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DOE OSTI2023

A hybrid deep neural operator/finite element method for ice-sheet modeling

One of the most challenging and consequential problems in climate modeling is to provide probabilistic projections of sea level rise. A large part of the uncertainty of sea level projections is due to uncertainty in ice sheet dynamics. At the moment, accurate quantification of the uncertainty is hindered by the cost of ice sheet computational models. In this work we develop a hybrid approach to approximate existing ice sheet models at a fraction of their cost. Our approach consists of replacing the finite element model for the momentum equations for the ice velocity, the most expensive part of an ice sheet model, with a Deep Operator Network, while we retain a classic finite element discretization for the evolution of the ice thickness. We show that the resulting hybrid model is very accurate and it is an order of magnitude faster than the traditional finite element model. Further, a distinctive feature of the proposed model, compared to other neural network approaches, is that it can handle high-dimensional parameter spaces (parameter fields) such as the basal friction at the bed of the glacier and can therefore be used for generating samples for uncertainty quantification. Further, we study the impact of hyper-parameters, number of unknowns and correlation length of the parameter distribution on the training and accuracy of the Deep Operator Network on a synthetic ice sheet model. We then target the evolution of the Humboldt glacier in Greenland and show that our hybrid model can provide accurate statistics of the glacier mass loss and can be effectively used to accelerate the quantification of uncertainty.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Quantitative and qualitative bone imaging: A review of synchrotron radiation microtomography analysis in bone research

All levels of the unique hierarchical structure of bone, consisting of collagen and hydroxyapatite crystals at the nanoscale to osteon/lamellae structures at the microscale, contribute to its characteristic toughness and material properties. Elements of bone's density and size contribute to bone quantity (or bone mass), whereas elements of bone's material composition, material properties, internal structure, and organization describe bone quality. Furthermore, bone quantity and quality can be degraded by factors such as aging, disease, treatments, and irradiation, compromising its ability to resist fracture and sustain loading. Accessing the morphology and architecture of bone at the microscale to quantify microstructural features and assess the degree of mineralization and path of crack propagation in bone provides crucial information on how these factors are influencing bone quantity and quality. Synchrotron radiation micro-computed tomography (SRμCT) was first used to assess bone structure at the end of the 1990's. One of the main advantages of the technique is that it enables accurate three-dimensional (3D), non-destructive quantification of structure while traditional histomorphometry on histological sections is inherantly destructive to the sample and two-dimensional (2D). Additionally, SRμCT uses monochromatic, high-flux X-ray beams to provide high-resolution and high-contrast imaging of bone samples. This allows the quantification of small microstructural features (e.g. osteocyte lacunae, canals, trabeculae, microcracks) and direct gray value compositional mapping (e.g. mineral quantification, cement lines) with greater speed and fidelity than lab-based micro-computed tomography. In this article, we review how SRμCT has been applied to bone research to elucidate the mechanisms by which bone aging, disease, and other factors affect bone fragility and resistance to fracture.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

An image-driven machine learning approach to kinetic modeling of a discontinuous precipitation reaction

Micrograph quantification is an essential component of several materials science studies. Machine learning methods, in particular convolutional neural networks, have previously demonstrated performance in image recognition tasks across several disciplines (e.g. materials science, medical imaging, facial recognition). Here, we apply these well-established methods to develop an approach to microstructure quantification for kinetic modeling of a discontinuous precipitation reaction in a case study on the uranium-molybdenum system. Prediction of material processing history based on image data (classification), calculation of area fraction of phases present in the micrographs (segmentation), and kinetic modeling from segmentation results were performed. Results indicate that convolutional neural networks represent microstructure image data well, and segmentation using the k-means clustering algorithm yields results that agree well with manually annotated images. Classification accuracies of original and segmented images are both 94% for a 5-class classification problem. Kinetic modeling results agree well with previously reported data using manual thresholding. The image quantification and kinetic modeling approach developed and presented here aims to reduce researcher bias introduced into the characterization process, and allows for leveraging information in limited image data sets.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Distinguishing fissile uranium isotopes using an active well neutron coincidence counter

Proposed thorium-based nuclear fuel cycles are likely to require quantification and verification of 233 U within nuclear material. Because of their similar fission cross sections, active neutron nondestructive assay (NDA) systems may respond similarly to 233 U and 235 U. Traditional safeguards equipment has been optimized for 235 U and 238 U quantification associated with conventional uranium/plutonium fuel cycles and may not be directly applicable to 233 U quantification when mixed with other actinides. This work used models of the large volume active well coincidence counter (LV-AWCC) at Oak Ridge National Laboratory to evaluate the performance of this neutron NDA system to differentiate fissile uranium isotopes. The models were developed to simulate NDA system performance in response to a number of triangular radiation signature training device sources within the central cavity or well. This work predicted that the LV-AWCC can effectively differentiate 233 U from 235 U in certain modes of operation. In active mode, the LV-AWCC with the cadmium liner results in different doubles count rates between the fissile isotopes for a given fissile uranium mass. Without the cadmium liner, the uranium isotopes provide a statistically indistinguishable doubles count rate response for the fissile masses considered in this work (up to approximately 150 g). The cadmium liner serves to harden the neutron interrogation spectrum, which better exploits the notable difference in the 233 U and 235 U fission cross sections at approximately 1 eV. In passive mode, the two fissile isotopes exhibit different doubles and singles count rates regardless of liner presence because the passive source strength of 233 U is approximately 2 orders of magnitude stronger than that of 235 U due to the shorter half-life and correspondingly higher (α, n) yield. We conclude that using neutron interrogation in the LV-AWCC, two measurements are needed to quantify 233 U content in mixed uranium items. The first measurement is used to determine the total fissile uranium mass using a mode that cannot distinguish fissile isotopes (i.e., where a similar response is observed for both fissile uranium isotopes such as active doubles without cadmium or using a thermal neutron interrogation source). In conclusion, the second measurement is used to determine the 233 U content by using a differentiating technique (e.g., passive doubles, passive doubles to singles ratio, active doubles with cadmium).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Fossil fuel CO 2 emissions over metropolitan areas from space: A multi-model analysis of OCO-2 data over Lahore, Pakistan

Urban areas, where gathering more than 55% of the global population, alone contributed to more than 70% of anthropogenic fossil fuel carbon dioxide (CO 2ff ) emissions. Accurate quantification of CO 2ff emissions from urban areas is of great importance to the formulation of global warming mitigation policies to achieve carbon neutrality by 2050. Satellite-based inversion techniques are unique among “top-down” approaches, potentially allowing us to track CO 2ff emission changes over cities globally. However, its accuracy is still limited by incomplete background information, cloud blockages, aerosol contaminations, and uncertainties in models and emission inventories used as prior. To evaluate the current potential of space-based quantification techniques, we present the first attempt to monitor long-term changes in CO 2ff emissions based on the OCO-2 satellite measurements of column-averaged dry-air mole fractions of CO 2 (X CO2 ) over a fast-growing Asian metropolitan area: Lahore, Pakistan. We first examined the OCO-2 data availability at global scale. About 17% of OCO-2 soundings are marked as high-quality soundings by quality flags over the global 70 most populated cities over the period 2014-2019. Cloud blockage and aerosol contamination are the two main causes of data loss. As an attempt to recover additional soundings, we evaluated the effectiveness of OCO-2 quality flags at the city level by comparing three flux quantification methods (WRF-Chem, X-STILT, and flux cross-sectional integration method), all based on the Open-Data Inventory for Anthropogenic Carbon dioxide (ODIAC) product. The satellite/bottom-up emissions (OCO-2/ODIAC) ratios of the high-quality tracks better converged across the three methods compared to the all-data tracks with reduced uncertainties in emissions. Thus, OCO-2 quality flags are useful filters of low-quality OCO-2 retrievals at local scales, although originally designed for global-scale studies. All three methods consistently suggested that the ratio medians are greater than 1, which implies that the ODIAC slightly underestimated the CO2ff emissions over Lahore. Additionally, our estimation of the a posteriori CO2ff emission trend was about 734 kt C/year (i.e., an annual 6.7% increase). 10,000 Monte Carlo simulations of the Mann-Kendall upward trend test showed that less than 10% prior uncertainty for 8 tracks (or less than 20% prior uncertainty for 25 tracks) is required to achieve a greater-than-50% trend significant possibility at a 95% confidence level. It implies that the trend is driven by the prior and not due to the assimilation of OCO-2 retrievals. The key to improving the role of satellite data in CO 2 emission trend detection lies in collecting more frequent high-quality tracks near metropolitan areas to achieve significant constraints from X CO2 retrievals.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Dispersion curve regression – assisted wideband local wavenumber analysis for characterizing three-dimensional (3D) profile of hidden corrosion damage

Corrosion as common damage in civil, petrochemical, nuclear, and aerospace structures affects the integrity and safety of the structures and may lead to catastrophic failures. This paper presents dispersion curve regression-assisted local wavenumber analysis method, which can analyze the time–space wavefield containing wideband information of wave-damage interaction and further extract the structural information carried by such wavefield for characterizing hidden corrosion damage in an isotropic plate. To acquire the time–space wavefield, a noncontact scanning laser Doppler vibrometer is used. In our analysis method, the acquired time–space wavefield is firstly processed to generate a local wavenumber function. The derived wavenumber function is further analyzed with a dispersion curve regression step, which searches in a set of theoretical frequency-wavenumber dispersion curves for different plate thicknesses and identifies the optimal plate thickness whose theoretical curve best matches the frequency-wavenumber relation contained in the local wavenumber function. By this means, a 3D profile including both in plane and thickness dimensions of the structure can be constructed for corrosion visualization and quantification. The experimental study demonstrates that our method can quantify the profile of hidden uniform corrosion in metal plates in terms of its in-plane shape and size as well as its out-of-plane depth in the subwavelength scale. Moreover, compared to previous Lamb wave-based corrosion inspection methods, our technique allows for noncontact 3D characterization of hidden corrosion from a far distance to the structure. Finally, we believe this work will inspire new 3D damage quantification methods that are based on wavefield analysis as well as enable potential applications for the quantification of hidden corrosion in civil, petrochemical, nuclear, and aerospace structures.

42 ENGINEERING↗

DOE OSTI2023

Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics

There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Here, in this paper, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments 1 offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

Min, Sehong↗

DOE OSTI2026

A Robust Methodology to Elucidate Kinetics of Room Temperature Electrochemical Propane Adsorption on Platinum

Electrocatalytic activation of alkanes can further decarbonize chemical manufacturing by leveraging affordable renewable electricity and readily available shale gas reserves in the United States. Earlier works have identified the unique role of Pt in adsorbing and activating alkanes, like propane, at room temperature in acidic, aqueous electrolytes, revealing spontaneous formation of deeply dehydrogenated propane-derived surface species with an intact C 3 - backbone. Although an adsorption mechanism was hypothesized, it has not been explicitly investigated to date, preventing the quantification of kinetic rate parameters. A robust methodology to investigate and benchmark propane adsorption kinetics on Pt is critical for the rational design of electrocatalysts that exhibit higher selectivity toward desired partially oxidized products. Herein, we analyze an oxidative current transience that appears during the adsorption of propane on Pt in aqueous electrochemical conditions and develop a methodology that elucidates the adsorption mechanism and enables quantification of rate parameters such as order dependences and apparent activation barriers. This method yields an expected first-order dependence with respect to propane concentration at low coverage and reveals a second-order dependence with respect to the concentration of surface active sites. Additionally, the apparent activation barrier for propane adsorption was calculated using an Arrhenius analysis of the current transience under temperature control. The experimentally measured activation barrier of 35 kJ mol –1 is in excellent agreement with the theoretical barrier calculated by density functional theory (DFT). The kinetic analysis was extended, via the use of transition state theory, to extract entropy and enthalpy of activation, yielding consistent results with the proposed two-step adsorption mechanism and DFT calculations. These results demonstrate reliable quantification of kinetic parameters for electrocatalytic activation of C–H bonds in alkanes that can be employed for rational catalyst development for a versatile range of electrocatalytic conditions.

alkane activation↗

DOE OSTI2025

Simulating Atmospheric Processes in Earth System Models and Quantifying Uncertainties With Deep Learning Multi‐Member and Stochastic Parameterizations

Abstract Deep learning is a powerful tool to represent subgrid processes in climate models, but many application cases have so far used idealized settings and deterministic approaches. Here, we develop stochastic parameterizations with calibrated uncertainty quantification to learn subgrid convective and turbulent processes and surface radiative fluxes of a superparameterization embedded in an Earth System Model (ESM). We explore three methods to construct stochastic parameterizations: (a) a single Deep Neural Network (DNN) with Monte Carlo Dropout; (b) a multi‐member parameterization; and (c) a Variational Encoder Decoder with latent space perturbation. We show that the multi‐member parameterization improves the representation of convective processes, especially in the planetary boundary layer, compared to individual DNNs. The respective uncertainty quantification illustrates that methods (b) and (c) are advantageous compared to a dropout‐based DNN parameterization regarding the spread of convective processes. Hybrid simulations with our best‐performing multi‐member parameterizations remained challenging and crash within the first days. Therefore, we develop a pragmatic partial coupling strategy relying on the superparameterization for condensate emulation. Partial coupling reduces the computational efficiency of hybrid Earth‐like simulations but enables model stability over 5 months with our multi‐member parameterizations. However, our hybrid simulations exhibit biases in thermodynamic fields and differences in precipitation patterns. Despite this, the multi‐member parameterizations enable improvements in reproducing tropical extreme precipitation compared to a traditional convection parameterization. Despite these challenges, our results indicate the potential of a new generation of multi‐member machine learning parameterizations leveraging uncertainty quantification to improve the representation of stochasticity of subgrid effects.

Behrens, Gunnar [Deutsches Zentrum für Luft‐ und R↗

DOE OSTI2019

Sparse Bayesian mass mapping with uncertainties: local credible intervals

ABSTRACT Until recently, mass-mapping techniques for weak gravitational lensing convergence reconstruction have lacked a principled statistical framework upon which to quantify reconstruction uncertainties, without making strong assumptions of Gaussianity. In previous work, we presented a sparse hierarchical Bayesian formalism for convergence reconstruction that addresses this shortcoming. Here, we draw on the concept of local credible intervals (cf. Bayesian error bars) as an extension of the uncertainty quantification techniques previously detailed. These uncertainty quantification techniques are benchmarked against those recovered via Px-MALA – a state-of-the-art proximal Markov chain Monte Carlo (MCMC) algorithm. We find that, typically, our recovered uncertainties are everywhere conservative (never underestimate the uncertainty, yet the approximation error is bounded above), of similar magnitude and highly correlated with those recovered via Px-MALA. Moreover, we demonstrate an increase in computational efficiency of $\mathcal {O}(10^6)$ when using our sparse Bayesian approach over MCMC techniques. This computational saving is critical for the application of Bayesian uncertainty quantification to large-scale stage IV surveys such as LSST and Euclid.

Price, M. A.↗

DOE OSTI2026

MAGIC: M arching Cubes Isosurface Uncertainty Visualization for G auss i an Uncertain Data With Spatial C orrelation

Here, in this paper, we study the propagation of data uncertainty through the marching cubes algorithm for isosurface visualization for correlated uncertain data. Consideration of correlation has been shown paramount for avoiding errors in uncertainty quantification and visualization in multiple prior studies. Although the problem of isosurface uncertainty with spatial data correlation has been previously addressed, there are two major limitations to prior treatments. First, there are no analytical formulations for uncertainty quantification of isosurfaces when the data uncertainty is characterized by a Gaussian distribution with spatial correlation. Second, as a consequence of the lack of analytical formulations,existing techniques resort to a Monte Carlo sampling approach, which is expensive and difficult to integrate into visualization tools. To address these limitations, we present a closed-form framework to efficiently derive uncertainty in marching cubes level-sets for Gaussian uncertain data with spatial correlation (MAGIC). To derive closed-form solutions, we leverage the Hinkley's derivation on the ratio of Gaussian distributions. With our analytical framework, we achieve a significant speed-up and enhanced accuracy of uncertainty quantification over classical Monte Carlo methods. We further accelerate our analytical solutions using many-core processors to achieve speed-ups up to 585× and integrability with production visualization tools for broader impact. We demonstrate the effectiveness of our correlation-aware uncertainty framework through experiments on meteorology, urban flow, and astrophysics simulation datasets.

Gaussian↗

DOE OSTI2021

jialiu232/MetaFunPrimer_paper_info

Genes belonging to the same functional group may include numerous and variable gene sequences, making characterizing and quantifying difficult. Therefore, high-throughput design tools are needed to simultaneously create primers for improved quantification of target genes. We developed MetaFunPrimer, a bioinformatic pipeline, to design primers for numerous genes of interest. This tool also enables gene target prioritization based on ranking the presence of genes in user-defined references, such as environment-specific metagenomes. Given inputs of protein and nucleotide sequences for gene targets of interest and an accompanying set of reference metagenomes or genomes, MetaFunPrimer generates primers for ranked genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 publicly available soil metagenomes. We demonstrate computationally that these amoA-AOB primers can cover 94% of the amoA-AOB genes observed in the 1,550 soil metagenomes compared with a 49% estimated coverage by previously published primers. Finally, we verified the utility of these primer sets in incubation experiments that used long-term nitrogen fertilized or unfertilized soils. High-throughput quantitative PCR (qPCR) results and statistical analyses showed significant differences in relative quantification patterns between the two soils, and subsequent absolute quantifications also confirmed that target genes enumerated by six selected primer pairs were significantly more abundant in the nitrogen-fertilized soils. This new tool gives microbial ecologists a new approach to assess functional gene abundance and related microbial community dynamics quickly and affordably.

Liu, Jia↗

DOE OSTI2020

Quantifying Uncertainties of Microscopic Nuclear Theories

The goal of this project was to produce modernized nuclear data libraries of light ion fusion reactions and actinide fission product yields. Such libraries are essential input in both stockpile science but also fundamental science (nucleosynthesis, superheavy nuclei). When such libraries are used to model complex processes involving exotic, very short-lived nuclei that have not been measured experimentally, the underlying nuclear data come from theoretical models, the predictive power of which needs to be quantified, together with its uncertainties. By teaming up nuclear theorists and statisticians, we built comprehensive theoretical frameworks based on the most fundamental theories of fusion and fission that we coupled for the first time with a Bayesian framework with machine learning techniques for uncertainty quantification. Our results include: (1) statistical emulators for neutron-alpha scattering, and the fission product mass yields of neutron-induced fission of 239 Pu, which will enable developers to generate random realizations of the corresponding data for uncertainty quantification (UQ) in applications; (2) the first complete and most accurate ab initio prediction of the S-factor for proton capture on 7 Be, which – combined with UQ – may become the recommended value at solar energies in the next review of solar fusion cross sections; (3) statistical emulators for fission mass yields in the neutron-induced fission of 239 Pu; (4) the first quantification of how uncertainties in nuclear forces impact fission properties that are relevant in nucleosynthesis simulations to explain how heavy elements are formed in the Cosmos.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

National User Resource for Biological Accelerator Mass Spectrometry Annual Report

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Evaluation of partial volume correction and analysis of longitudinal [ 18 F]GTP1 tau PET imaging in Alzheimer's disease using linear mixed-effects models

Purpose: We evaluated the impact of partial volume correction (PVC) methods on the quantification of longitudinal [ 18 F]GTP1 tau positron-emission tomography (PET) in Alzheimer's disease and the suitability of describing the tau pathology burden temporal trajectories using linear mixed-effects models (LMEM). Methods: We applied van Cittert iterative deconvolution (VC), 2-compartment, and 3-compartment, and the geometric transfer matrix plus region-based voxelwise methods to data acquired in an Alzheimer's disease natural history study over 18 months at a single imaging site. We determined the optimal PVC method by comparing the standardized uptake value ratio change (%ΔSUVR) between diagnostic and tau burden–level groups and the longitudinal repeatability derived from the LMEM. The performance of LMEM analysis for calculating %ΔSUVR was evaluated in a natural history study and in a multisite clinical trial of semorinemab in prodromal to mild Alzheimer's disease by comparing results to traditional per-visit estimates. Results: The VC, 2-compartment, and 3-compartment PVC methods had similar performance, whereas region-based voxelwise overcorrected regions with a higher tau burden. The lowest within-subject variability and acceptable group separation scores were observed without PVC. The LMEM-derived %ΔSUVR values were similar to the per-visit estimates with lower variability. Conclusion: The results indicate that the tested PVC methods do not offer a clear advantage or improvement over non-PVC images for the quantification of longitudinal [ 18 F]GTP1 PET data. LMEM offers a robust framework for the longitudinal tau PET quantification with low longitudinal test–retest variability. Clinical trial registration: NCT02640092 and NCT03289143.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Picometer-Precision Atomic Position Tracking through Electron Microscopy

The modern aberration-corrected scanning electron microscopes have successfully achieved direct visualization of atomic columns with sub-angstrom resolution. With this significant progress, advanced image quantification and analysis is still at its early stages. In this work, we present the complete pathway for the metrology of atomic resolution STEM images. This includes: 1) tips for acquiring high-quality STEM images; 2) denoising and drift-correction for enhancing measurement accuracy; 3) obtaining initial atom positions; 4) indexing the atoms based on unit cell vectors; 4) quantifying the atom column positions with either 2D-gaussian single peak fitting or 5) multi-peak fitting routines for slightly overlapping atomic columns; 6) quantification of lattice distortion/strain within the crystal structures or at the defects/interfaces where the lattice periodicity is disrupted, and 7) some common methods to visualize and present the analysis. Furthermore, a simple self-developed free MATLAB app (EASY-STEM) with a graphical user interface (GUI) will be introduced that can help with the analysis of STEM images without the need for writing dedicated analysis code or software. The advanced data analysis methods presented here can be applied for the local quantification of defect relaxations, local structural distortions, local phase transformations, and non-centrosymmetry in a wide range of materials.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Orphaned oil and gas well methane emission rates quantified using Gaussian plume inversions of ambient observations

Abstract. Annually, ∼ 3.6 million abandoned oil and gas wells in the US emit a combined ∼ 2.6 Tg methane (CH4), adversely affecting climate and regional air quality. However, these estimates depend on emission factors derived from measuring subpopulations of wells that vary by orders of magnitude due to very limited field sampling and poorly characterized distributions. Currently, US protocols to remediate orphaned wells lacks standardized quantification methods needed to both prioritize plugging and account for emission reductions. Therefore, sensitive, reliable, affordable, and scalable CH4 flux quantification methods are needed. We report the use of a simple Gaussian plume method where the dispersion parameters are constrained by in situ ground measurements of CH4 concentration at four locations 7.5–49 m downwind of the orphan well as well as local winds to estimate the leak rate from an orphan well. We derive a flux of 10.53 ± 1.16 kg CH4 h−1 during a venting procedure in April 2023 that agrees with the directly measured volumetric flow rate of 9.00 ± 0.25 kg CH4 h−1. This is 71 % greater than the 5.3 kg CH4 h−1 flux measured 7 months prior. Additionally, we discovered a secondary leak through the surface casing inferred as 0.43–0.67 kg CH4 h−1 both by our ground Gaussian analysis and by transecting the plume with an uncrewed aerial system (UAS). We show that in situ determination of the dispersion parameters used in our Gaussian inversions allows us to measure methane emissions to 15 % accuracy, significantly reducing errors when compared to the standard practice of assuming stability class. Our results help develop simpler methods and protocols for robust orphan well emission quantification that can be used for reporting.

Follansbee, Emily↗