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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗
DOE OSTI2024

Circulating levels of micronutrients and risk of osteomyelitis: a Mendelian randomization study

Background Few observational studies have investigated the effect of micronutrients on osteomyelitis, and these findings are limited by confounding and conflicting results. Therefore, we conducted Mendelian randomization (MR) analyses to evaluate the association between blood levels of eight micronutrients (copper, selenium, zinc, vitamin B12, vitamin C, and vitamin D, vitamin B6, vitamin E) and the risk of osteomyelitis. Methods We performed the two-sample and multivariable Mendelian randomization (MVMR) to investigate causation, where instrument variables for the predictor (micronutrients) were derived from the summary data of micronutrients from independent cohorts of European ancestry. The outcome instrumental variables were used from the summary data of European-ancestry individuals ( n = 486,484). The threshold of statistical significance was set at p < 0.00625. Results We found a significant causal association that elevated zinc heightens the risk of developing osteomyelitis in European ancestry individuals OR = 1.23 [95% confidence interval (CI) [1.07, 1.43]; p = 4.26E-03]. Similarly, vitamin B6 showed a similar significant causal effect on osteomyelitis as a risk factor OR = 2.78 (95% CI [1.34, 5.76]; p = 6.04E-03; in the secondary analysis). Post-hoc analysis suggested this result (vitamin B6). However, the multivariable Mendelian randomization (MVMR) provides evidence against the causal association between zinc and osteomyelitis OR = 0.98(95% CI [−0.11, 0.07]; p = 7.20E-1). After searching in PhenoScanner, no SNP with confounding factors was found in the analysis of vitamin B6. There was no evidence of a reverse causal impact of osteomyelitis on zinc and vitamin B6. Conclusion This study supported a strong causal association between vitamin B6 and osteomyelitis while reporting a dubious causal association between zinc and osteomyelitis.

Zhang, Xu↗
DOE OSTI2024

Changing effects of external forcing on Atlantic–Pacific interactions

Recent studies have highlighted the increasingly dominant role of external forcing in driving Atlantic and Pacific Ocean variability during the second half of the 20th century. This paper provides insights into the underlying mechanisms driving interactions between modes of variability over the two basins. We define a set of possible drivers of these interactions and apply causal discovery to reanalysis data, two ensembles of pacemaker simulations where sea surface temperatures in either the tropical Pacific or the North Atlantic are nudged to observations, and a pre-industrial control run. We also utilize large-ensemble means of historical simulations from the Coupled Model Intercomparison Project Phase 6 (CMIP6) to quantify the effect of external forcing and improve the understanding of its impact. A causal analysis of the historical time series between 1950 and 2014 identifies a regime switch in the interactions between major modes of Atlantic and Pacific climate variability in both reanalysis and pacemaker simulations. A sliding window causal analysis reveals a decaying El Niño–Southern Oscillation (ENSO) effect on the Atlantic as the North Atlantic fluctuates towards an anomalously warm state. The causal networks also demonstrate that external forcing contributed to strengthening the Atlantic's negative-sign effect on ENSO since the mid-1980s, where warming tropical Atlantic sea surface temperatures induce a La Niña-like cooling in the equatorial Pacific during the following season through an intensification of the Pacific Walker circulation. The strengthening of this effect is not detected when the historical external forcing signal is removed in the Pacific pacemaker ensemble. The analysis of the pre-industrial control run supports the notion that the Atlantic and Pacific modes of natural climate variability exert contrasting impacts on each other even in the absence of anthropogenic forcing. The interactions are shown to be modulated by the (multi)decadal states of temperature anomalies of both basins with stronger connections when these states are “out of phase”. We show that causal discovery can detect previously documented connections and provides important potential for a deeper understanding of the mechanisms driving changes in regional and global climate variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Modular flow in JT gravity and entanglement wedge reconstruction

It has been shown in recent works that JT gravity with matter with two boundaries has a type II ∞ algebra on each side. As the bulk spacetime between the two boundaries fluctuates in quantum nature, we can only define the entanglement wedge for each side in a pure algebraic sense. As we take the semiclassical limit, we will have a fixed long wormhole spacetime for a generic partially entangled thermal state (PETS), which is prepared by inserting heavy operators on the Euclidean path integral. Under this limit, with appropriate assumptions of the matter theory, geometric notions of the causal wedge and entanglement wedge emerge in this background. In particular, the causal wedge is manifestly nested in the entanglement wedge. Different PETS are orthogonal to each other, and thus the Hilbert space has a direct sum structure over sub-Hilbert spaces labeled by different Euclidean geometries. The full algebra for both sides is decomposed accordingly. From the algebra viewpoint, the causal wedge is dual to an emergent type III 1 subalgebra, which is generated by boundary light operators. To reconstruct the entanglement wedge, we consider the modular flow in a generic PETS for each boundary. We show that the modular flow acts locally and is the boost transformation around the global RT surface in the semiclassical limit. It follows that we can extend the causal wedge algebra to a larger type III 1 algebra corresponding to the entanglement wedge. Within each sub-Hilbert space, the original type II ∞ reduces to type III 1 .

2D Gravity↗
DOE OSTI2025

Quantum Gravity and Laser Interferometry: Towards Observable Predictions

Understanding quantum gravity remains one of the deepest challenges in modern physics, as direct experimental access to Planck-scale effects is beyond current technological reach. However, recent theoretical advances indicate that quantum fluctuations of spacetime may produce measurable effects in precision experiments, particularly near causal horizons. This opens new avenues for testing quantum gravity phenomena through high-precision measurement techniques. This dissertation develops multiple theoretical models to characterize these effects and examines their potential observational signatures in future gravitational wave interferometers. We begin by investigating the role of quantum fluctuations in near-horizon geometries through the lens of the AdS/CFT correspondence, which provides a powerful framework for understanding the interplay between quantum field theory and general relativity via holographic principles. By modeling stochastic energy-momentum sources in Rindler-AdS spacetime, we demonstrate that vacuum fluctuations transform the Einstein equations into a Langevin-type stochastic differential equation, leading to potentially observable fluctuations in photon traversal times. Extending this approach to Minkowski spacetime, we establish a correspondence between gravitational shockwaves and fluid dynamics, showing that near-horizon perturbations satisfy an equation analogous to that governing incompressible fluids, thereby reinforcing the membrane paradigm and hydrodynamic analogies in the context of the fluid/gravity duality. Furthermore, we construct the covariant phase space of a spherically symmetric causal diamond in Minkowski spacetime, identifying two fundamental charges that govern its evolution. These results provide a foundation for quantizing causal horizons and understanding their microscopic degrees of freedom. Building upon these theoretical developments, we further examine a related stochastic phenomenon: the gravitational wave memory background arising from the cumulative memory steps produced by supermassive black hole mergers. After reviewing the standard stochastic gravitational wave background, gravitational memory effects, and BMS symmetries, we model the stochastic memory background using a Brownian motion framework. We show that while the cumulative memory background initially appears above the sensitivity curve of space-based interferometers like LISA, the realistic subtraction of individually resolvable merger events substantially suppresses the residual signal, making its detection more challenging. This highlights the critical importance of source subtraction when evaluating the detectability of gravitational memory effects. By bridging fundamental theory with experimental prospects, this dissertation contributes to the ongoing effort to uncover the quantum nature of spacetime through precision measurement techniques. Whether through detecting quantum spacetime fluctuations, gravitational memory backgrounds, or probing the symmetries of causal horizons, the pursuit of observable quantum gravity phenomena continues to expand the frontiers of both theory and experiment.

Zhang, Yiwen [Caltech] (ORCID:0000000323559416)↗
DOE OSTI2025

Assessing the cumulative effects of nearshore habitat restoration actions for multiple populations of juvenile salmon in Whidbey Basin, Washington: foundation and approach for synthesis and evaluation

Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Targeted seed EMS mutagenesis reveals a basic helix–loop–helix transcription factor underlying male sterility in sorghum

Abstract Forward genetic screens of mutant populations are fundamental for functional genomics studies. However, isolating independent mutant alleles to molecularly identify causal genes is challenging in species recalcitrant to genetic manipulation. Here, we demonstrate that classic seed ethyl methanesulfonate (EMS) mutagenesis coupled with genome sequencing can overcome this limitation in sorghum. We used this method to generate new mutant alleles of sorghum MALE STERILE 8 (MS8) and identified the causal locus for the ms8 phenotype as Sobic.004G270900, which encodes the sorghum ortholog of maize bhlh122, a basic helix–loop–helix (bHLH) transcription factor required for male fertility in maize. Bulked segregant analysis mapped ms8-1 to a region on chromosome 4 containing Sobic.004G270900. Seeds from heterozygous MS8/ms8-1 plants were mutagenized and screened for chimeric inflorescences containing sectors with white, sterile anthers resembling the ms8-1 homozygous phenotype. DNA sequencing of sterile and fertile sectors from a single chimeric inflorescence revealed two mutations in Sobic.004G270900 within the sterile sector, but not the fertile sector. Isolation of this loss-of-function allele (ms8-2) established Sobic.004G270900 as the causative locus for male sterility in the ms8 mutant. We generated additional alleles of MS8 in a different genetic background using CRISPR/Cas9-based gene editing, where deletions in Sobic.004G270900 also resulted in male sterility. Our work identified a gene underlying male sterility in sorghum and provides a novel and straightforward genetic tool for researchers who lack access to advanced transformation facilities to validate gene candidates. Unlike gene editing, no prior knowledge of candidate genes is required for targeted seed EMS mutagenesis to aid identification of causal loci.

Genetics & Heredity↗
DOE OSTI2024

Complementarity for a dynamical black hole

Black hole complementarity posits that the interior of a black hole is not independent from its Hawking radiation. This leads to an apparent violation of causality: the interior can be acausally affected by operators acting solely on the radiation. We argue that this perspective is misleading and that the black hole interior must be viewed as existing in the causal past of the Hawking radiation, despite the fact that they are spacelike separated in the semiclassical description. Consequently, no operation on the Hawking radiation—no matter how complex—can affect the experience of an infalling observer. The black hole interior and the radiation only appear spacelike separated in the semiclassical description because an infalling observer’s ability to access complex information is limited; the chaotic dynamics on the horizon, as viewed from the exterior, then converts any effect caused by such an observer to information in the Hawking radiation which cannot be accessed at the semiclassical level. We arrive at the picture described above by considering a unitary exterior description in which the flow of information is strictly causal, which we extend to apply throughout the entire history of black hole evolution, including its formation. This description uses the stretched event horizon as an inner edge of spacetime, on which the information inside is holographically encoded. We argue that the global spacetime picture arises from coarse graining over black hole microstates, and discuss its relationship with the exterior description.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Efficiently Computable Limits on EPR Pair Generation in Quantum Broadcast Channels

We investigate the generation of EPR pairs between three observers in a general causally structured setting, where communication occurs via a noisy quantum broadcast channel. The most general quantum codes for this setup take the form of tripartite quantum channels. Since the receivers are constrained by causal ordering, additional temporal relationships naturally emerge between the parties. These causal constraints enforce intrinsic no-signalling conditions on any tripartite operation, ensuring that it constitutes a physically realizable quantum code for a quantum broadcast channel. We analyze these constraints and, more broadly, characterize the most general quantum codes for communication over such channels. We examine the capabilities of codes that are fully no-signalling among the three parties, positive partial transpose (PPT)-preserving, or both, and derive simple semidefinite programs to compute the achievable entanglement fidelity. We then establish a hierarchy of semidefinite programming converse bounds -- both weak and strong -- for the capacity of quantum broadcast channels for EPR pair generation, in both one-shot and asymptotic regimes. Notably, in the special case of a point-to-point channel, our strong converse bound recovers and strengthens existing results. Finally, we demonstrate how the PPT-preserving codes we develop can be leveraged to construct PPT-preserving entanglement combing schemes, and vice versa.

FOS: Physical sciences↗
DOE OSTI2024

Further adoption of conservation tillage can increase maize yields in the western US Corn Belt

Conservation tillage can reduce soil erosion, increase soil health, and decrease labor and fuel input costs. Despite these benefits, potential yield impacts remain an important concern for farmers considering adoption. Previous research suggests that conservation tillage is likely to have the largest yield benefits in more arid conditions, but a lack of field-level analyses across climatic, management and soil conditions limits confidence in such predictions. Satellite imagery provides the opportunity to monitor agricultural lands at sub-field resolution across large spatial scales and wide environmental gradients. Here we investigate the maize yield impacts of conservation tillage in the semi-arid western US Corn Belt, using sub-field resolution datasets on tillage practices and crop yields derived from satellite data spanning four states (Nebraska, Kansas, South Dakota, and North Dakota) between 2008 and 2020. On these datasets, we estimate heterogenous yield outcomes for several thousand maize fields across gradients in climate, soil quality and irrigation status by using a causal forests analysis, an adaptation of the random forests machine-learning algorithm for causal inference on observational data. We find that long-term adoption of conservation tillage increased rainfed maize yields by an average of 9.9% in the region. Impacts on irrigated yields were small and not statistically significant. These results, along with an analysis of variables related to greater than average yield benefits, indicate that improved water infiltration and retention are the primary reasons for conservation tillage benefits. Despite yield benefits, many fields estimated to see increased yields under long term low till have not adopted the practice. Therefore, we identify specific counties likely to benefit most from increased levels of adoption. Our results strengthen the understanding of the impacts of conservation agriculture on crop yields and help define environments and counties most likely to benefit from conservation tillage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Quantum area fluctuations from gravitational phase space

We study the gravitational phase space associated to a stretched horizon within a finite-sized causal diamond in (d + 2)-dimensional spacetimes. By imposing the Raychaudhuri equation, we obtain its constrained symplectic form using the covariant phase space formalism and derive the relevant quantum commutators by inverting the symplectic form and quantizing. Finally, we compute the area fluctuations of the causal diamond by taking a Carrollian limit of the stretched horizon in pure Minkowski spacetime, and derive the relationship $\left\langle {\left(\Delta A\right)}^2\right\rangle \ge \frac{2\pi G}{d}\left\langle A\right\rangle$, showing that the variance of the area fluctuations is proportional to the area itself.

classical theories of gravity↗
DOE OSTI2024

Hidden zeros for particle/string amplitudes and the unity of colored scalars, pions and gluons

Recent years have seen the emergence of a new understanding of scattering amplitudes in the simplest theory of colored scalar particles — the Tr(Φ 3 ) theory — based on combinatorial and geometric ideas in the kinematic space of scattering data. In this paper we report a surprise: far from the toy model it appears to be, the “stringy” Tr(Φ 3 ) amplitudes secretly contains the scattering amplitudes for pions, as well as non-supersymmetric gluons, in any number of dimensions. The amplitudes for the different theories are given by one and the same function, related by a simple shift of the kinematics. This discovery was spurred by another fundamental observation: the tree-level Tr(Φ 3 ) field theory amplitudes have a hidden pattern of zeros when a special set of non-planar Mandelstam invariants is set to zero. These zeros are not manifest in Feynman diagrams but are made obvious by the connection of these amplitudes to the new understanding of associahedra arising from “causal diamonds” in kinematic space. Furthermore, near these zeros, the amplitudes simplify, by factoring into a non-trivial product of smaller amplitudes. Remarkably the amplitudes for pions and gluons are observed to also vanish in the same kinematical locus. These properties for Tr(Φ 3 ) amplitudes hold and further generalize to the “stringy” Tr(Φ 3 ) amplitudes. The “kinematic causal diamond” picture suggests a unique shift of the kinematic data that preserves the zeros, and this shift is precisely the one that unifies colored scalars, pions, and gluons into a single object. We will focus in this paper on explaining the hidden zeros and factorization properties and the connection between all the colored theories, working for simplicity at tree level. Subsequent works will describe this new formulation for the Non-linear Sigma Model and non-supersymmetric Yang-Mills theory, at all loop orders.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Indicators of carbon alteration (ICAs) suggest patterns in reservoir methane emissions

Reservoir operations influence emissions via multiple causal pathways. In this paper, we quantify indicators of carbon alteration (ICAs) focused on methane. ICAs were chosen to reflect the potential for methane emission along four causal pathways: 1) water column mixing, 2) wet-dry cycles in sediment, 3) sediment redistribution, and 4) vegetation. We developed algorithms to calculate ICAs for three reservoirs along a longitudinal gradient in the Tennessee River basin of the southeast US. The ICAs revealed interesting longitudinal patterns. Indicators of both methane production and destruction increased downstream. The potential for ebullitive methane emissions driven by sub-daily water level fluctuations and emissions mediated by vegetation were higher in downstream mainstem reservoirs than in the upstream tributary reservoir. Along the remaining two pathways, longitudinal patterns were equivocal (sediment pathway) or suggested decreased emissions downstream (water-column mixing). We also observed seasonal patterns and, by combining ICAs, inferred times when ramping could be achieved with lower risk of emissions. The ICAs demonstrated here are the first step in quantifying mechanistic relationships between reservoir operation and methane emissions. In future, they may lead to improved operations in reservoir cascades and regional-scale estimates of emissions that account for differences among reservoirs.

Greenhouse gases↗
DOE OSTI2025

Unsupervised discovery of extreme weather events using universal representations of emergent organization

Spontaneous self-organization is ubiquitous in systems far from thermodynamic equilibrium. While organized structures that emerge dominate transport properties, universal representations that identify and describe these key objects remain elusive. Here, we introduce a theoretically grounded framework for describing emergent organization that, via data-driven algorithms, is constructive in practice. Its building blocks are spacetime lightcones that embody how information propagates across a system through local interactions. We show that predictive equivalence classes of lightcones—local causal states—capture organized behaviors in complex spatiotemporal systems. Employing an unsupervised physics-informed machine learning algorithm and a high-performance computing implementation, we demonstrate automatically discovering organized structures in two real-world domain science problems. We show that local causal states identify vortices and track their power-law decay behavior in two-dimensional fluid turbulence. We then show how to detect and track familiar extreme weather events—hurricanes and atmospheric rivers—and discover other novel structures associated with precipitation extremes in high-resolution climate data at the grid-cell level.

Rupe, Adam [Pacific Northwest National Laboratory ↗
DOE OSTI2025

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗
DOE OSTI2025

Decoding crops one cell at a time: from cell atlases to single-cell genetics

Understanding the mechanisms underlying key agricultural traits remains a central challenge in crop research, but recent advances in technologies are providing powerful tools to address this issue. Among these, single-cell and spatial transcriptomics have revealed tissue heterogeneity and spatial organization, offering unique insights into cellular gene expression dynamics and the coordinated activity of multiple cell types. These approaches help uncover how specific cell types contribute to agricultural traits and refine candidate loci lists through integration with trait-associated loci. Additionally, single-cell and spatial transcriptomics have the potential to serve as cell-level readout platforms integrating cellular perturbations, enabling high-throughput discovery of causal relationships between genotype and gene expression at the cellular level in plants. Successful implementation will accelerate the identification of key genetic variants for crop improvement. Furthermore we review lessons learned from application of single-cell screening in mammalian cells, highlight major technical and biological barriers to its use in plants, and outline potential strategies to overcome these challenges. Together, the widespread application and integration of single-cell and spatial transcriptomics with other technologies enable not only the descriptive cataloging of cell states but also the causal interrogation of sequence functions and regulatory networks at cell type resolution, ultimately advancing gene function studies and accelerating crop improvement.

Cellular heterogeneity↗