our analysis yields estimates of the second-degree harmonic radial Love number h(sub 2) at the M2 tide of 0.604 + i0.005 +/- 0.002. The most likely explanation for the rotational variations are the effects of ocean tides, but there may also be some contributions from atmospheric tides, the effects of triaxiality of Earth, and the equatorial second-degree-harmonic components of the core- mantle boundary.

Herring, Thomas A.↗

NASA NTRS2007

Inter-annual and Long-term Temperature Variations in the Mesopause Region at High Latitudes Generated by the Stratospheric QBO

The Numerical Spectral Model (NSM) simulates the Quasi-biennial Oscillation (QBO) that dominates the zonal circulation of the lower stratosphere at low latitudes. In the model, the QBO is generated with parameterized small-scale gravity waves (GW), which are partially augmented in 3D with planetary waves owing to baroclinic instability. Due to GW filtering, the QBO extends into the upper mesosphere, evident in UARS zonal wind and TIMED temperature measurements. While the QBO zonal winds are confined to equatorial latitudes, even in simulations with latitude-independent wave source, the associated temperature variations extend to high latitudes. The meridional circulation redistributes some of the QBO energy to focus it partially onto the Polar Regions. The resulting QBO temperature variations away from the equator tend to increase at higher altitudes to produce inter-annual variations that can exceed 5 K in the polar mesopause region -- and our 3D model simulations show that the effect is variable from year to year and can produce large differences between the two hemispheres, presumably due to interactions involving the seasonal variations. Modeling studies with the NSM have shown that long-term variations can also be generated by the QBO interacting with the seasonal cycles through OW node-filtering. A 30-month QBO, optimally synchronized by the 6-month Semi-Annual Oscillation (SAO), thus produces a 5-year or semi-decadal (SD) oscillation -- and observational evidence for that has been provided by a recent analysis of stratospheric NCEP data. In a simulation with the 2D version of the NSM, this SD oscillation extends into the upper mesosphere, and we present results to show that the related temperature variations could contribute significantly to the long-term variations of the polar mesopause region. Quasi-decadal variations could furthermore arise from the modeled solar cycle modulations of the QBO and 12-month annual oscillation. Our numerical results are discussed in the context of the observed low summer temperatures reproduced by the model, to demonstrate that the above interannual and long-term variations could contribute significantly to the climatology of Polar Mesospheric Clouds (PMC) investigated by the Aeronomy of Ice in the Mesosphere (AIM) mission.

Mayr, Hans G.↗

DOE OSTI2026

Variation in supercurrent connectivity and vortex pinning of state-of-the-art pulsed laser deposited RE Ba 2 Cu 3 O 7- x coated conductors

REBa 2 Cu 3 O 7-x (REBCO, RE: rare earth) coated conductors (CCs) suffer from great critical current I c differences between different manufacturers, I c variations within individual manufacturers, and often significant lengthwise fluctuations. The understanding of such variations is complicated by the lack of a direct correlation between I c and the critical current density J c . In fact, although J c is the fundamental property determined by the local vortex pinning landscape, I c is often limited by variable current blocking mechanisms. An important practical complexity is commercial practices of performing J c and I c evaluations based on I c at 77 K and self-field (sf), where connectivity variation dominates over vortex pinning variations. However, at higher fields and lower temperatures, vortex pinning becomes more complex and highly variable, making predictions of I c and J c at arbitrary temperature T, magnetic field H, and field orientation θ, quite uncertain. To address some aspects of this problem, we conducted detailed spool-to-spool performance characterization on recently manufactured REBCO CCs. Despite J c (77 K, sf) varies by only ∼11%, J c (77 K, 1 T) of its minimum and maximum (for H//ab-plane) show variations of ∼21% and ∼32%, respectively. This emphasizes the shortcoming in using J c (77 K, sf) as parameter for evaluating even the low field performance. An even more remarkable spool-to-spool J c variation of ∼68% was observed at 20 K and 15 T for H//ab-plane. To identify the origin of such lack of reproducibility we performed microstructural characterizations, which revealed, within the REBCO layer, large variation in the density of copper oxide (CuO x ) particles ranging from 0.1 to 2 μm in size. We believe that they play a decisive role in reducing the effective cross-section of the REBCO layer by not simply blocking current themselves, but also by nucleating off-axis REBCO grains, whose misoriented grain boundaries adversely impact REBCO grain-to-grain connectivity. The REBCO growth associated with high density CuO x particles also leads to the more disordered spatial arrangement of BaHfO 3 precipitate arrays, which, when self-aligning along the ab-planes, generate stronger pinning enhancing J c (H//ab) at all temperatures. In this way, we established that variations of both connectivity and vortex pinning are thus directly coupled. Our results also explain why the so-called ‘lift-factor’, typically defined by the ratio between I c (T, H) and I c (77 K, sf), frequently turns out to be unreliable.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Laminar-to-turbulent flame transition and cycle-to-cycle variations in large eddy simulation of spark-ignition engines

This paper investigates the effect of laminar-to-turbulent flame transition modeling on the prediction of cycle-to-cycle variations (CCVs) in large eddy simulation (LES) of spark-ignition (SI) engines. A laminar-to-turbulent flame transition model that describes the non-equilibrium sub-filter flame speed evolution during an early stage of flame kernel growth is developed. In the present model, the flame transition is characterized by the flame kernel size at which the flame transition ends, defined here as the flame transition scale. The proposed model captures the effects that variations in a turbulent flow field have on the evolution of early-stage burning rates, through variations in the flame transition scale. The proposed flame transition model is combined with the front propagation formulation (FPF) method and a spark-ignition model to predict CCVs in a gasoline direct injection SI engine. It is found that multi-cycle LES with the proposed flame transition model reproduces experimentally-observed CCVs satisfactorily. When the transition model is not considered or when variations in the transition process are neglected, CCVs are significantly under-predicted for the case considered here. These results indicate the importance of modeling the laminar-to-turbulent flame transition and the effect of turbulence on the transition process, when predicting CCVs, under certain engine conditions. The LES results are also used to analyze sources for variations in the flame transition. It is found, for the present engine case, that the most important source is the cycle-to-cycle variation in the turbulence dissipation rate, which is used to measure the strength of turbulence in the proposed model, near a spark plug. The large-scale velocity field and the variations of the laminar flame speed due to the mixture composition and thermal stratification are also found to be important factors to contribute to the variations in the flame transition.

42 ENGINEERING↗

DOE OSTI2024

Incorporating Diurnal and Meter-Scale Variations of Ambient CO 2 Concentrations in Development of Direct Air Capture Technologies

To be implemented on climate-relevant scales, direct air capture of CO 2 (DAC) will require large capital-intensive facilities and careful attention to cost minimization. In making decisions among potential sites for DAC facilities, all of the factors that will impact process cost and efficiency should be considered. In this paper we focus on a factor that has previously received little attention in the DAC community, namely variations in atmospheric conditions on hourly time scales and length scales of meters. We present data curated from extensive previous studies of biosphere-atmosphere fluxes with observations of CO 2 concentration, temperature, and relative humidity (RH) with hourly resolution from many sites in North America. These include locations where typical diurnal variations in CO 2 concentration during summer months exceeds 150 ppm. These variations are larger than the seasonal variations that exist between averaged CO 2 concentrations in winter and summer, and they are highly correlated with diurnal variations in temperature and RH. Diurnal variations are dependent on the height above ground at which CO 2 concentrations are measured, with smaller variations existing at heights of 10 m or more than at ground level. We illustrate the potential implications of these short-term variations for the operation and optimization of a DAC process with process-level calculations for a specific adsorption-based process using amine-rich adsorbents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Narum, Shawn R.↗

DOE OSTI2025

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Abstract Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript’s impacts on plant metabolism has employed data from controlled environments. Here, we generated and analyzed data on the variation in the abundance of 26 metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies (GWAS)) and transcripts (using both transcriptome-wide association studies (TWAS) and an explainable artificial intelligence (AI) approach based on random forest (RF)) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

Mathivanan, Ramesh Kanna↗

DOE OSTI2022

Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks

Background Genome-wide Association Studies (GWAS) aims to uncover the link between genomic variation and phenotype. They have been actively applied in cancer biology to investigate associations between variations and cancer phenotypes, such as susceptibility to certain types of cancer and predisposed responsiveness to specific treatments. Since GWAS primarily focuses on finding associations between individual genomic variations and cancer phenotypes, there are limitations in understanding the mechanisms by which cancer phenotypes are cooperatively affected by more than one genomic variation. Results This paper proposes a network representation learning approach to learn associations among genomic variations using a prostate cancer cohort. The learned associations are encoded into representations that can be used to identify functional modules of genomic variations within genes associated with early- and late-onset prostate cancer. The proposed method was applied to a prostate cancer cohort provided by the Veterans Administration’s Million Veteran Program to identify candidates for functional modules associated with early-onset prostate cancer. The cohort included 33,159 prostate cancer patients, 3181 early-onset patients, and 29,978 late-onset patients. The reproducibility of the proposed approach clearly showed that the proposed approach can improve the model performance in terms of robustness. Conclusions To our knowledge, this is the first attempt to use a network representation learning approach to learn associations among genomic variations within genes. Associations learned in this way can lead to an understanding of the underlying mechanisms of how genomic variations cooperatively affect each cancer phenotype. This method can reveal unknown knowledge in the field of cancer biology and can be utilized to design more advanced cancer-targeted therapies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

Tropical forests harbor a large diversity of closely related tree species that can thrive across habitats. This biodiversity has been found to correspond to large functional diversity in aboveground traits, and likely also relates to belowground trait variation. Globally, root trait (co-)variation is driven by different belowground resource strategies of species, environmental variation, and phylogeny; however, these patterns mostly reflect observations from temperate biomes and remain unconfirmed in tropical trees. We examine phylogenetic and environmental effects on root trait (co-)variation of trees across habitats in an Amazonian rainforest. Roots of 218 tree species from ten dominant families were sampled across three major habitats near Manaus, Brazil. We quantified five morphological and architectural root traits to (i) investigate how they reflected different resource strategies across species, (ii) compare them between families and superorders to test phylogenetic effects, and (iii) compare them between habitats to determine environmental effects on root trait expressions and variability. Root traits discriminated species along a tradeoff between root diameter and root branching and, secondly, due to variation in root tissue density. Our results further show weak phylogenetic effects on tropical tree root variation, for example, families from the same superorder showed large divergence in their root traits, while those from different superorders often overlapped in their root morphology and architecture. Root traits differed significantly between habitats but habitat type had only little effect on overall root trait variation. Our work suggests that the dimensions and drivers that underlie (co-)variation in tropical root traits may differ from global patterns defined by mostly temperate datasets. Due to (a)biotic environmental differences, different root trait dimensions may underlie the belowground functional diversity in (Neo)tropical forests, and we found little evidence for the strong phylogenetic conservatism observed in root traits in temperate biomes. We highlight important avenues for future research on tropical roots in order to determine the degree of, and shifts in functional diversity belowground as communities and environments change in tropical forests.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1985

Solar UV radiation variations and their stratospheric and climatic effects

Nimbus-7 SBUV measurements of the short-term solar UV variations caused by solar rotation and active-region evolution have determined the amplitude and wavelength dependence for the active-region component of solar UV variations. Intermediate-term variations lasting several months are associated with rounds of major new active regions. The UV flux stays near the peak value during the current solar cycle variation for more than two years and peaks about two years later than the sunspot number. Nimbus-7 measurements have observed the concurrent stratospheric ozone variations caused by solar UV variations. There is now no doubt that solar UV variations are an important cause of short- and long-term stratospheric variations, but the strength of the coupling to the troposphere and to climate has not yet been proven.

Donnelly, R. F.↗