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At least 559 records · Page 31

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗

Discovering New Strong Gravitational Lenses in the DESI Legacy Imaging Surveys

We have conducted a search for new strong gravitational lensing systems in the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys' Data Release 8. We use deep residual neural networks, building on previous work presented by Huang et al. These surveys together cover approximately one-third of the sky visible from the Northern Hemisphere, reaching a z-band AB magnitude of ~22.5. We compile a training sample that consists of known lensing systems as well as non-lenses in the Legacy Surveys and the Dark Energy Survey. After applying our trained neural networks to the survey data, we visually inspect and rank images with probabilities above a threshold. In this work, we present 1210 new strong lens candidates.

79 ASTRONOMY AND ASTROPHYSICS↗

Resonance Parameter Evaluation of n + 88 Sr reactions for ENDF/B-VIII.1 Library

An evaluation of n+ 88 Sr reactions up to 950 keV was compiled from a publicly available set of resonance parameters. Starting from the repository of the ENDF/B-VIII.0 library, an evaluated nuclear data file was assembled and submitted for inclusion to the Evaluated Nuclear Data File (ENDF)/B-VIII.1 release. This evaluation features an external function representation defined by pole strengths and R ∞ parameters over the entire resolved resonance range. This work improves the modeling of the R-matrix parameterization from multi-Level Breit-Wigner resonance parameters to Reich-Moore formalism, and it also extends thrice the upper energy range of the current ENDF/B-VIII.0 resolved resonance evaluation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

FY 2026 Midyear Report: Seismic Monitoring of Underground Vibration Sources Using Distributed Acoustic Sensing and Seismometers

Safeguards-relevant temporal changes in underground facilities can be observed using geophysical monitoring techniques. Seismic waves, in particular, provide valuable insights into subsurface activities and can serve as an important tool for detecting anomalous events that may indicate containment breaches at geological repositories. This midyear report summarizes ongoing efforts to automatically and rapidly detect and locate anomalous vibration signals that could be indicative of potential containment breaches. Previous work during FY25 focused on compiling continuous seismic datasets from two underground sites and developing a database of continuous waveforms and ground-truth event data derived from multiple sensing modalities. Building on this foundation, we are adapting anomaly detection and geolocation algorithms to explore methods for monitoring underground activities using two relatively low-maintenance sensing technologies: a dense surface geophone array deployed at the Pleasant Gap mine in Pennsylvania, and a three-dimensional fiber-optic cable array for distributed acoustic sensing (DAS) installed in the subsurface at the Sanford Underground Research Facility (SURF) in South Dakota. This report summarizes work conducted during the first two quarters of FY26, during which we refined a dynamic power spectral density (PSD)-based detector, applied it independently to each geophone station, and then combined the per‑station detections with density-based spatial clustering of applications with noise (DBSCAN) to cluster events and produce spatial maps over a nine‑day interval. In addition, we outline plans for a field trial at the Waste Isolation Pilot Plant (WIPP) in New Mexico to compare traditional seismic monitoring approaches with DAS techniques and to evaluate the benefits of combined data analysis. Activities during the past two quarters have included the preparation and submission of a Field Test Plan to WIPP for approval, as well as submission to headquarters for review and feedback.

58 GEOSCIENCES↗

SALT3: An Improved Type Ia Supernova Model for Measuring Cosmic Distances

Abstract A spectral-energy distribution (SED) model for Type Ia supernovae (SNe Ia) is a critical tool for measuring precise and accurate distances across a large redshift range and constraining cosmological parameters. We present an improved model framework, SALT3, which has several advantages over current models—including the leading SALT2 model (SALT2.4). While SALT3 has a similar philosophy, it differs from SALT2 by having improved estimation of uncertainties, better separation of color and light-curve stretch, and a publicly available training code. We present the application of our training method on a cross-calibrated compilation of 1083 SNe with 1207 spectra. Our compilation is 2.5× larger than the SALT2 training sample and has greatly reduced calibration uncertainties. The resulting trained SALT3.K21 model has an extended wavelength range 2000–11,000 Å (1800 Å redder) and reduced uncertainties compared to SALT2, enabling accurate use of low- z I and iz photometric bands. Including these previously discarded bands, SALT3.K21 reduces the Hubble scatter of the low- z Foundation and CfA3 samples by 15% and 10%, respectively. To check for potential systematic uncertainties, we compare distances of low (0.01 < z < 0.2) and high (0.4 < z < 0.6) redshift SNe in the training compilation, finding an insignificant 3 ± 14 mmag shift between SALT2.4 and SALT3.K21. While the SALT3.K21 model was trained on optical data, our method can be used to build a model for rest-frame NIR samples from the Roman Space Telescope. Our open-source training code, public training data, model, and documentation are available at https://saltshaker.readthedocs.io/en/latest/ , and the model is integrated into the sncosmo and SNANA software packages.

79 ASTRONOMY AND ASTROPHYSICS↗

Compiler and Runtime Approaches to Enable Large-Scale Irregular Programs. Final report, July 2013 - July 2019

While regular algorithms, characterized by operations on dense matrices and arrays, have long been the mainstay of scientific, high-performance computing, irregular algorithms, which feature unpredictable accesses to pointer-based data structures, are becoming increasingly common in high performance computing, arising in graph analysis, data mining and visualization, among other domains. Unfortunately, the defining characteristics of irregular applications, their dynamic, unpredictable, data-dependent access patterns and data layouts, make achieving high performance on large scale systems difficult. Scaling applications to peta- and exa-scale requires carefully controlling communication and data movement and placement, an inherently difficult task when access patterns and data layouts are unpredictable! Most irregular applications that attain high performance must be painstakingly hand-written and hand-tuned, with few common principles or paradigms uniting various implementations and easing future development. Despite the increasing importance of irregular applications, there is little programmer knowledge, and even less compiler ability, devoted to optimizing them. This project aims to solve these problems. By allowing programmers to write irregular applications in high level forms, with at most a few annotations highlighting key structural properties, programmers can focus on developing their algorithms and methods. The compiler and run-time system can take on the tedious task of optimizing the application for execution at large scales, and can automatically provide efficient implementations. This will provide portability and ease maintenance for existing irregular applications, but, more importantly, open up whole new domains of computational science to large-scale, high-performance simulation codes.

97 MATHEMATICS AND COMPUTING↗

A new data-driven map predicts substantial undocumented peatland areas in Amazonia

Tropical peatlands are among the most carbon-dense terrestrial ecosystems yet recorded. Collectively, they comprise a large but highly uncertain reservoir of the global carbon cycle, with wide-ranging estimates of their global area (441 025–1700 000 km 2 ) and below-ground carbon storage (105–288 Pg C). Substantial gaps remain in our understanding of peatland distribution in some key regions, including most of tropical South America. Here we compile 2413 ground reference points in and around Amazonian peatlands and use them alongside a stack of remote sensing products in a random forest model to generate the first field-data-driven model of peatland distribution across the Amazon basin. Our model predicts a total Amazonian peatland extent of 251 015 km 2 (95th percentile confidence interval: 128 671–373 359), greater than that of the Congo basin, but around 30% smaller than a recent model-derived estimate of peatland area across Amazonia. The model performs relatively well against point observations but spatial gaps in the ground reference dataset mean that model uncertainty remains high, particularly in parts of Brazil and Bolivia. For example, we predict significant peatland areas in northern Peru with relatively high confidence, while peatland areas in the Rio Negro basin and adjacent south-western Orinoco basin which have previously been predicted to hold Campinarana or white sand forests, are predicted with greater uncertainty. Similarly, we predict large areas of peatlands in Bolivia, surprisingly given the strong climatic seasonality found over most of the country. Very little field data exists with which to quantitatively assess the accuracy of our map in these regions. Data gaps such as these should be a high priority for new field sampling. This new map can facilitate future research into the vulnerability of peatlands to climate change and anthropogenic impacts, which is likely to vary spatially across the Amazon basin.

54 ENVIRONMENTAL SCIENCES↗

Elucidating and predicting the dynamic evolution of water and land systems due to natural and energy-related forcings

Focal Area(s): 3. Insight gleaned from complex data (both observed and simulated) using AI, big data analytics, and other advanced methods, including explainable AI and physics- or knowledge-guided AI; & 1. Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization, unsupervised learning (including deep learning), and hardware-related efforts involving AI (e.g., edge computing). Science Challenge: Interactions between water, land, and energy systems are complex and occur on a variety of scales, ranging from local to basinal to regional. Accurately predicting the behavior of ground water and surface water systems for 5-10 years and beyond requires an understanding of the current system and the ability to model both the natural system at scale and human-induced forcings related to energy and other activities. Artificial intelligence and machine learning (AI/ML) combined with modern compilation and integration efforts for U.S. groundwater and surface water systems present potential solutions to bolstering detailed physics-based models of these systems. Big data tied with ML and physics-based modeling can drive breakthroughs in understanding the earth system, but research is often impeded by data access (e.g., privacy issues), quality, formats, gaps, multi-source, multi-scale, integration, and spatiotemporal challenges. Effective integration of real data and simulated (synthetic) data that fill gaps is critical. Overcoming these complex data and model integration challenges will enable a transformational approach to acquiring enhanced understanding of environmental systems.

54 ENVIRONMENTAL SCIENCES↗

Refining the Census of the Upper Scorpius Association with Gaia

We have refined the census of stars and brown dwarfs in the Upper Sco association (∼10 Myr, ∼145 pc) by (1) updating the selection of candidate members from our previous survey to include the high-precision astrometry from the second data release of Gaia, (2) obtaining spectra of a few hundred candidate members to measure their spectral types and verify their youth, and (3) assessing the membership (largely with Gaia astrometry) of 2020 stars toward Upper Sco that show evidence of youth in this work and previous studies. We arrive at a catalog of 1761 objects that are adopted as members of Upper Sco. The distribution of spectral types among the adopted members is similar to those in other nearby star-forming regions, indicating a similar initial mass function. In previous studies, we have compiled mid-infrared photometry from the Wide-field Infrared Survey Explorer and the Spitzer Space Telescope for members of Upper Sco and used those data to identify the stars that show evidence of circumstellar disks; we present the same analysis for our new catalog of members. As in earlier work, we find that the fraction of members with disks increases with lower stellar masses, ranging from ≲10% for >1 M {sub ⊙} to ∼22% for 0.01–0.3 M {sub ⊙}. Finally, we have estimated the relative ages of Upper Sco and other young associations using their sequences of low-mass stars in M{sub G{sub R{sub P}}} versus G {sub BP} − G {sub RP}. This comparison indicates that Upper Sco is a factor of two younger than the β Pic association (21–24 Myr) according to both nonmagnetic and magnetic evolutionary models.

79 ASTRONOMY AND ASTROPHYSICS↗

The Foundational Industry Energy Dataset: Unit-level Characterization and Derived Energy Estimates for Industrial Facilities in 2017

The Foundational Industry Energy Dataset (FIED) addresses several of the areas of growing disconnect between the demands of industrial energy analysis and the state of industrial energy data by providing unit-level characterization by facility. Each facility is identified by a unique registryID, based on the U.S. Environmental Protection Agency (EPA) Facility Registry Service, and includes its coordinates and other geographic identifiers. Energy-using units are characterized by design capacity, as well as their estimated energy use, greenhouse gas emissions, and physical throughput using 2017 data from the EPA's National Emissions Inventory and Greenhouse Gas Reporting Program. An overview of the derivation methods is provided in a separate technical report which will be linked after publication. The Python code used to compile the dataset is available in a GitHub repository. An updated 2020 version is under development.

Array↗

Energy Levels of Light Nuclei A=13

Experimental nuclear spectroscopic data are evaluated for the 7 known nuclides of mass 13 (Li, Be, B, C, N, O, F). Detailed information is compiled and presented for each reaction and decay experiment. The results are combined and used to provide a set of recommended values that include level energies, spins and parities, half-lives of levels, decay branching ratios, and other nuclear properties. Furthermore, this work supersedes the earlier work by Fay Ajzenberg-Selove (1990Aj01) published in Nuclear Physics A 523 (1991) 1. Earlier reviews were published in (1986Aj01, 1981Aj01, 1976Aj04, 1970Aj04, 1959Aj76).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Formalization of Core Why3 in Coq

Intermediate verification languages like Why3 and Boogie have made it much easier to build program verifiers, transforming the process into a logic compilation problem rather than a proof automation one. Why3 in particular implements a rich logic for program specification with polymorphism, algebraic data types, recursive functions and predicates, and inductive predicates; it translates this logic to over a dozen solvers and proof assistants. Accordingly, it serves as a backend for many tools, including Frama-C, EasyCrypt, and GNATProve for Ada SPARK. But how can we be sure that these tools are correct? The alternate foundational approach, taken by tools like VST and CakeML, provides strong guarantees by implementing the entire toolchain in a proof assistant, but these tools are harder to build and cannot directly take advantage of SMT solver automation. As a first step toward enabling automated tools with similar foundational guarantees, we give a formal semantics in Coq for the logic fragment of Why3. We show that our semantics are useful by giving a correct-by-construction natural deduction proof system for this logic, using this proof system to verify parts of Why3's standard library, and proving sound two of Why3's transformations used to convert terms and formulas into the simpler logics supported by the backend solvers.

97 MATHEMATICS AND COMPUTING↗

Data from "A Bayesian Record Linkage Approach to Applications in Tree Demography Using Overlapping LiDAR Scans"

Processed LiDAR data and environmental covariates from 2015 and 2019 LiDAR scans in the Vicinity of Snodgrass Mountain (Western Colorado, USA), in a geographic subset used in primary analysis for the research paper.This package contains LiDAR-derived canopy height maps for 2015 and 2019, crown polygons derived from the height maps using a segmentation algorithm, and environmental covariates supporting the model of forest growth. Source datasets include August 2015 and August 2019 discrete-return LiDAR point clouds collected by Quantum Geospatial for terrain mapping purposes on behalf of the Colorado Hazard Mapping Program and the Colorado Water Conservation Board. Both datasets adhere to the USGS QL2 quality standard. The point cloud data were processed using the R package lidR to generate a canopy height model representing maximum vegetation height above the ground surface, using a pit-free algorithm.This dataset was compiled to assess how spatial patterns of tree growth in montane and subalpine forests are influenced by water and energy availability. Understanding these growth patterns can provide insight into forest dynamics in the Southern Rocky Mountains under changing climatic conditions.This dataset contains .tif, .csv, and .txt files. This dataset additionally includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata; and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.

54 ENVIRONMENTAL SCIENCES↗

Neutron elastic and inelastic cross section measurements on silicon from 0.8--8 MeV

Neutron elastic and inelastic scattering differential cross sections were measured at angles between 30° and 155° with incident neutron energies between 0.8 and 8 MeV. The measured differential scattering cross sections are compared to existing measurements and the ENDF/B-VIII.0, the JEFF-3.3, and the JENDL-4.0 data evaluations, as well as theoretical calculations from the TALYS-1.95 nuclear reaction code. Our results are reasonably well described by values from the ENDF/B-VIII.0 and JEFF-3.3 compilations. However, below 4 MeV, our backward-angle elastic scattering results tend to be lower than database/calculated values, suggesting that less recoil damage would occur than expected. Above 6 MeV, larger backward-angle cross sections are observed suggesting the opposite. Deexcitation γ rays produced in the inelastic scattering process were also studied for neutron energies between 1.9 and 4.5 MeV. Inelastic neutron scattering cross sections deduced from 28 Si(n,n1γ) γ-ray projection cross sections confirm our 28 Si(n,n1) results. To the extent that data from GELINA and our experimental results can be compared, we have excellent agreement between the inelastic neutron scattering cross sections.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Solovay-Kitaev algorithm and randomized compilation

This paper discusses a technique for randomizing over synthesized one-qubit gate sequences in order to mitigate coherent errors in fault-tolerant circuits. We present simulated and experimental data showing that randomization can reduce the trace distance to the target state.

Widzowski Maupin, Oliver Gabriel [Sandia National ↗

Review: Pre-Darcy flows in low-permeability porous media

The widely used Darcy’s law specifies a linear relation between the Darcy velocity of fluid flow and the pressure gradient that drives the flow. However, studies have shown that Darcy velocity can exhibit a nonlinear dependence on the pressure gradient in low-permeability porous media such as clay and shale when the pressure gradient is adequately low. This phenomenon is referred to as low-velocity non-Darcian flow or pre-Darcy flow. This paper provides a comprehensive review of the theories, experimental data, and modeling methods for pre-Darcy flow in low-permeability porous media. The review begins by outlining the fundamental mechanisms underlying pre-Darcy flow that regulate the unique characteristics such as nonlinear dependence of the Darcy velocity on the pressure gradient and its relevance to fluid–rock interactions. The review then proceeds to present a thorough compilation of experimental investigations performed in various low-permeability geomaterials including tight sandstones, shales, and clays. Next, empirical and theoretical models and simulation methods that have been developed to fit and interpret experimental data are reviewed. Finally, the review underscores the challenges encountered in conducting and interpreting pre-Darcy flow experiments and suggests future research directions. By analyzing previous experimental investigations, this review aims to offer a valuable resource for researchers and practitioners seeking to enhance their understanding of fluid dynamics in low-permeability geomaterials. This provides insights into the application of pre-Darcy flow in numerous natural and engineered processes such as shale oil and gas recovery, contaminant transport in low-permeability aquifers, and geological disposal of nuclear waste.

58 GEOSCIENCES↗

Assessing hydrogen supply chains: An integrated review of leakage and energy efficiency studies

This paper examines hydrogen leakage and efficiency across the supply chain for liquid, gaseous, and mixed hydrogen systems. These factors are crucial for assessing hydrogen's role in mitigating emissions and facilitating a clean energy transition. Drawing on a comprehensive review of existing literature and model-based analysis, the study compiles leakage rates and efficiency metrics at each stage of the supply chain: production, storage, transmission, distribution, and end-use. These data inform system scenarios that estimate the impact of leakage on overall performance and climate benefits. The analysis also identifies persistent data gaps, particularly for liquid and mixed system configurations, and outlines priorities for future research. A comparison of hydrogen system types shows that gaseous pathways generally achieve the highest efficiencies (28 %–39 %) and the lowest leakage rates (∼4.5 %) across the supply chain. Liquid hydrogen systems, while favorable for long-distance and high-volume transport due to their higher energy density, exhibit lower efficiency (∼28 %) and a greater leakage potential (∼12 %). Mixed systems, which combine gaseous and liquid elements (e.g., pipeline transmission followed by liquefaction and truck distribution), show compounded energy losses and moderate-to-high leakage rates (6.8 %–9.4 %), highlighting trade-offs associated with added system complexity. The study highlights opportunities for technological advancements, including optimizing liquefaction, enhancing insulation for storage and transportation, and refining refueling equipment. These improvements are crucial for maximizing the climate benefits of hydrogen. The results offer actionable insights for researchers, industry, and policymakers working to develop low-leakage, high-efficiency hydrogen infrastructure.

08 HYDROGEN↗

Meta-analysis of biogas upgrading to renewable natural gas through biological CO 2 conversion

Biogas upgrading through CO 2 conversion by hydrogenotrophic methanogenesis is receiving an increasing attention worldwide because of the demand for renewable natural gas. Herein, a holistic and statistical study of the operation conditions, driving forces, performances, and potential implementation of biogas upgrading via biological CO 2 conversion was conducted. Based on a systematic review and meta-analysis of 46 existing publications that were selected from 1475 papers, we have compiled a global dataset of CO 2 bioconversion biogas upgrading, encompassing 308 study cases. Subsequently, we employed a rigorous analytical framework incorporating data processing and mixed effects linear regression analysis to examine the dataset. This analysis revealed a significant positive relationship between the H 2 :CO 2 ratio and the methane percentage in the upgraded biogas when using the study as a random effect. Furthermore, we performed meta-analysis on observations taken when the ratio was close to 4:1 and found that ex situ reactors (91.93% [88.11%, 95.75%]) can perform better than in situ reactors (84.74% [80.69%, 88.80%]). No evidence of differential performance was found based on the present dataset between different temperature regimes or operation modes. Furthermore, those findings establish a database that will contribute to a deeper understanding of the biogas upgrading via biological CO 2 conversion.

Biogas upgrading↗