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At least 163 records · Page 9

Assessment of Clonal Expansion Using CarcSeq Measurement of Lung Cancer Driver Mutations and Correlation With Mouse Strain- and Sex-Related Incidence of Spontaneous Lung Neoplasia

Quantification of variation in levels of spontaneously occurring cancer driver mutations (CDMs) was developed to assess clonal expansion and predict future risk of neoplasm development. Specifically, an error-corrected next-generation sequencing method, CarcSeq, and a mouse CarcSeq panel (analogous to human and rat panels) were developed and used to quantify low-frequency mutations in a panel of amplicons enriched in hotspot CDMs. Mutations in a subset of panel amplicons, Braf, Egfr, Kras, Stk11, and Tp53, were related to incidence of lung neoplasms at 2 years. This was achieved by correlating median absolute deviation (MAD) from the overall median mutant fraction (MF) measured in the lung DNA of 16-week-old male and female, B6C3F1 and CD-1 mice (10 mice/sex/strain) with percentages of spontaneous alveolar/bronchioloalveolar adenomas and carcinomas reported in bioassay control groups. A total of 1586 mouse lung mutants with MFs > x 10-4 were recovered. The ratio of nonsynonymous to synonymous mutations was used to assess the proportion of recovered mutations conferring a positive selective advantage. The greatest ratio was observed in what is considered the most lung tumor-sensitive model examined, male B6C3F1 mice. Of the recurrent, nonsynonymous mouse mutations recovered, 55.5% have been reported in human tumors, with many located in or around the mouse equivalent of human cancer hotspot codons. MAD for the same subset of amplicons measured in normal human lung DNA samples showed a correlation of moderate strength and borderline significance with age (a cancer risk factor), as well as age-related cumulative lung cancer risk, suggesting MAD may inform species extrapolation.

Toxicology↗

Meta-uncertainty for particle image velocimetry

Uncertainty quantification for Particle Image Velocimetry (PIV) is critical for comparing experimentally measured flow fields with Computational Fluid Dynamics (CFD) results, and model design and validation. However, PIV features a complex measurement chain with coupled, non-linear error sources, and quantifying the uncertainty is challenging. Multiple assessments show that none of the current methods can reliably measure the actual uncertainty across a wide range of experiments, and estimates can vary. Because the current methods differ in assumptions regarding the measurement process and calculation procedures, it is not clear which method is best to use for an experiment where the error distribution is unknown. To address this issue, we propose a method to estimate an uncertainty method's sensitivity and reliability, termed the Meta-Uncertainty. The novel approach is automated, local, and instantaneous, and based on perturbation of the recorded particle images. We developed an image perturbation scheme based on adding random unmatched particles to the interrogation window pair considering the signal-to-noise (SNR) of the correlation plane. Each uncertainty scheme's response to several trials of random particle addition is used to estimate a reliability metric, defined as the rate of change of the inter-quartile range (IQR) of the uncertainties with increasing levels of particle addition. We also propose applying the meta-uncertainty as a weighting metric to combine uncertainty estimates from individual schemes, based on ideas from the consensus forecasting literature. We use planar and stereo PIV measurements across a range of canonical flows to assess the performance of the uncertainty schemes. Further, a novel method is introduced to assess an uncertainty scheme's performance based on a quantile comparison of the error and uncertainty distributions, generalizing the current method of comparing the RMS of the two distributions. Here, the results show that the combined uncertainty method outperforms the individual methods, and this work establishes the meta-uncertainty as a useful reliability assessment tool for PIV uncertainty quantification.

47 OTHER INSTRUMENTATION↗

Bottom-up and Top-Down Uncertainty Quantification for Measurements

Several recent papers address improved uncertainty quantification (UQ) for measurements used in nuclear safeguards. This paper reviews progress and presents new results for bottom-up (first principles) and top-down (empirical) UQ for safeguards, where the main quantitative measure of uncertainty is the total measurement error standard deviation (SD), which includes both random and systematic error components. The five main UQ topics addressed here include: (1) impact of making data-driven choices in SD estimation; (2) use of approximate Bayesian computation (ABC) for both bottom-up and top-down UQ; (3) computational calibration; (4) revisions to the guide to the expression of uncertainty in measurement (GUM), and (5) critique of a recently-suggested “Unified Theory of Measurement Errors and Uncertainties.”

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

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↗

Pyrrole‐Imine Macrocycle: Self‐Organizing Cross‐Reactive Anion Receptor and Sensor

Self-organizing macrocyclic receptor-sensors for phosphorus oxyanions, phosphates, and phosphonates comprising imine moieties were prepared by condensation of dipyrrolylmethane dicarbaldehyde with diethylene triamine. The incorporation of flexible ethylene moieties endows the macrocycle with unprecedented flexibility and ability to accommodate numerous phosphorus oxyanions from orthophosphate to large anions such as ATP or phosphonate glyphosate. The anion binding was elucidated by NMR titrations, low-temperature NMR, and NOESY NMR. The incorporation of dansyl fluorophore enables sensing of anions using the fluorescence signal, whereas the changes in fluorescence intensity, width of the fluorescence band, and position of the maxima are analyte-specific and useful in recognition and identification of eleven different P-oxyanions in water. The affinity (K assoc ) for Na + salts was H 2 PO 4 − ≈ Methylphosphonate > H 2 P 2 O 7 2− > Phenylphosphonate- > Glyphosate 2− > AMP 2− > ADP 2− > ATP 2− . Interestingly, phosphonates, including methylphosphonate and glyphosate anions, were also found to display a strong affinity (K assoc ∼10 6 M −1 ) while halides, nitrate, carbonates, or hydrogen sulfate did not show a significant affinity. The determined fluorescence spectral parameters were used to classify the 12 analytes (11 anions and water) using Linear Discriminant Analysis (LDA). Quantification was performed using LDA and Support Vector Machine (SVM), and the phosphonate concentrations in unknown samples were determined with an error of 3.5% or lower.

anions↗

Stochastic Optimization and Uncertainty Quantification of Natrium-based Nuclear-Renewable Energy Systems for Flexible Power Applications in Deregulated Markets

Rapid integration of variable renewable energy sources (VRES) has made modeling and stochastic optimization of hybrid energy systems crucial for studying their long-term performance and viability. However, most studies have focused on just historical data, which may be unreliable for capturing short-term fluctuations, rare events, and long-term patterns of energy demand, price, and the variability of renewable energy sources. For this study, optimal synthetic time series models were developed using Wasserstein distance. The models were validated by comparing the key statistical measures against those of the historical data. They were then used to optimize the integrated Natrium-style advanced energy systems and their long-term (30 years) economics. The stochastic model performs bi-level optimization to find the optimal sizes for the balance of plant and thermal energy storage, while also optimizing energy dispatch to achieve the maximum net present value. In studies of two deregulated markets (California ISO and the Electric Reliability Council of Texas), the integrated Natrium-style system performed better in CAISO than in ERCOT, given higher and more consistent electricity prices during peak-demand periods. The potentially enlarged cost associated with the variable operation and maintenance of the TES system also plays a significant role in driving the system sizing, thus its impacts on the system are investigated in detail through comparison against a baseline case. The study also finds that the bi-level optimization results based on stochastic gradient descent closely match the grid search results. The uncertainty quantification of the stochastic signals provides further NPV-related insights and probability distributions for the case studies. The normal standard error of the mean of NPV for the case with and without TES VOM for CAISO were found to be 7.73M (plus-minus sign) 1.09M USD and 104.99M (plus-minus sign) 1.25M USD, respectively based on a 95% confidence. Given the relatively small NPV variance based on 150 samples, the analysis affords the most robust possible prediction of the techno-economic performance of the integrated Natrium-style energy systems.

25 ENERGY STORAGE↗

Generalized Bayesian MARS: Tools for Stochastic Computer Model Emulation

The multivariate adaptive regression spline (MARS) approach of Friedman and its Bayesian counterpart are effective approaches for the emulation of computer models. The traditional assumption of Gaussian errors limits the usefulness of MARS, and many popular alternatives, when dealing with stochastic computer models. Here, we propose a generalized Bayesian MARS (GBMARS) framework which admits the broad class of generalized hyperbolic distributions as the induced likelihood function. This allows us to develop tools for the emulation of stochastic simulators which are parsimonious, scalable, and interpretable and require minimal tuning, while providing powerful predictive and uncertainty quantification capabilities. GBMARS is capable of robust regression with t distributions, quantile regression with asymmetric Laplace distributions, and a general form of “Normal-Wald” regression in which the shape of the error distribution and the structure of the mean function are learned simultaneously. We demonstrate the effectiveness of GBMARS on various stochastic computer models, and we show that it compares favorably to several popular alternatives.

97 MATHEMATICS AND COMPUTING↗

Weighted greedy-optimal design of computer experiments for kernel-based and Gaussian process model emulation and calibration

This article is concerned with the approximation of high-dimensional functions by kernel-based methods. Motivated by uncertainty quantification, which often necessitates the construction of approximations that are accurate with respect to a probability density function of random variables, we aim at minimizing the approximation error with respect to a weighted $L^p$-norm. We present a greedy procedure for designing computer experiments based upon a weighted modification of the pivoted Cholesky factorization. The method successively generates nested samples with the goal of minimizing error in regions of high probability. Numerical experiments validate that this new importance sampling strategy is superior to other sampling approaches, especially when used with non-product probability density functions. We also show how to use the proposed algorithm to efficiently generate surrogates for inferring unknown model parameters from data.

97 MATHEMATICS AND COMPUTING↗

Optimization of algorithmic errors in analog quantum simulations

Due to rapidly improving quantum computing hardware, Hamiltonian simulations of relativistic lattice field theories have seen a resurgence of attention. Furthermore, this computational tool requires turning the formally infinite-dimensional Hilbert space of the full theory into a finite-dimensional one. For gauge theories, a widely used basis for the Hilbert space relies on the representations induced by the underlying gauge group, with a truncation that keeps only a set of the lowest dimensional representations. This works well at large bare gauge coupling, but becomes less efficient at small coupling, which is required for the continuum limit of the lattice theory. In this work, we develop a new basis suitable for the simulation of an SU(2) lattice gauge theory in the maximal tree gauge. In particular, we show how to perform a Hamiltonian truncation so that the eigenvalues of both the magnetic and electric gauge-fixed Hamiltonian are mostly preserved, which allows for this basis to be used at all values of the coupling. Little prior knowledge is assumed, so this may also be used as an introduction to the subject of Hamiltonian formulations of lattice gauge theories.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Uncertainty Quantification in Scientific ML

The intricate interactions between data sampling, model selection and the inherent randomness in complex systems strongly emphasize the need for a rigorous characterization of ML algorithms. In conventional statistics, uncertainty quantification (UQ) provides this characterization by measuring how accurately a model reflects the physical reality and by studying the impact of different error sources on the prediction.

97 MATHEMATICS AND COMPUTING↗

The Fluid Dynamics Uncertainty Quantification Challenge Problem: XFOIL vs. MFOIL

Uncertainty quantification (UQ) has become more critical in aerospace engineering due to the growing dependence on computational tools for design optimization and performance analyses of aerospace vehicles. Even though the significance of UQ in assessing the credibility of computational analyses is well recognized, its costs and complexity impede its integration into standard practices, particularly in computational fluid dynamics (CFD) and other fluid analyses. This paper presents a UQ study for low-fidelity computational aerodynamics analyses with XFOIL and mfoil (i.e., the MATLAB version of XFOIL with several implementation modifications); these tools are utilized widely in both research and education. The main contributions of this paper are as follows: 1) improved precision in quantifying the uncertainty of the baseline Monte Carlo results used to benchmark surrogate modeling techniques for UQ, 2) quantification of the effect of the implementation differences between XFOIL and mfoil on solution quantities of interest (QoIs), such as lift and pitching moment coefficients, and 3) development of an open-source UQ library for use with XFOIL and mfoil, which has educational values and helps promote UQ for fluid analyses with aerospace applications. Results and discussions revolve around cases 1-4 of the challenge problem posed by the AIAA Fluid Dynamics Technical Committee’s Uncertainty Quantification Discussion Group (UQDG). In case 3, this work employs CFDverify, an open-source solution verification software, to quantify the discretization error and evaluate the extrapolated QoIs based on the grid convergence index (GCI). This UQ study differentiates itself from previous studies in the rigor of handling baseline Monte Carlo uncertainty and in including mfoil, which is a more accessible alternative to XFOIL. Finally, despite the growing computing power, low-fidelity computational tools remain valuable, such as for aerodynamic shape optimization at Mach numbers below 0.65 and low-to-mid Reynolds numbers.

Lay, Aidan S [University of Tennessee, Knoxville (↗

Quantitative 14 N NMR with Monte Carlo Uncertainty Analysis of Nitrate/Nitrite in Alkaline Nuclear Waste

While monitoring of nitrate and nitrite concentrations is important for managing corrosion in nuclear waste systems, existing analytical methods are hindered by turbidity, spectral interference, and delays from sample handling. Here, we demonstrate quantitative 14 N nuclear magnetic resonance (qNMR) spectroscopy as a direct, matrix-tolerant approach for nitrate and nitrite detection at natural abundance. Monte Carlo resampling was integrated into the workflow to quantify random error, establish precision–time tradeoffs, and separate noise-limited uncertainty from systematic bias arising from shimming, transmitter offset, or excitation pulse conditions. Quantification of nitrate and nitrite were validated in controlled alkaline matrix challenges and in 18-component Hanford-type simulants. These results establish 14 N qNMR as a practical, uncertainty-bounded tool for monitoring redox-active nitrogen species in chemically complex environments and provide a generalizable framework for quantitative analysis of quadrupolar nuclei.

Graham, Trent R. [Pacific Northwest National Labor↗

SLS Integrated Modal Test Uncertainty Quantification using the Hybrid Parametric Variation Method

Uncertainty in structural loading during launch is a significant concern in the development of spacecraft and launch vehicles. Small variations in launch vehicle and payload mode shapes and their interaction can result in significant variation in system loads. In many cases involving large aerospace systems it is difficult, not economical, or impossible to perform a system modal test. However, it is still vital to obtain test results that can be compared with analytical predictions to validate models. Instead, the “Building Block Approach” is used in which system components are tested individually. Component models are correlated and updated to agree as best they can with test results. The Space Launch System consists of a number of components that are assembled into a launch vehicle. Finite element models of the components are developed, reduced to Hurty/Craig-Bampton models and assembled to represent different phases of flight. The only opportunity to obtain modal test data from an assembled Space Launch System will be during the Integrated Modal Test. There is always uncertainty in every model, which flows into uncertainty in predicted system results. Uncertainty Quantification is used to determine statistical bounds on prediction accuracy based on model uncertainty. For the Space Launch System, model uncertainty is at the Hurty/Craig-Bampton component level. Uncertainty in the Hurty/Craig-Bampton components is quantified using the hybrid parametric variation approach that combines parametric and nonparametric uncertainty. Uncertainty in model form is one of the biggest contributors to uncertainty in complex built-up structures. This type of uncertainty cannot be represented by variations infinite element model input parameters and thus cannot be included in a parametric approach. However, model-form uncertainty can be modeled using a nonparametric approach based on random matrix theory. The hybrid parametric variation method requires the selection of dispersion values for the Hurty/Craig-Bampton fixed-interface eigenvalues, and the Hurty/Craig-Bampton stiffness matrices. Component test/analysis frequency error is used to identify the fixed-interface eigenvalue dispersions, while test/analysis cross-orthogonality is used to identify stiffness dispersion values. The hybrid parametric variation uncertainty quantification approach is applied to the Space Launch System Integrated Modal Test configuration. Monte Carlo analysis is performed, and statistics are determined for modal correlation metrics, frequency response from Integrated Modal Test shakers to selected accelerometers, as well as other metrics for determining how well target modes are excited and identified. If the predicted uncertainty envelopes future Integrated Modal Test results, then there will be increased confidence in the utility of the component-based hybrid parametric variation uncertainty quantification approach.

Uncertainty Quantification↗

Uncertainty quantification of transition operators in the empirical shell model

While empirical shell model calculations have successfully described low-lying nuclear data for decades, only recently has significant effort been made to quantify the uncertainty in such calculations. Here, in this study, we quantify the statistical error in effective parameters for transition operators in empirical calculations in the sd (1s 1/2 -0d 3/2 -0d 5/2 ) valence space, specifically the quenching of Gamow-Teller transitions, effective charges for electric quadrupole (E2) transitions, and the effective orbital and spin couplings for magnetic dipole (M1) transitions and moments. We find the quenching factor for Gamow-Teller transitions relative to free-space values is tightly constrained. For effective M1 couplings, we found isoscalar components more constrained than isovector. This detailed quantification of uncertainties, while highly empirical, nonetheless is an important step towards interpretation of experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Automatic identification and quantification of dense microcracks in high-performance fiber-reinforced cementitious composites through deep learning-based computer vision

Highlights: • A method is presented to detect, locate, quantify, and visualize dense microcracks in HPFRCC. • Quantification of dense microcracks is realized using deep learning method for the first time. • The presented method uses deep learning models that are trained using a realistic dataset size. • The presented method has a high computation efficiency for identifying and quantifying cracks. • The presented method provides crack width with errors up to 50 μm and a R{sup 2} value of 0.984. High-performance fiber-reinforced cementitious composites (HPFRCCs) feature high mechanical strengths, crack resistance, and durability. Under excessive loading, HPFRCCs demonstrate dense microcracks that are difficult to identify using existing methods. This study presents a computer vision method for identification, quantification, and visualization of microcracks in HPFRCCs based on deep learning. The presented method integrates multiple deep learning models and computer vision techniques in a hierarchical architecture. The crack pattern (e.g., number, width, and spacing of cracks) are automatically determined from pictures without human intervention. This study shows that the presented method achieves an accuracy of 0.992 for crack detection and an accuracy finer than 50 μm (R{sup 2} > 0.984) for quantification of crack width when deep learning models are trained using only 200 pictures of HPFRCCs and 200 pictures of conventional concrete with incorporation of data augmentation. The presented method is expected to be also applicable to other materials featuring complex cracks.

36 MATERIALS SCIENCE↗

Synthetic method of analogues for emerging infectious disease forecasting

The Method of Analogues (MOA) has gained popularity in the past decade for infectious disease forecasting due to its non-parametric nature. In MOA, the local behavior observed in a time series is matched to the local behaviors of several historical time series. The known values that directly follow the historical time series that best match the observed time series are used to calculate a forecast. This non-parametric approach leverages historical trends to produce forecasts without extensive parameterization, making it highly adaptable. However, MOA is limited in scenarios where historical data is sparse. This limitation was particularly evident during the early stages of the COVID-19 pandemic, where the emerging global epidemic had little-to-no historical data. In this work, we propose a new method inspired by MOA, called the Synthetic Method of Analogues (sMOA). sMOA replaces historical disease data with a library of synthetic data that describe a broad range of possible disease trends. This model circumvents the need to estimate explicit parameter values by instead matching segments of ongoing time series data to a comprehensive library of synthetically generated segments of time series data. We demonstrate that sMOA has competitive performance with state-of-the-art infectious disease forecasting models, out-performing 78% of models from the COVID-19 Forecasting Hub in terms of averaged Mean Absolute Error and 76% of models from the COVID-19 Forecasting Hub in terms of averaged Weighted Interval Score. Additionally, we introduce a novel uncertainty quantification methodology designed for the onset of emerging epidemics. Developing versatile approaches that do not rely on historical data and can maintain high accuracy in the face of novel pandemics is critical for enhancing public health decision-making and strengthening preparedness for future outbreaks.

97 MATHEMATICS AND COMPUTING↗

A novel conditional generative model for efficient ensemble forecasts of state variables in large-scale geological carbon storage

Integrating monitoring data to efficiently update reservoir pressure and CO 2 plume distribution forecasts presents a significant challenge in geological carbon storage (GCS) applications. Inverse modeling techniques are commonly used to fuse observational data and refine reservoir model parameters, thereby improving state variable forecasts. However, these techniques often rely on linear or Gaussian assumptions, which can limit their effectiveness in accurately predicting state variables. Moreover, simulating large-scale three-dimensional (3D) GCS problems is computationally expensive, making iterative runs in inverse problems prohibitive. To address these challenges, we propose a conditional generative model utilizing the score-based diffusion method for real-time 3D pressure and saturation field distribution predictions. Our approach involves solving the score function with a mini-batch-based Monte Carlo estimator to generate labeled data. This data is subsequently employed to train a fully connected neural network, enabling it to learn the conditional sample generator within a supervised learning framework. This method enables the rapid generation of a large ensemble of predictions, facilitating comprehensive uncertainty quantification of state variables. Here we applied our method to forecast the dynamic 3D distributions of pressure and saturation fields over a 30-year injection period. The statistical assessment with low root mean square error (RMSE) values demonstrates that our method can accurately predict the spatiotemporal distributions of both pressure and saturation fields. Moreover, the developed conditional generative model shows high computational efficiency by generating 100 ensemble forecasts of 3D state variables in less than 10 min. The consistency between ensemble averages and ground truth values further illustrates the model’s capability to capture state variable dynamics during the CO 2 plume injection process. Notably, the ground truth values fall within the ensemble forecasts, indicating that our uncertainty quantification effectively captures variability and potential noise in the observations. Thus, the developed conditional generative model proves to be a more efficient, accurate, and practical tool for GCS applications, facilitating timely risk analysis and informed decision-making.

58 GEOSCIENCES↗

Effects of grain size and porosity on cladding failure in high-burnup UO 2 : A sensitivity and uncertainty study

Isotopic taggants are being studied to aid in the provenance assessment of nuclear materials. However, these taggants must be selected such that they do not adversely affect fuel performance during normal operation or accident scenarios. Taggants are known to affect the fuel’s grain size and porosity. In the work described in this paper, the BISON fuel performance code was used to assess the potential effects of taggants (i.e., grain size and porosity) on fuel rod behavior and cladding failure during a high-burnup, large-break loss-of-coolant accident. Here, 281 individual fuel rods from the same reactor core were modeled for a sensitivity study, a parametric study, and uncertainty quantification. The cladding failure predictions often exhibited stochastic behavior. After additional study, it was found that the cladding failure model is highly sensitive to residual error inherent to numerical approximation solvers. Some strategies to mitigate this sensitivity are discussed. The study found no relationship between known taggant effects and cladding failure status. However, taggants were found to affect the time and location of failure in certain rods. In conclusion, future work to continue investigating and validating these findings is briefly discussed.

Doped UO 2↗