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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Outgrowth of erlotinib-resistant subpopulations recapitulated in patient-derived lung tumor spheroids and organoids

A model that recapitulates development of acquired therapeutic resistance is needed to improve oncology drug development and patient outcomes. To achieve this end, we established methods for the preparation and growth of spheroids from primary human lung adenocarcinomas, including methods to culture, passage, monitor growth, and evaluate changes in mutational profile over time. Primary lung tumor spheroids were cultured in Matrigel® with varying concentrations of erlotinib, a small molecule kinase inhibitor of epidermal growth factor receptor (EGFR) that is ineffective against KRAS mutant cells. Subtle changes in spheroid size and number were observed within the first two weeks of culture. Spheroids were cultured for up to 24 weeks, during which time interactions between different cell types, movement, and assembly into heterogeneous organoid structures were documented. Allele-specific competitive blocker PCR (ACB-PCR) was used to quantify low frequency BRAF V600E, KRAS G12D, KRAS G12V, and PIK3CA H1047R mutant subpopulations in tumor tissue residue (TR) samples and cultured spheroids. Mutant subpopulations, including multiple mutant subpopulations, were quite prevalent. Twelve examples of mutant enrichment were found in eight of the 14 tumors analyzed, based on the criteria that a statistically-significant increase in mutant fraction was observed relative to both the TR and the no-erlotinib control. Of the mutants quantified in erlotinib-treated cultures, PIK3CA H1047 mutant subpopulations increased most often (5/14 tumors), which is consistent with clinical observations. Thus, this ex vivo lung tumor spheroid model replicates the cellular and mutational tumor heterogeneity of human lung adenocarcinomas and can be used to assess the outgrowth of mutant subpopulations. Spheroid cultures with characterized mutant subpopulations could be used to investigate the efficacy of lung cancer combination therapies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

ABSTRACT RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3′ untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5′ and 3′ UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator. IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO 2 and sunlight into useful products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Enriching Load Data Using Micro-PMUs and Smart Meters

In modern distribution systems, load uncertainty can be fully captured by micro-PMUs, which can record high-resolution data; however, in practice, micro-PMUs are installed at limited locations in distribution networks due to budgetary constraints. In contrast, smart meters are widely deployed but can only measure relatively low-resolution energy consumption, which cannot sufficiently reflect the actual instantaneous load volatility within each sampling interval. In this paper, we have proposed a novel approach for enriching load data for service transformers that only have low-resolution smart meters. The key to our approach is to statistically recover the high-resolution load data, which is masked by the low-resolution data, using trained probabilistic models of service transformers that have both high- and low-resolution data sources, i.e., micro-PMUs and smart meters. The overall framework consists of two steps: first, for the transformers with micro-PMUs, a Gaussian Process is leveraged to capture the relationship between the maximum/minimum load and average load within each low-resolution sampling interval of smart meters; a Markov chain model is employed to characterize the transition probability of known high-resolution load. Next, the trained models are used as teachers for the transformers with only smart meters to decompose known low-resolution load data into targeted high-resolution load data. The enriched data can recover instantaneous load uncertainty and significantly enhance distribution system observability and situational awareness. Here, we have verified the proposed approach using real high- and low-resolution load data.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Data for Transposon Signatures of Allopolyploid Genome Evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

Genomics↗
DOE OSTI2024

STAT7 v1.2 Verification and Validation Report

This report documents the software testing which has been performed for the STAT7 Version 1.2 (hereafter STAT7 v1.2) software, a code for the statistical propagation of uncertainties in steady-state thermal hydraulics (TH) analysis of plate-fueled research and test reactors. The key capabilities addressed in this testing were selected based on the use of the software for analysis work supporting the conversion to low-enriched uranium fuel of U.S. High-Performance Research Reactors (USHPRR) such as the Massachusetts Institute of Technology Research Reactor (MITR-II). This testing scope includes comparison of the code’s statistical processing capabilities using statistical tests, comparison of coolant property evaluations to NIST data tables, and systematic comparison of key TH solver capabilities to the results of hand calculations and to predictions from PLTEMP/ANL Version 4.4. The good agreement achieved in this testing campaign, within the acceptance criteria of a 1% relative difference, also demonstrates that these capabilities have been implemented in STAT7 v1.2 correctly.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

STAT7 v2.0 Verification and Validation Report

This report documents the software testing which has been performed for STAT7 Version 2.0 (hereafter STAT7 v2.0), a code for the statistical propagation of uncertainties in steady-state thermal hydraulics (TH) analysis of plate-fueled research and test reactors. The key capabilities addressed in this testing were selected based on the use of the software for analysis work supporting the conversion to low-enriched uranium fuel of U.S. High-Performance Research Reactors (USHPRR) such as the Massachusetts Institute of Technology Research Reactor (MITR-II). This testing scope includes comparison of the code’s statistical processing capabilities using statistical tests, comparison of coolant property evaluations to NIST data tables, and systematic comparison of key TH solver capabilities to the results of hand calculations and to predictions from PLTEMP/ANL Version 4.4. The

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

A new generation of uranium coincidence fast neutron collars for assay of LWR fresh fuel assemblies

The active uranium neutron coincidence collar provides a means of non-destructively assaying the fissile linear density of Light Water Reactor fresh fuel assemblies containing low enriched uranium. These neutron collars can operate in two modes: a thermal and a fast mode. In fast mode, a neutron collar has an added cadmium (Cd) liner in the sample cavity of the detector to reduce the impact of the burnable poison (thermal neutron absorber) on the detector signal (doubles). The main advantage for operating in fast mode is a detected signal that is less dependent of the burnable neutron poison content and thus less dependent on facility operator declarations. The drawback is that operating in fast mode requires a longer measurement time (~hour vs tens of minutes for thermal mode) to achieve the statistically needed precision in the measurements. The trend in the modern reactor fuel assemblies is moving to higher burnup by using higher initial enrichment and, consequently, a higher number of burnable poison rods to compensate the initial neutron reactivity. The increase of the burnable poison loading has motivated the development of a new generation of high efficiency fast neutron collars to allow practical measurements in-field by nuclear inspectors. This paper describes the development and performance evaluation of a new generation of neutron collars, for both boiling water reactor (BWR) and pressurized water reactor (PWR) fuels, jointly developed between the US Department of Energy, through Los Alamos National Laboratory, and the Euratom Safeguards Directorate of the European Commission. In this work, we present here calibrations with reference fuel assemblies at Los Alamos National Laboratory as well as the results of in-field measurement campaigns in fuel fabrication plants with modern commercial fuel assemblies. The experimental results show that a typical PWR verification can be made in a total time of 30 min with an uncertainty in the measured mass of 2% at one standard deviation (1σ). A BWR verification can be made in 47 min with an uncertainty in the measured mass of 1.9% at 1σ, or a total time of 20 min with 1σ uncertainty in the measured mass of 2.5%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

NE-COST plug-in: Expanding ACCERT's Capabilities for Life-Cycle Cost Modeling

The Algorithm for the Capital Cost Estimation of Reactor Technologies (ACCERT) is a structured methodology and software tool designed to simplify and standardize cost estimation for nuclear reactor technologies [1]. By utilizing a relational database structure and modular cost estimation algorithms, ACCERT delivers a robust, flexible, and scalable framework for evaluating costs across various reactor types and configurations [2]. The recent integration of the NE-COST plugin further expands ACCERT’s scope by introducing detailed life-cycle cost modeling and probabilistic analysis of uncertainties. This addition enables users to evaluate costs across front-end processes such as uranium enrichment and fabrication, as well as back-end activities including waste disposal and geologic storage. Through Monte Carlo statistical cost simulations, the plugin provides probabilistic insights into cost ranges, offering critical decision-making support for stakeholders including reactor developers, policymakers, and researchers.

Zhou, Jia↗
DOE OSTI2026

Conserved Macromolecular Architecture of Poplar Secondary Cell Walls Revealed by ssNMR and Atomistic Modeling

The macromolecular architecture of plant secondary cell walls governs wood's mechanical and biochemical properties, yet its natural intra-species variability remains poorly characterized. Here, we combined 13C solid-state NMR (ssNMR), multivariate statistical analysis, and molecular modeling to profile nanoscale structure across 13 genetically diverse Populus trichocarpa genotypes grown in 13C-enriched atmospheres. SsNMR-derived phenotypes spanning composition, structure, mobility, and inter-polymer proximities reveal a conserved architecture, with a subtle yet coordinated variation organizing into dominant structural and secondary mobility axes. A representative atomistic model captures these features and reproduces experimental metrics. Molecular dynamics simulations support a weak but consistent positive correlation between cellulose abundance and crystalline-like order, with interior cellulose chains enriched in tg (trans-gauche) conformations without expanding crystalline cores. Together, experiment and simulation reveal a genetically buffered, broadly conserved nanoscale architecture across genotypes, where subtle fine-tuning of cellulose bundling and matrix packing balances mechanical performance with biological function.

09 BIOMASS FUELS↗
DOE OSTI2020

Multi-scale microstructural investigation of a laser 3D printed Ni-based superalloy

The heterogeneous microstructure of a laser 3D printed Ni-based superalloy was examined at multiple length scales. The sub-millimeter-sized columnar crystal grains are composed of micron-sized cellular colonies. The crystal grains grow in epitaxy with the substrate under the large temperature gradient and high cooling rate. The cell boundaries, decorated with γ/γ' eutectics, μ-phase precipitates and high density of dislocations, show enrichment of γ' forming elements and low-angle misorientations. Dislocations trapped in the intra-cellular regions are characterized as statistically stored dislocations with no detectable contribution to lattice curvature, and are the results of the interaction between dislocations and γ' precipitates.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Atom Probe Tomography Investigation of Clustering in Model P 2 O 5 -Doped Borosilicate Glasses for Nuclear Waste Vitrification

Atom probe tomography (APT) has been utilized to investigate the microstructure of two model borosilicate glasses designed to understand the solubility limits of phosphorous pentoxide (P 2 O 5 ). This component is found in certain high-level radioactive defence wastes destined for vitrification, where phase separation can potentially lead to a number of issues relating to the processing of the glass and its long-term chemical and structural stability. The development of suitable focused ion beam (FIB)-preparation routes and APT analysis conditions were initially determined for the model glasses, before examining their detailed microstructures. In a 3.0 mol% P 2 O 5 -doped glass, both visual inspection and sensitive statistical analysis of the APT data show homogeneous microstructures, while raising the content to 4.0 mol% initiates the formation of phosphorus-enriched nanoscale precipitates. This study confirms the expected inhomogeneities and phase separation of these glasses and offers routes to characterizing these at near-atomic scale resolution using APT.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

STAT7 v1.2 User Guide: The STAT7 Code for Statistical Propagation of Uncertainties in Steady-State Thermal Hydraulics Analysis of Plate-Fueled Reactors

The STAT7 software was developed to perform steady-state, single-phase thermal hydraulics analysis of plate-fueled reactors based on statistical propagation of uncertainties. Application of the software is for non-power research and test reactors, including conversion to low-enriched uranium fuel of U.S. High-Performance Research Reactors such as Massachusetts Institute of Technology Research Reactor. Since it can be necessary to repeat analysis during fuel reloading, STAT7 accommodates flexibility in analyzing many realistic aspects of reactor fuel management. STAT7 uses a Monte Carlo approach to model uncertainty in common fuel fabrication parameters and other key reactor operating parameters required for thermal hydraulics analyses of research and test reactors. These safety calculations are ultimately intended to protect against high fuel plate temperatures due to critical heat flux, or onset of flow instability. STAT7 supports water properties based on the IAPWS-IF97 functions (The International Association for the Properties of Water and Steam Industrial Formulation 1997 for the Thermodynamic Properties of Water and Steam) in addition to the fit functions. STAT7 predicts axial profiles of fuel, cladding, and coolant temperature along a lateral stripe that runs the full length of the fuel plate from the bottom to the top. STAT7 can simultaneously analyze all of the axial nodes of all of the fuel plates and all of the coolant channels for one latera stripe of a fuel element. Power splits are calculated for each axial node of each plate to determine how much of the power goes out each face of the plate. By running STAT7 multiple times, full core analysis can be performed by analyzing the margin to onset of nucleate boiling and onset of flow instability for each axial node of each stripe of each plate of each fuel element in the core.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Modeling the Photoelectrochemical Evolution of Lead-Based, Mixed-Halide Perovskites Due to Photosegregation

Lead-based, mixed-halide perovskites such as methylammonium lead iodide-bromide [MAPb(I 1-x Br x ) 3 ] undergo anion photosegregation under illumination. This is observed as low band gap photoluminescence from photogenerated iodine-rich domains due to favorable band offsets that induce carrier funneling into them. Unfortunately, theoretical rationalizations of mixed-halide photosegregation are complicated by biases inherent to photoluminescence-based observations. Recent compositionally-weighted X-ray diffraction (XRD) measurements now reveal broad distributions of photosegregated stoichiometries not captured by existing photosegregation models. To better bridge experiment and theory, we perform kinetic Monte Carlo (KMC) simulations of photosegregation within the context of a band gap-based thermodynamic model, which has previously accounted for numerous experimental observations. Our KMC simulations are modified to consider high carrier density Fermi-Dirac statistics that result from carrier funneling and accumulation within photosegregated I-rich domains. Obtained KMC results reproduce broad x terminal distributions seen experimentally and illustrate how they are characterized by a central, heavily I-enriched stoichiometry. I-rich domain “drifting” during photosegregation rationalizes the long photosegregation timescales seen experimentally with drifting simultaneously producing a wake of variable stoichiometry I-rich inclusions that form the lion’s share of stoichiometric heterogeneities seen in compositionally-weighted XRD measurements. These simulations and accompanying rationalizations further reveal a general criterion for realizing favorable free energies to induce demixing. Central to the criterion is the statistical occupation of low gap inclusions in the parent alloy by excitations. Furthermore, the resulting model thus provides a general framework for conceptualizing mixed-halide perovskite light and temperature sensitivities, mediated by photocarriers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica , a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Transposon signatures of allopolyploid genome evolution

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

amsession/Kmer-based-Subgenome-Mapping

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

Session, Adam↗
DOE OSTI2025

STAT7 v2.0 User Guide

The STAT7 software was developed to perform steady-state, single-phase thermal hydraulics analysis of plate-fueled reactors based on statistical propagation of uncertainties. Application of the software includes non-power research and test reactor analysis, and it has been used for the conversion to low- enriched uranium fuel of U.S. High Performance Research Reactors such as the Massachusetts Institute of Technology Research Reactor. Since it can be necessary to repeat reactor safety analysis, such as during fuel reloading, STAT7 accommodates flexibility in analyzing many practical aspects of reactor fuel management. STAT7 uses a Monte Carlo approach to model uncertainty in common fuel fabrication parameters and other key reactor operating parameters required for reactor thermal hydraulics analysis. These safety calculations are ultimately intended to protect against high fuel plate temperatures due to critical heat flux, or onset of flow instability. STAT7 supports water properties based on the IAPWS-IF97 functions (The International Association for the Properties of Water and Steam Industrial Formulation 1997 for the Thermodynamic Properties of Water and Steam) in addition to fitted functions. STAT7 predicts axial profiles of fuel, cladding, and coolant temperature along a lateral stripe that runs the full length of the fuel plate from the bottom to the top. STAT7 can simultaneously analyze every axial node in each lateral stripe of all fuel plates and coolant channels in every fuel element of an entire reactor core. Power splits are calculated for each axial node of each plate to determine how much of the power goes out each face of the plate. In a single execution, STAT7 can be used to perform full core analysis by analyzing the margin to onset of nucleate boiling and onset of flow instability for each axial node of each stripe of each plate of each fuel element in the core.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Direct cross section measurement of 102 Pd ⁢(𝛾,𝑝) and 102 Pd ⁢(𝛾,𝛼) for the astrophysical 𝑝 process

Background: A handful of neutron-deficient stable nuclei, known as the “p nuclei,” cannot be produced through astrophysical neutron capture processes. Instead, some of these nuclei are proposed to be produced by 𝛾-induced reactions on existing r- and s-process seeds. The specific astrophysical site or sites are not yet identified, however, with uncertainties in the cross sections of these 𝛾-induced reactions playing a role. Databases of reaction rates for astrophysical simulations often rely on theoretical statistical model calculations, such as Hauser-Feshbach, for rates where no experimental information is known. However, reasonable variations in the choice of parametrizations of various nuclear properties can create order-of-magnitude variations in the final predicted cross sections and reaction rates, which are then propagated through the models to the predicted final abundances. Purpose: To better constrain these statistical model calculations and ultimately reduce the uncertainties from the nuclear physics on our understanding of the p nuclei, a measurement of the cross sections of 𝛾-induced reactions on the p-nucleus 102 Pd was undertaken. This work represents the first measurement of its kind, using segmented silicon detectors to measure prompt charged particle emission from 𝛾-induced reactions. Methods: Quasimonoenergetic gamma beams from the High Intensity 𝛾 Source facility bombarded an enriched 102 Pd target. A segmented silicon array was arranged to detect the particles emitted from (𝛾,𝑝) and (𝛾,𝛼) reactions. Results: Reaction cross sections were deduced at multiple 𝛾-beam energies between 10 and 19 MeV, and compared to statistical model calculations using talys-1.96. The 102 Pd ⁢(𝛾,𝑝)⁢ 101 Rh reaction cross section was reasonably well reproduced by a subset of photon strength functions and level densities, though the strength to the ground state of 101 Rh was underestimated at higher incident gamma energies. The 102 Pd ⁢(𝛾,𝛼)⁢ 98 Ru was in general overpredicted by the various alpha-nucleus optical model potentials. Conclusions: While the theoretical cross sections used to model the (𝛾,𝑝) reactions for the p process may be reasonable, a more careful approach is needed in the case of (𝛾,𝛼). Further work to probe gamma-induced reaction cross sections at and near the p nuclei is warranted.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗