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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

DAISY Complement Protein ML-Ready Data

A total of 172 children from the DAISY study with multiple plasma samples collected over time, with up to 23 years of follow-up, were characterized via proteomics analysis. Of the children there were 40 controls and 132 cases. All 132 cases had measurements across time relative to IA. Sampling was not consistent for all children. There were 47 of the children who had samples taken and evaluated prior to IA (Pre-IA), and 131 children had measurements at or after IA, but prior to diagnosis of clinical T1D (Post-IA). The control children were frequency matched on HLA genotypes and age and sex with an observed lower frequency of first degree relatives within the control group versus the cases For machine learning the children that will develop islet autoantibodies the 40 control and 47 Pre-IA children were down-selected to a single sample time point. For the 40 control children this was the earliest sample collected and for the 47 Pre-IA children it was a random selection of the first or second time point prior to the detection of autoantibodies to assure the age distributions were not significantly different.

Webb-Robertson, Bobbie-Jo M↗
DOE OSTI2026

Efficient many-jet event generation with flow matching

We apply for the first time, to the best of our knowledge, the flow matching method to the problem of phase-space sampling for event generation in high-energy collider physics. By training the model to remap the random numbers used to generate the momenta and helicities of the scattering matrix elements as implemented in the portable partonic event generator pepper, we find substantial efficiency improvements in the studied processes. We focus our study on the highest final-state multiplicities in Drell-Yan and top-antitop pair production used in simulated samples for the Large Hadron Collider, which computationally are the most relevant ones. We find that the unweighting efficiencies improve by factors of 184 and 25, respectively, when compared to the standard approach of using a vegas-based optimization. We also compare continuous normalizing flows trained with flow matching against the previously studied normalizing flows based on coupling layers and find that the former leads to better results, faster training and a better scaling behavior across the studied multiplicity range, while the latter evaluate faster. When combining the advantages of both methods using the regflow approach, we find parton-level unweighted event generation walltime gains of about a factor of 10 at the highest final-state multiplicities.

Bothmann, E. [CERN; Gottingen U.] (ORCID:000000016↗
DOE OSTI2025

The polarized-signal density matrix: A practical way to recover molecular frame information from isotropic samples

We present a novel approach to model ultrafast time-dependent nonlinear optical polarization sensitive signals emitted from randomly oriented molecules. By projecting the laboratory-frame analyzer polarization axis into the molecular-frame and linking that axis with the density matrix through a tensor product, we demonstrate an approach to find a specific molecular orientation that yields a good approximation to simulated four-wave mixing signals produced by the same model but with averaging over molecular orientation.

Thurston, Richard L↗
DOE OSTI2016

STRUCTURAL STUDIES OF EIGHT BRIGHT RIMMED CLOUDS IN THE SOUTHERN HEMISPHERE

We carried out deep- and wide-field near- and mid-infrared observations for a sample of eight bright-rimmed clouds (BRCs). Supplemented with the Spitzer archival data, we have identified and classified 44 to 433 young stellar objects (YSOs) associated with these BRCs. The Class I sources are generally located toward the places with higher extinction and are relatively closer to each other than the Class II sources, confirming that the young protostars are usually found in regions with denser molecular material. On the other hand the comparatively older population, Class II objects, are more randomly found throughout the regions, which can be due to their dynamical evolution. Using the minimal sampling tree analyses, we have extracted 13 stellar cores of eight or more members, which contain 60% of the total YSOs. The typical core is ∼0.6 pc in radii and somewhat elongated (aspect ratio of 1.45), of relatively low stellar density (surface density 60 pc{sup −2}), consisting of a small (35) number of YSOs of relatively young sources (66% Class I), and partially embedded (median A{sub K} = 1.1 mag). But the cores show a wide range in their mass distribution (∼20 to 2400 M {sub ⊙}), with a median value of around 130 M {sub ⊙}. We found the star-formation efficiencies in the cores to be between 3% and 30% with an average of ∼14%, which agrees with the efficiencies needed to link the core mass function to the initial mass function. We also found a linear relation between the density of the clouds and the number of YSOs. The peaked nearest neighbor spacing distributions of the YSOs and the ratio of Jeans lengths to the YSO separations indicates a significant degree of non-thermally driven fragmentation in these BRCs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

An adaptive Hessian approximated stochastic gradient MCMC method

Bayesian approaches have been successfully integrated into training deep neural networks. One popular family is stochastic gradient Markov chain Monte Carlo methods (SG-MCMC), which have gained increasing interest due to their ability to handle large datasets and the potential to avoid overfitting. Although standard SG-MCMC methods have shown great performance in a variety of problems, they may be inefficient when the random variables in the target posterior densities have scale differences or are highly correlated. Here, we present an adaptive Hessian approximated stochastic gradient MCMC method to incorporate local geometric information while sampling from the posterior. The idea is to apply stochastic approximation (SA) to sequentially update a preconditioning matrix at each iteration. The preconditioner possesses second-order information and can guide the random walk of a sampler efficiently. Instead of computing and saving the full Hessian of the log posterior, we use limited memory of the samples and their stochastic gradients to approximate the inverse Hessian-vector multiplication in the updating formula. Moreover, by smoothly optimizing the preconditioning matrix via SA, our proposed algorithm can asymptotically converge to the target distribution with a controllable bias under mild conditions. To reduce the training and testing computational burden, we adopt a magnitude-based weight pruning method to enforce the sparsity of the network. Our method is user-friendly and demonstrates better learning results compared to standard SG-MCMC updating rules. The approximation of inverse Hessian alleviates storage and computational complexities for large dimensional models. Numerical experiments are performed on several problems, including sampling from 2D correlated distribution, synthetic regression problems, and learning the numerical solutions of heterogeneous elliptic PDE. The numerical results demonstrate great improvement in both the convergence rate and accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Sampling Size Optimization for Bioburden Density Estimation in Planetary Protection

Planetary protection (PP) is a discipline that focuses on minimizing the biological contamination of spacecraft to ensure compliance with international policy. Precise estimation of bioburden - the total number of microbes in or on spacecraft hardware – and the bioburden density are of utmost importance for PP. Such estimation is the way concordance with requirements is demonstrated, and it is critical for quantifying the potential risk of inadvertently contaminating other planetary bodies. Although a suite of molecular techniques have been used to thoroughly characterize and profile the microbiome of various cleanroom environments and spacecraft, the gold standard remains the physical enumeration of microbes via culturing of samples directly taken from spacecraft and associated surfaces. However, due to technical, budgetary, and programmatic constraints, only a manageable portion (around 10%) of the entire spacecraft surface is directly sampled with cotton swabs or wipes. To generate the bioburden current best estimate (CBE) for components not directly verifiable, the accepted approach is to apply a NASA-defined bioburden estimate based on the components’ manufacturing or assembly environment. This approach utilizes a prespecified bioburden density estimation that applies a maximum value across the total surface area of the specified component. For hardware components that underwent similar assembly processes, an implied bioburden is adopted for all components, based on a direct verification of a representative component within the same lot. Once all components have a CBE, the bioburden estimates are generated. In previous publication [ 1], we have shown that statistical risks quantifying the accuracy of the estimates for sampled, prespecified, and implied components can be derived and ranked. For mean squared error (MSE) function, the risks are available analytically and hence a cost function can be obtained to optimize the risks with respect to the sampling area and sampling cost. Since the sampling area and sampling cost are two complimentary variables, their sum will have a well-defined minimum. This paper presents the multivariate optimization of the integrated risk of an empirical Bayes estimator to determine the optimal sampling schedule for a given number of components. It is assumed that given a number of components, N, the bioburden density for each component can either be sampled, implied, or prespecified. The multivariate optimization searches through different options to sample, imply or prespecify the bioburden density for a component, and account for the component’s surface area and cost of sampling. The idea of the optimization is based on the observation that the statistical risk of using an estimator is a monotonically decreasing function of the sampled area. The larger the sampled area, the lower the risk of using the estimator as the estimator becomes more and more accurate as the sampling area increases. On the other hand, the cost of sampling is monotonically increasing as the sampled surface grows. This makes the risk and total cost of sampling complimentary variables which can be counterbalanced to achieve an optimal overall value with respect to the sampled surface. In this paper, the integrated risk has been used to quantify the accuracy of the estimator. This risk has been selected because it depends on neither the true value of the parameter nor on the collected data. The cost of each sample was also available to obtain the total cost of sampling of N components. The paper will present the results based on computer-simulated data as well as the data collected during the InSight mission. The computer-simulated data have N components with randomly generated total areas and each component assigned to one of the three categories according to the method of estimating of bioburden density: sampled, implied, or prespecified. The cost of sampling is also available. The cost of sampling is estimated based on a cost model provided by the planetary protection group at JPL. For this paper, the overall cost was assumed to be a linear function of exposure. The optimization process finds the allocation of the components to the three categories that minimizes the tradeoff between integrated risk and total cost. For the InSight data, a set of components is selected representing all three categories, and optimization is performed to determine if the performed allocation was optimal or if a better allocation could have been obtained. To the best of our knowledge, this work is the first attempt not only perform an accurate estimation of bioburden density but also do it in an optimal way.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Highly-defective nanocrystals of ZnS formed via dissimilatory bacterial sulfate reduction: A comparative study with their abiogenic analogues

The physicochemical properties of a (nano)mineral are strongly affected by its formation processes, and thus, may indicate the (nano)mineral’s formation environment and mechanism. This correlation, although relevant to a myriad of geological, environmental, and material-science processes, has not yet been fully appreciated and systematically explored. In this study, using the Zn–S system, we demonstrate that biological and abiotic processes at similar experimental conditions can produce distinctive particle size, morphology, and crystal structure in the formed ZnS. Specifically, bacterial sulfate reduction led to the formation of highly-defective nanocrystals of mixed sphalerite and wurtzite in a range of ~4–12 nm. By comparison, the abiotic procedures of titration- or diffusion-controlled precipitation resulted in the formation of polycrystalline aggregates that contained randomly-oriented, ultrafine crystals below ~2–3 nm. The poor crystallinity in the abiogenic samples, regardless of the sulfide addition rates, reveals an overall nucleation-dominated, crystal growth-restricted pathway for the formation of ZnS from low-temperature aqueous solutions. The difficulty in the ZnS crystallization likely stems from the intrinsic surface instability of the ZnS growth units (i.e., in the form of nanoclusters) resulting from the dipole–dipole interactions of the unit with surrounding water molecules. In the biogenic samples, the ZnS crystallinity was significantly improved, indicating that the presence of bacterial metabolites somehow promoted the crystallization process. With evidence for the enlarged {1 1 1} planes in the biogenic nanocrystals, we attribute this enhancement mainly to the selective interaction of the bacterial metabolites with polar faces of the ZnS growth units, which might have effectively screened the dipole moments in the growth units and enabled their crystallographic assembly. By revealing the intrinsic difficulty and specific pathways for the ZnS crystallization, we also present viable explanations for the exclusive occurrence of structural defects in {1 1 1} planes of the biogenic nanocrystals. The findings of our study provide insight into the origin and fate of metal sulfide nanoparticles in the environment, and have implications for biomineralization, bioremediation of metal-contaminated sites, and bacterial production of functional nanomaterials.

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

Distributionally Safe Path Planning: Wasserstein Safe RRT

In this paper, we propose a Wasserstein metric-based random path planning algorithm. Wasserstein Safe RRT (W-Safe RRT) provides finite-sample probabilistic guarantees on the safety of a returned path in an uncertain obstacle environment. Vehicle and obstacle states are modeled as distributions based upon state and model observations. Additionally, we define limits on distributional sampling error so the Wasserstein distance between a vehicle state distribution and obstacle distributions can be bounded. This enables the algorithm to return safe paths with a confidence bound through combining finite sampling error bounds with calculations of the Wasserstein distance between discrete distributions. W-Safe RRT is compared against a baseline minimum encompassing ball algorithm, which ensures balls that minimally encompass discrete state and obstacle distributions do not overlap. The improved performance is verified in a 3D environment using single, multi, and rotating non-convex obstacle cases, with and without forced obstacle error in adversarial directions, showing that W-Safe RRT can handle poorly modeled complex environments.

42 ENGINEERING↗
DOE OSTI2022

Do Machine Learning Approaches Offer Skill Improvement for Short-Term Forecasting of Wind Gust Occurrence and Magnitude?

Abstract Wind gusts, and in particular intense gusts, are societally relevant but extremely challenging to forecast. This study systematically assesses the skill enhancement that can be achieved using artificial neural networks (ANNs) for forecasting of wind gust occurrence and magnitude. Geophysical predictors from the ERA5 reanalysis are used in conjunction with an autoregressive term in regression and ANN models with different predictors, and varying model complexity. Models are derived and assessed for the warm (April–September) and cold (October–March) seasons for three high passenger volume airports in the United States. Model uncertainty is assessed by deriving models for 1000 different randomly selected training (70%) and testing (30%) subsets. Gust prediction fidelity in independent test samples is critically dependent on inclusion of an autoregressive term. Gust occurrence probabilities derived using five-layer ANNs exhibit consistently higher fidelity than those from regression models and shallower ANNs. Inclusion of the autoregressive term and increasing the number of hidden layers in ANNs from 1 to 5 also improve the model performance for gust magnitudes (lower RMSE, increased correlation, and model standard deviations that more closely approximate observed values). Deeper ANNs (e.g., 20 hidden layers) exhibit higher skill in forecasting strong (17–25.7 m s −1 ) and damaging (≥25.7 m s −1 ) wind gusts. However, such deep networks exhibit evidence of overfitting and still substantially underestimate (by 50%) the frequency of strong and damaging wind gusts at the three airports considered herein. Significance Statement Improved short-term forecasting of wind gusts will enhance aviation safety and logistics and may offer other societal benefits. Here we present a rigorous investigation of the relative skill of models of wind gust occurrence and magnitude that employ different statistical methods. It is shown that artificial neural networks (ANNs) offer considerable skill enhancement over regression methods, particularly for strong and damaging wind gusts. For wind gust magnitudes in particular, application of deeper learning networks (e.g., five or more hidden layers) offers tangible improvements in forecast accuracy. However, deeper networks are vulnerable to overfitting and exhibit substantial variability with the specific training and testing data subset used. Also, even deep ANNs reproduce only half of strong and damaging wind gusts. These results indicate the need for future work to elucidate the dynamical mechanisms of intense wind gusts and advance solutions to their prediction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Single-shot imaging with randomized structured illumination at a free electron laser

Stroboscopic nanoscale imaging with free electron laser light is revolutionizing our understanding of fast dynamics in heterogeneous systems. The short wavelength of X-ray and extreme ultraviolet radiation makes it possible to achieve nanoscale resolution, while resonance with atomic transitions gives access to electronic and magnetic degrees of freedom. Here, we report on our implementation of a recently developed imaging method, randomized probe imaging, at a free electron laser. The advantage of randomized probe imaging over existing methods is its compatibility with extended and strongly scattering samples. Our implementation delivers robust single-shot reconstructions at up to a full-pitch resolution of 400 nm over a field of view with a 40 µm diameter. We also demonstrate single-shot imaging of magnetic domain structures using circular dichroism at resonance, paving the way to future time-resolved studies of magnetic dynamics, shock physics, and the dynamics of collective electronic phases.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

Corn Stover Harvest, Tillage, and Cover Crop Effects on Soil Health Indicators

Monitoring soil health indicators (SHI) will help ensure that corn (Zea mays L.) stover harvest is sustainable. This study examines SHI changes after 5 yr of growing continuous corn with either chisel plow or no-tillage practices and harvesting 0, ~35, or ~60% of the stover. Two no-tillage treatments with a cereal rye (Secale cereale L.) cover crop and stover harvest rates of ~35 or ~60% were evaluated. All eight treatments were replicated four times in a randomized complete block design at an 11-ha site in Boone County, IA. Soil samples were collected following grain and stover harvest from 0- to 5- and 5- to 15-cm depth increments. Particulate organic matter C (POM-C) decreased when stover was removed or the soil was chisel plowed. No-till with 0% stover removal had 10 mg g –1 POM-C in the 0- to 5-cm soil layer, which was 1.9-fold higher than in other treatments. Potentially mineralizable N (PMN) was greater under cover crop treatments. Average PMN values were 56.9 and 45.5 µg g –1 PMN for no-till with cereal rye at 0- to 5- and 5- to 15-cm depths, respectively, compared with 17.5 and -3.7 µg g –1 PMN for the same no-till treatments without cereal rye. Other soil properties did not respond to increasing levels of stover removal. At this location and at the studied removal rates, 5 yr of harvesting corn stover did not decrease soil health, but POM-C data suggest that changes may be occurring. Long-term monitoring should continue to assess corn stover harvest sustainability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Modeling the Swift BAT trigger algorithm with machine learning

To draw inferences about gamma-ray burst (GRB) source populations based on Swift observations, it is essential to understand the detection efficiency of the Swift burst alert telescope (BAT). This study considers the problem of modeling the Swift/BAT triggering algorithm for long GRBs, a computationally expensive procedure, and models it using machine learning algorithms. A large sample of simulated GRBs from Lien et al. is used to train various models: random forests, boosted decision trees (with AdaBoost), support vector machines, and artificial neural networks. The best models have accuracies of ≳97% (≲3% error), which is a significant improvement on a cut in GRB flux, which has an accuracy of 89.6% (10.4% error). These models are then used to measure the detection efficiency of Swift as a function of redshift z, which is used to perform Bayesian parameter estimation on the GRB rate distribution. We find a local GRB rate density of n{sub 0}∼0.48{sub −0.23}{sup +0.41} Gpc{sup −3} yr{sup −1} with power-law indices of n{sub 1}∼1.7{sub −0.5}{sup +0.6} and n{sub 2}∼−5.9{sub −0.1}{sup +5.7} for GRBs above and below a break point of z{sub 1}∼6.8{sub −3.2}{sup +2.8}. This methodology is able to improve upon earlier studies by more accurately modeling Swift detection and using this for fully Bayesian model fitting.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

3FGL demographics outside the galactic plane using supervised machine learning: pulsar and dark matter subhalo interpretations

Nearly one-third of the sources listed in the Third Fermi Large Area Telescope (LAT) catalog (3FGL) remain unassociated. It is possible that predicted and even unanticipated gamma-ray source classes are present in these data waiting to be discovered. Taking advantage of the excellent spectral capabilities achieved by the Fermi LAT, we use machine-learning classifiers (Random Forest and XGBoost) to pinpoint potentially novel source classes in the unassociated 3FGL sample outside the Galactic plane. Here we report a total of 34 high-confidence Galactic candidates at |b|⩾5{sup ∘}. The currently favored standard astrophysical interpretations for these objects are pulsars or low-luminosity globular clusters hosting millisecond pulsars (MSPs). Yet these objects could also be interpreted as dark matter annihilation taking place in ultra-faint dwarf galaxies or dark matter subhalos. Unfortunately, Fermi LAT spectra are not sufficient to break degeneracies between the different scenarios. Careful visual inspection of archival optical images reveals no obvious evidence for low-luminosity globular clusters or ultra-faint dwarf galaxies inside the 95% error ellipses. If these are pulsars, this would bring the total number of MSPs at |b|⩾5{sup ∘} to 106, down to an energy flux ≈4.0 × 10{sup −12} erg cm{sup −2} s{sup −1} between 100 MeV and 100 GeV. We find this number to be in excellent agreement with predictions from a new population synthesis of MSPs that predicts 100–126 high-latitude 3FGL MSPs depending on the choice of high-energy emission model. If, however, these are dark matter substructures, we can place upper limits on the number of Galactic subhalos surviving today and on dark matter annihilation cross sections. These limits are beginning to approach the canonical thermal relic cross section for dark matter particle masses below ∼100 GeV in the bottom quark (b b-bar ) annihilation channel.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Enabling probabilistic learning on manifolds through double diffusion maps

Here, we present a generative learning framework for probabilistic sampling that extends Probabilistic Learning on Manifolds (PLoM), which is designed to generate statistically consistent realizations of a random vector in a finite-dimensional Euclidean space, informed by a (representative) set of observations. In its original form, PLoM constructs a reduced-order probabilistic model by combining three main components: (a) kernel density estimation to approximate the underlying probability measure, (b) Diffusion Maps to characterize the manifold of the data, and (c) a reduced-order Itô Stochastic Differential Equation (ISDE) to sample from the learned distribution. However, its sampling dynamics are posed in the ambient space and the retained number of reduced coordinates is chosen by projection-reconstruction error. In practice, this often (i) requires more coordinates than the data’s intrinsic dimension to achieve stable sampling and (ii) lacks a smooth, basis-independent lifting back to the data domain; moreover, standard Diffusion Maps emphasize harmonic eigenfunctions and can miss non-harmonic latent structure. We address these limitations by decoupling geometry learning from sampling: a first Diffusion Maps pass identifies non-harmonic coordinates on which we formulate a full-order ISDE directly in the latent space, while Double Diffusion Maps captures multiscale geometric features and Geometric Harmonics (GH) learns a smooth lifting map to the ambient variables that is independent of the particular diffusion basis. This hybrid design preserves the system’s dynamical richness with a compact geometric representation and enables principled out-of-sample inference. The effectiveness and robustness of the proposed method are illustrated through two numerical studies: one based on data generated from two-dimensional Hermite polynomial functions and another based on high-fidelity simulations of a detonation wave in a reactive flow.

Double diffusion maps↗
DOE OSTI2023

Stochastic modeling and statistical calibration with model error and scarce data

This paper introduces a procedure to assess the predictive accuracy of stochastic models subject to model error and sparse data. Model error is introduced as uncertainty on the coefficients of appropriate polynomial chaos expansions (PCE). The error associated with finite sample size allows us to conceive of these coefficients as statistics of the data that we describe as random variables whose influence on output quantities of interest is evaluated through the extended polynomial chaos expansion (EPCE). A Bayesian data assimilation scheme is introduced to update these expansions by considering the resulting nested chaos expansion as a hierarchical probabilistic model. Stochastic models of quantities of interest (QoI) are thus constructed and efficiently evaluated. Here, the Metropolis–Hastings Markov chain Monte Carlo procedure is used to sample the posterior. Two illustrative analytical and numerical problems are used to demonstrate the proposed approach.

Bayesian inference↗
DOE OSTI2021

Randomized Algorithms for Scientific Computing (RASC)

Randomized algorithms have propelled advances in artificial intelligence (AI) and represent a foundational research area in advancing AI for Science. Future advancements in DOE Office of Science priority areas such as climate science, astrophysics, fusion, advanced materials, combustion, and quantum computing all require randomized algorithms for surmounting challenges of complexity, robustness, and scalability. Advances in data collection and numerical simulation have changed the dynamics of scientific research and motivate the need for randomized algorithms. For instance, advances in imaging technologies such as X-ray ptychography, electron microscopy, electron energy loss spectroscopy, or adaptive optics lattice light-sheet microscopy collect hyperspectral imaging and scattering data in terabytes, at breakneck speed enabled by state-of-the-art detectors. The data collection is exceptionally fast compared with its analysis. Likewise, advances in high-performance architectures have made exascale computing a reality and changed the economies of scientific computing in the process. Floating-point operations that create data are essentially free in comparison with data movement. Thus far, most approaches have focused on creating faster hardware. Ironically, this faster hardware has exacerbated the problem by making data still easier to create. Under such an onslaught, scientists often resort to heuristic deterministic sampling schemes (e.g., low-precision arithmetic, sampling every nth element) and sacrifice potentially valuable accuracy. Dramatically better results can be achieved via randomized algorithms, reducing the data size as much as or more than naive deterministic subsampling can achieve, while retaining the high accuracy of computing on the full data set. By randomized algorithms we mean those algorithms that employ some form of randomness in internal algorithmic decisions to accelerate time to solution, increase scalability, or improve reliability. Examples include matrix sketching for solving large-scale least-squares problems (see Figure 1) and stochastic gradient descent for training machine learning models. We are not recommending heuristic methods but rather randomized algorithms that have certificates of correctness and probabilistic guarantees of optimality and near-optimality. Such approaches can be useful beyond acceleration, for example, in understanding how to avoid measure zero worst-case scenarios that plague methods such as QR matrix factorization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Intensity of sample processing methods impacts wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes

Wastewater SARS-CoV-2 surveillance has been deployed since the beginning of the COVID-19 pandemic to monitor the dynamics in virus burden in local communities. Genomic surveillance of SARS-CoV-2 in wastewater, particularly efforts aimed at whole genome sequencing for variant tracking and identification, are still challenging due to low target concentration, complex microbial and chemical background, and lack of robust nucleic acid recovery experimental procedures. The intrinsic sample limitations are inherent to wastewater and are thus unavoidable. Here, we use a statistical approach that couples correlation analyses to a random forest-based machine learning algorithm to evaluate potentially important factors associated with wastewater SARS-CoV-2 whole genome amplicon sequencing outcomes, with a specific focus on the breadth of genome coverage. We collected 182 composite and grab wastewater samples from the Chicago area between November 2020 to October 2021. Samples were processed using a mixture of processing methods reflecting different homogenization intensities (HA + Zymo beads, HA + glass beads, and Nanotrap), and were sequenced using one of the two library preparation kits (the Illumina COVIDseq kit and the QIAseq DIRECT kit). Technical factors evaluated using statistical and machine learning approaches include sample types, certain sample intrinsic features, and processing and sequencing methods. The results suggested that sample processing methods could be a predominant factor affecting sequencing outcomes, and library preparation kits was considered a minor factor. Finally, a synthetic SARS-CoV-2 RNA spike-in experiment was performed to validate the impact from processing methods and suggested that the intensity of the processing methods could lead to different RNA fragmentation

60 APPLIED LIFE SCIENCES↗