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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

An application of survival analysis to disruption prediction via Random Forests

One of the most pressing challenges facing the fusion community is adequately mitigating or, even better, avoiding disruptions of tokamak plasmas. However, before this can be done, disruptions must first be predicted with sufficient warning time to actuate a response. The established field of survival analysis provides a convenient statistical framework for time-to-event (i.e. time-to-disruption) studies. This paper demonstrates the integration of an existing disruption prediction machine learning algorithm with the Kaplan-Meier estimator of survival probability. Specifically discussed are the implied warning times from binary classification of disruption databases and the interpretation of output signals from Random Forest algorithms trained and tested on these databases. This survival analysis approach is applied to both smooth and noisy test data to highlight important features of the survival and hazard functions. In addition, this method is applied to three Alcator C-Mod plasma discharges and compared to a threshold-based scheme for triggering alarms. In one case, both techniques successfully predict the disruption; although, in another, neither warns of the impending disruption with enough time to mitigate. For the final discharge, the survival analysis approach could avoid the false alarm triggered by the threshold method. Limitations of this analysis and opportunities for future work are also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Dark Energy Survey Year 3 results: optimized $w$CDM simulation-based inference with weak lensing map-level hybrid statistics

We present cosmological constraints from the Dark Energy Survey Year 3 (DES Y3) weak lensing data using hierarchical hybrid statistics within a Bayesian simulation-based inference framework that is based on the Gower Street simulations. To maximize the precision of the inference, we have developed a new, information-theory based, data compression of the weak lensing maps to just seven highly informative summary statistics. The hybrid scheme exploits the high information content of the power spectrum, compressing both the power spectrum and neural-based summaries that are designed to extract further information. Our simulation-based approach enables principled forward modelling of all major sources of systematic uncertainty and survey properties into realistic mock observations, including the survey mask, photometric redshift uncertainties, intrinsic galaxy alignments, multiplicative shear calibration bias, source galaxy clustering, non-Gaussian shape noise, and non-linear structure formation. The summary statistics are then used in a Bayesian simulation-based inference pipeline. The inference is validated through coverage tests and checks for robustness against baryonic feedback. Assuming a $w$CDM cosmology, our analysis yields $S_8 = 0.808 \pm 0.017$, $Ω_{\rm m} = 0.325 \pm 0.024$, and $w < -0.766$ (marginalized posterior 68 per cent credible intervals). This rigorous combination of information theory, physics- and neural network-based extreme data compression, and principled Bayesian analysis improves the figure of merit for $(Ω_{\rm m}, S_8, w)$ by 60 per cent over the previous state-of-the-art, and by almost a factor of 3 over two-point analyses of the same data. They are the most precise joint constraints on $(Ω_{\rm m}, S_8, w)$ from weak gravitational lensing data alone of any survey to date. We intend to apply this analysis to the more recent DES Y6 data.

Williamson, J. [University Coll. London]↗
DOE OSTI2024

How do mirror charge radii constrain density dependence of the symmetry energy?

It has recently been suggested that differences in the charge radii of mirror nuclei (Δ$R^{mirr}_{ch}$) are strongly correlated with the neutron-skin thickness ($R_{skin}$) of neutron-rich nuclei and with the slope of the symmetry energy ($L$). To test this assumption, we present ab initio calculations of $R_{skin}$ in 48 Ca and 208 Pb, Δ$R^{mirr}_{ch}$ in 36 Ca$-$ 36 S, 38 Ca$-$ 38 Ar, 41 Sc$-$ 41 Ca, 48 Ni$-$ 48 Ca, 52 Ni$-$ 52 Cr, and 54 Ni$-$ 54 Fe mirror pairs, and $L$. Employing the recently developed 34 chiral interaction samples, identified by the history matching approach, we conduct rigorous statistical analysis of correlations among Δ$R^{mirr}_{ch}$, $R_{skin}$ and $L$, accounting for quantified uncertainties from low-energy constants of chiral interaction, chiral effective field theory truncation and many-body method approximation. The ab initio results reveal an appreciable Δ$R^{mirr}_{ch}$ $-$ $L$ correlation in $fp$-shell mirror pairs. However, contrary to previous studies, the present calculation finds that the studied $sd$-shell mirror pairs do not exhibit any Δ$R^{mirr}_{ch}$ $-$ $L$ correlation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

A probabilistic-phase field model for the fracture of brittle materials

Abstract We develop a computational method to determine the failure probability of brittle materials under general mechanical loading conditions. The method is a combination of two parts: (1) numerical simulations of materials with multiple cracks using phase field theory, where the complete fracture process is viewed as ‘damage percolation’ along critical paths or clusters of cracks, rather than the traditional weak-link failure mechanism of Weibull, and (2) an extension of the Batdorf statistical theory of fracture to finite domains, where it is implemented within the finite element framework. The results of phase-field simulations at the ‘percolation threshold’ are used as failure data in the Batdorf theory to determine the overall probability of failure. The input to this approach is the size distribution of cracks in a pristine material. An example is shown, where alumina samples that were previously tested by Abe and coworkers (Abeet al2003J. Am. Ceram. Soc.861019–21) in four-point loading are compared to the results of our numerical simulations. The approach developed here has the advantage of being extendable to more complex thermomechanical loading.

Materials Science↗
DOE OSTI2024

Improved Subseasonal Forecasting of Extreme Polar Vortices Using Machine Learning

Our research was focused on forecasting the position and shape of the winter stratospheric polar vortex at a subseasonal timescale of 15 days in advance. To achieve this, we employed both statistical and neural network machine learning techniques. The analysis was performed on 42 winter seasons of reanalysis data provided by NASA giving us a total of 6,342 days of data. The state of the polar vortex for determined by using geometric moments to calculate the centroid latitude and the aspect ratio of an ellipse fit onto the vortex. Timeseries for thirty additional precursors were calculated to help improve the predictive capabilities of the algorithm. Feature importance of these precursors was performed using random forest to measure the predictive importance and the ideal number of precursors. Then, using the precursors identified as important, various statistical methods were tested for predictive accuracy with random forest and nearest neighbor performing the best. An echo state network, a type of recurrent neural network that features sparsely connected hidden layer and a reduced number of trainable parameters that allows for rapid training and testing, was also implemented for the forecasting problem. Hyperparameter tuning was performed for each methods using a subset of the training data. The algorithms were trained and tuned on the first 41 years of data, then tested for accuracy on the final year. In general, the centroid latitude of the polar vortex proved easier to predict than the aspect ratio across all algorithms. Random forest outperformed other statistical forecasting algorithms overall but struggled to predict extreme values. Forecasting from echo state network suggested a strong predictive capability past 15 days, but further work is required to fully realize the potential of recurrent neural network approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

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

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

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Hydrogen Dispersion Modeling for Development of Smart Distributed Monitoring

Studying hydrogen dispersion is crucial for ensuring the safe and effective deployment of hydrogen as an energy carrier. This study presents a comprehensive CFD modeling framework for simulating hydrogen dispersion at a real-world hydrogen production, storage, and utilization facility. Utilizing the Hydrogen Research Facility under the Advanced Research on Integrated Energy Systems (ARIES) at the National Renewable Energy Laboratory's (NREL) Flatirons campus, controlled hydrogen releases at 27 kg-H2/hr were simulated. The model incorporated site-specific atmospheric conditions, including hourly wind speeds and temperatures recorded between 8 AM and 8 PM from October to December 2023. To reduce computational demands, a statistical reduction technique was applied to condense the dataset to 100 representative scenarios, validated by statistical tests for wind speeds and power law coefficients. Simulations were conducted using the Reynolds-Averaged Navier-Stokes equations. Results demonstrated that wind speed substantially influences hydrogen dispersion, with low wind conditions forming concentrated clouds and higher wind speeds stretching the plume. Additionally, clustering analysis informed optimal sensor placement at various elevations with up to 10 sensor locations on each elevation. This framework offers a robust approach for understanding hydrogen behavior in ambient conditions and informing detection strategies.

08 HYDROGEN↗
DOE OSTI2021

Nonlinear proper orthogonal decomposition for convection-dominated flows

Autoencoder techniques find increasingly common use in reduced order modeling as a means to create a latent space. This reduced order representation offers a modular data-driven modeling approach for nonlinear dynamical systems when integrated with a time series predictive model. In this Letter, we put forth a nonlinear proper orthogonal decomposition (POD) framework, which is an end-to-end Galerkin-free model combining autoencoders with long short-term memory networks for dynamics. By eliminating the projection error due to the truncation of Galerkin models, a key enabler of the proposed nonintrusive approach is the kinematic construction of a nonlinear mapping between the full-rank expansion of the POD coefficients and the latent space where the dynamics evolve. We test our framework for model reduction of a convection-dominated system, which is generally challenging for reduced order models. Our approach not only improves the accuracy, but also significantly reduces the computational cost of training and testing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Convergent Concordant Mode Approach for Molecular Vibrations: CMA-2

The concordant mode approach (CMA) is a promising new scheme for dramatically increasing the system size and level of theory achievable in quantum chemical computations of molecular vibrational frequencies. Here, we achieve advances in the CMA hierarchy by computations targeting CCSD(T)/cc-pVTZ (coupled cluster singles and doubles with perturbative triples using a correlation-consistent polarized-valence triple-ζ basis set) benchmarks within the G2 molecular test set, executing a statistical analysis for 1501 frequencies from 111 compounds and then separately solving the refractory case of pyridine. First, MP2/cc-pVTZ (second-order Møller–Plesset perturbation theory with the same basis set) proves to be an excellent and preferred choice for generating the underlying (Level B) normal modes of the CMA scheme. Utilizing this Level B within the CMA-0A method reproduces the 1501 benchmark frequencies with a mean absolute error (MAE) of only 0.11 cm –1 and an attendant standard deviation of 0.49 cm –1 . Second, a convergent CMA-2 method is constituted that allows efficient computation of higher level (Level A) frequencies to any reasonable accuracy threshold by using only Hartree–Fock (HF) and MP2 or density functional theory (DFT) data to generate ξ parameters, which select the sparse off-diagonal force field elements for explicit evaluation at Level A. When Level B = MP2/cc-pVTZ, a cutoff of ξ = 0.02 provides an average maximum absolute error per molecule of only 0.17 cm –1 by incurring merely a 33% increase in average cost over CMA-0A. This CMA-2 method also eradicates the 4 problematic CMA-0A outliers of pyridine with even less effort (ξ = 0.04, 22% increase). Finally, the newly developed CMA procedures are shown to be highly successful when applied to 1-(1H-pyrrol-3-yl)ethanol, a new test molecule with diverse types of vibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Assessment of EPRI’s Tan Delta Approach to Manage Cables in Submerged Environments: Statistical Review of EPRI Data

Research conducted by the Electric Power Research Institute (EPRI) and other research institutions have concluded that water-trees are one of the leading degradation mechanisms that contribute to the loss of dielectric insulation strength in medium-voltage cable insulating materials in wet or submerged environments. The electrochemical reactions are caused by the combined effect of water presence and relatively high electrical stress. Records of cable failures provided by the licensees in response to Generic Letter (GL) 2007-01 (NRC 2007) have called into question the reliability of medium voltage cables in wetted or submerged environments. EPRI’s dissipation factor or Tan Delta testing guidelines and acceptance criteria have been adopted by most nuclear power plant operators as the primary tool for condition monitoring of medium voltage cables in wet or submerged environments. EPRI has been collecting member data since late 2009 to analyze and provide feedback to members, validate the EPRI-developed acceptance criteria guidelines, support analysis of test results, recommend appropriate actions for the "action required" category, and gather candidate cables for EPRI-sponsored forensic research on causes for insulation degradation. EPRI has collected data from 37 nuclear sites, which represent 44 operating units. The test results have been organized by insulation type, such as cross-linked polyethylene (XLPE); butyl rubber; black, pink, and brown ethylene-propylene rubber (EPR); and compact insulation (black and pink EPR)1. The data have been analyzed, and follow-up information was obtained from members for “action required” test results. EPRI has also performed correlations between Tan Delta tests and the information gathered under the EPRI forensic research on medium-voltage cables. In addition, EPRI has developed guidance by cable insulation type on how to systematically analyze Tan Delta test results. The analysis described here reviewed the two primary EPRI reports (EPRI 3002000557 and EPRI 3002005321) as well as two precedent EPRI reports (EPRI 1028262 and EPRI 1021070) that were cited in the primary reports. The principal results and conclusions from the project analyses are provided.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

An Applied Strategy for Using Empirical and Hybrid Models in Online Monitoring

The monitoring of plant equipment for failure prediction is one of the key contributors to operation and maintenance (O&M) costs for a nuclear power plant (NPP) because O&M monitoring depends on labor-intensive activities that are required to meet high equipment reliability standards. These activities rely primarily on humans for information gathering, condition diagnosis, and predictive analysis. Online monitoring aims to automate these activities by relying on sensors to replace human information gathering and machine learning to replace human analysis and decision making. To facilitate automated monitoring, a systematic strategy for anomaly detection is needed to optimally use the available sensor data, empirical models, and physics-supported models. This strategy is essential to provide credible reasoning on why and when an empirical (i.e., purely data-driven) versus hybrid (i.e., physics-supported) approach should be used and to determine the ideal mix of these two approaches for a defined anomaly detection scope. The extant methods usually adopt an ad hoc trial-and-error approach that, in addition to being time-consuming and costly, is also highly subjective; it is impacted by the background and the skill set of the personnel making the decisions. Thus, such an approach cannot guarantee an optimum outcome. This represents the motivation of the current research effort, which is focused on devising a scientifically supported strategy for the optimum selection of anomaly detection methods. This report presents a detailed assessment of the main anomaly detection techniques within the empirical or hybrid method streams. Empirical methods include pattern, statistical, and causal inference. Hybrid methods include the use of physics models to train and test data methods, reduce data dimensionality, reduce data-model complexity, augment data, and reduce empirical uncertainty; hybrid methods also include the use of data to tune physics models. The listed techniques within these two streams represent the vast majority of techniques performed for anomaly detection. Using the techniques as outcomes, a strategy was developed to enable a systematic decision-making process to lead to one of these techniques. The strategy is driven by key decision points related to data relevance, simple modeling feasibility, data inference, physics-modeling value, data dimensionality, physics knowledge, method of validation, performance, data availability and suitability for training and testing, cause-effect, entropy inference, and model fitting. Each of these decision points in the strategy is explained in detail in this report with examples, along with the scientific basis behind the decisions and outcomes in common and simplified terminology. The strategy is developed for use by any NPP staff with basic engineering or science knowledge. A user-friendly graphical state flow diagram was also developed as a visual presentation of the strategy. The strategy was tested and demonstrated through two pilot projects for the application of anomaly detection at an NPP. Each pilot had two use cases: an initial case in which certain decisions were made that resulted in one or more empirical techniques and a revised use case where one or more key decisions were modified resulting in using a set of hybrid methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

The STAT7 Code for Statistical Propagation of Uncertainties in Steady State Thermal Hydraulics Analysis of Plate Fueled Reactors

The STAT7 software was developed to perform steady-state thermal hydraulic analyses. Application of the software is for non-power research and test reactors, including conversion to low-enriched uranium fuel of U.S. High-Performance Research Reactors such as MITR-II. Since it can be necessary to repeat analysis during fuel reloading, STAT7 accommodates flexibility in analyzing many realistic aspects of reactor fuel management. STAT7 uses a Monte Carlo approach to model common fabrication parameters and other key reactor analysis uncertainties required for research and test reactor thermal hydraulic analyses. These safety calculations are ultimately intended to protect against high fuel plate temperatures due to critical heat flux or departure from nucleate boiling or onset of flow instability; but additional margin is obtained by basing the limiting safety settings on avoiding onset of nucleate boiling. STAT7 can simultaneously analyze all of the axial nodes of all of the fuel plates and all of the coolant channels for one lateral stripe of a fuel element. The stripes run the length of the fuel, from the bottom to the top. Power splits are calculated for each axial node of each plate to determine how much of the power goes out each face of the plate. By running STAT7 multiple times, full core analysis can be performed by analyzing the margin to onset of nucleate boiling and onset of flow instability for each axial node of each stripe of each plate of each element in the core.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

A spatially-resolved model of neutron-irradiated tungsten coupling stochastic cluster dynamics and finite deformation plasticity

Structural materials used in nuclear reactors face severe degradation in mechanical properties, such as hardening and embrittlement. At the microscopic scale, this occurs due to creation and accumulation of irradiation-induced defects and their interaction with system dislocations. Although techniques exist which can model evolution of irradiation defects, for instance kinetic transport theory-based models, their interaction with mechanical deformation of the bulk material has not been investigated extensively. In this work, we demonstrate a novel spatially-resolved multiscale coupling between microscopic irradiation defect evolution, modeled using Stochastic Cluster Dynamics (SCD) and macroscopic mechanical deformation modeled using a finite-deformation plasticity model. SCD is used to determine the statistically averaged defect cluster spacing, dependent on operating conditions such as irradiation dose and temperature. This acts as an initial condition that governs the critical resolved shear stress of dislocation glide in the macroscopic plasticity model. This framework is used to predict mechanical behavior in post-mortem test of irradiated Tungsten samples, which has found its importance as structural material used in nuclear reactors. The results obtained using the coupled approach are in good agreement with experimental data of uniaxial tension tests. The model is able to capture the effect of temperature and irradiation dose on the material hardening. Two methods are proposed to estimate hardness – using Tabor's Law relating uniaxial yield stress to hardness and from flat-punch simulations. The results are in reasonable agreement with hardness data from micro-indentation experiments of irradiated Tungsten samples. Finally, the model is also able to reveal microstructural details such as spatial variation in defect density and local stress.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

Natural Gas Drilling near the Underground Nuclear Test Site of Rulison, Colorado - 19571

In 1969, the Project Rulison test was conducted in western Colorado using a nuclear device to stimulate natural gas production by fracturing low-permeability, gas-bearing rock. The presence of radionuclides (specifically tritium) in the produced gas persisted above acceptable levels, and the test was abandoned. Advances in hydrofracturing technology over the past 10-15 years have revolutionized the extraction of hydrocarbons from low-permeability formations, leading to a significant increase of drilling in the Rulison area. Drilling activity nearing the Rulison site has raised concerns that remnant radioactivity might be encountered. The site, now under the care of the US Department of Energy (DOE), is protected by a 16-hectare (40 acre) institutional control boundary (Lot 11) that prohibits drilling or extraction of materials below 1830 meters (6000 feet) within the lot boundary. Drilling within 0.8 kilometer (0.5 mile) of the site requires a hearing before the Colorado Oil and Gas Conservation Commission. DOE recommends that gas developers adopt a conservative, staged drilling approach, allowing gas reserves near the Rulison site to be recovered in a manner that minimizes the likelihood of encountering contamination. The staged approach calls for collecting data from wells away from the site before drilling closer. For instance, the wells 1.2 kilometer (0.75 mile) west of the site did not encounter any unexpected geologic conditions and now have 8 years of production without encountering any detonation-related radionuclides. The next set of wells would be 0.8 kilometer (0.5 mile) west of the site. This sequential method drills first at locations with a low probability of encountering contamination and then moves closer. This process protects public safety while allowing the collection of additional data to confirm that contamination has not migrated beyond the 16-hectare (40-acre) institutional control boundary. The staged drilling approach was simulated with a modeling effort that estimates the current extent of contamination and the potential for production-induced contaminant migration to nearby wells. The model incorporates geologic data from nearby wells and was calibrated to production data from both the reentry well production testing (1970-1971) and the wells 1.2 kilometer (0.75 mile) from the site that began producing in 2010. The geologic data include both sand/shale distribution statistics as well as the tendency of hydrofractures to preferentially propagate east and west due to the regional stress field. The model results indicate that it is unlikely that wells near the site would ever encounter site-related radionuclides. (authors)

03 NATURAL GAS↗
DOE OSTI2022

Failure evaluation of neutron-irradiated SiC/SiC composites by underwater acoustic emission

Here, understanding the statistical properties of mechanical properties of non-irradiated and neutron-irradiated SiC/SiC composites is essential for component design. This study aims to evaluate the detailed damage accumulation behavior of composites focusing on two fracture parameters: proportional limit stress (PLS) and acoustic emission (AE) onset stress. The developmental underwater AE technique, which is benefit in non-contact in-situ failure monitoring method during mechanical testing and in handle of the irradiated material, was first applied to evaluate damage accumulation behavior. Two types of chemical vapor infiltration SiC/SiC composites were used: one reinforced with Hi-Nicalon Type-S SiC fiber and one reinforced with Tyranno-SA3 SiC fiber in the form of satin-woven 2D fabrics with pyrolytic carbon interface. Neutron irradiation in the High Flux Isotope Reactor at Oak Ridge National Laboratory reached a fluence of 30 dpa at a temperature of 620–670°C. Four-point flexural tests were conducted to evaluate post-irradiation strength. Weibull statistics did not suggest marked degradation of composite strength. Detailed failure behavior evaluated by AE demonstrated no irradiation-induced change of the AE onset stress (i.e., crack initiation equivalent stress). Failure probability analysis suggests that increasing the reliability of composites (i.e., the Weibull modulus rather than strength itself) is essential to expanding the design margin and benefiting from a probabilistic design approach.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Joint cosmic density reconstruction from photometric and spectroscopic samples

ABSTRACT We reconstruct the dark matter density field from spatially overlapping spectroscopic and photometric redshift catalogues through a field-level forward modelling approach. Instead of directly inferring the underlying density field, we find the best-fitting initial Gaussian fluctuations that will evolve into the observed cosmic volume. To account for the substantial uncertainty of photometric redshifts we employ a differentiable continuous Poisson process. As an initial test, we construct a mock based on the upcoming Prime Focus Spectrograph combined with photometric sample modelled on the Subaru Hyper Suprime-Cam. Depending on the statistic of interest, we find improvements in cosmic structure classification equivalent to 50–100 per cent more spectroscopic targets by combining relatively sparse spectroscopic with dense photometric samples.

Horowitz, B.↗
DOE OSTI2018

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly, Clostridium difficile strains harboring this gene are at higher abundance in formula-fed infants than C. difficile strains lacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have higher replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data to five principal components classified by boosted decision trees. Among the genes involved in predicting whether an organism increased in relative abundance after treatment are those that encode subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics treatment and predict how organisms in the gut microbiome will respond to antibiotic administration.

59 BASIC BIOLOGICAL SCIENCES↗