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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Tunable phononic bandgap materials designed via topology optimization

Topology optimization is used to design phononic bandgap materials that are tunable by mechanical deformation. A periodic media is considered, which due to the assumption of length scale separation, allows the dispersion relations to be obtained by analyzing a single unit cell subjected to Floquet–Bloch boundary conditions. A finite macroscopic deformation is applied to the unit cell to affect its geometry and hence dispersion. We tune the dispersion–deformation relation to our liking by solving a topology optimization problem using nonlinear programming. The adjoint method is employed to compute the sensitivities, and the non-differentiability of degenerate eigenvalues is avoided using symmetric polynomials. Several tunable phononic crystal designs are presented. Also, a verification analysis is performed, wherein the optimized design is interpreted and analyzed using a conforming finite element mesh.

42 ENGINEERING↗
DOE OSTI2021

TROPOMI NO 2 in the United States: A Detailed Look at the Annual Averages, Weekly Cycles, Effects of Temperature, and Correlation With Surface NO 2 Concentrations

Abstract Observing the spatial heterogeneities of NO 2 air pollution is an important first step in quantifying NO X emissions and exposures. This study investigates the capabilities of the Tropospheric Monitoring Instrument (TROPOMI) in observing the spatial and temporal patterns of NO 2 pollution in the continental United States. The unprecedented sensitivity of the sensor can differentiate the fine‐scale spatial heterogeneities in urban areas, such as emissions related to airport/shipping operations and high traffic, and the relatively small emission sources in rural areas, such as power plants and mining operations. We then examine NO 2 columns by day‐of‐the‐week and find that Saturday and Sunday concentrations are 16% and 24% lower respectively, than during weekdays. We also analyze the correlation of daily maximum 2‐m temperatures and NO 2 column amounts and find that NO 2 is larger on the hottest days (>32°C) as compared to warm days (26°C–32°C), which is in contrast to a general decrease in NO 2 with increasing temperature at moderate temperatures. Finally, we demonstrate that a linear regression fit of 2019 annual TROPOMI NO 2 data to annual surface‐level concentrations yields relatively strong correlation ( R 2 = 0.66). These new developments make TROPOMI NO 2 satellite data advantageous for policymakers and public health officials, who request information at high spatial resolution and short timescales, in order to assess, devise, and evaluate regulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Study of $Z \rightarrow ll\gamma$ decays at $\sqrt{s}$ = 8 TeV with the ATLAS detector

This paper presents a study of $Z \rightarrow ll\gamma$ decays with the ATLAS detector at the Large Hadron Collider. The analysis uses a proton–proton data sample corresponding to an integrated luminosity of 20.2 fb -1 collected at a centre-of-mass energy $\sqrt{s}$ = 8 TeV. Integrated fiducial cross-sections together with normalised differential fiducial cross-sections, sensitive to the kinematics of final-state QED radiation, are obtained. The results are found to be in agreement with state-of-the-art predictions for final-state QED radiation. First measurements of $Z \rightarrow ll\gamma\gamma$ decays are also reported.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Measurement accuracy and spatial resolution of a distributed temperature sensor based on a two-pulse differential coherent reflectometer

We present a model and numerical simulation of a distributed temperature sensor based on a two-pulse differential coherent optical time-domain reflectometer (COTDR). The differential phase measured using a phase-sensitive Rayleigh reflectometer is shown to have a regular component, which is a linear function of temperature, and a random component, which is related to a random distribution of scattering centres in the fibre and restricts the accuracy of measurements of variations in temperature. Measurement accuracy can be improved by reducing the relative contribution of the random component via a decrease in pulse duration and/or an increase in the time delay between pulses. The spatial resolution of a differential two-pulse phase-sensitive reflectometer is shown to be determined by the time delay between pulses and to vary little with pulse duration. At a typical pulse duration (200 ns) and delay time (300 ns), the accuracy in measurements of variations in temperature in the 0.1-K range is 2 % and the spatial resolution is about 30 m. (fibre-optic sensors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Towards reverse mode automatic differentiation of Kokkos-based codes

Derivative computation is a key component of optimization, sensitivity analysis, uncertainty quantification, and the solving of nonlinear problems. Automatic differentiation (AD) is a powerful technique for evaluating such derivatives, and in recent years, has been integrated into programming environments such as Jax, PyTorch, and TensorFlow to support derivative computations needed for training of machine learning models, facilitating wide-spread use of these technologies. The C++ language has become the de facto standard for scientific computing due to numerous factors, yet language complexity has made the wide-spread adoption of AD technologies for C++ difficult, hampering the incorporation of powerful differentiable programming approaches into C++ scientific simulations. This is exacerbated by the increasing emergence of architectures, such as GPUs, with limited memory capabilities and requiring massive thread-level concurrency. C++ AD tools must effectively use these environments to bring novel scientific simulations to next-generation DOE experimental and observational facilities. In this project, we investigated source transformation-based automatic differentiation using LLVM compiler infrastructure to automatically generate portable and efficient gradient computations of Kokkos-based code. We have demonstrated that our proposed strategy is feasible by investigating the usage of a prototype LLVM-based source transformation tool to generate gradients of simple functions made of sequences of simple Kokkos parallel regions. Speedups of up to 500x compared to Sacado were observed on NVIDIA V100 GPU.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Resource-Adaptive Federated Text Generation with Differential Privacy

In cross-silo federated learning (FL), sensitive text datasets remain confined to local organizations due to privacy regulations, making repeated training for each downstream task both communication-intensive and privacy-demanding. A promising alternative is to generate differentially private (DP) synthetic datasets that approximate the global distribution and can be reused across tasks. However, pretrained large language models (LLMs) often fail under domain shift, and federated finetuning is hindered by computational heterogeneity: only resource-rich clients can update the model, while weaker clients are excluded, amplifying data skew and the adverse effects of DP noise. We propose a flexible participation framework that adapts to client capacities. Strong clients perform DP federated finetuning, while weak clients contribute through a lightweight DP voting mechanism that refines synthetic text. To ensure the synthetic data mirrors the global dataset, we apply control codes (e.g., labels, topics, metadata) that represent each client’s data proportions and constrain voting to semantically coherent subsets. This two-phase approach requires only a single round of communication for weak clients and integrates contributions from all participants. Experiments show that our framework improves distribution alignment and downstream robustness under DP and heterogeneity.

Wang, Jiayi [ORNL]↗
DOE OSTI2021

Which nuclear data can be validated with LLNL pulsed-sphere experiments?

It is shown here that 14-MeV D+T LLNL pulsed-sphere experiments bring complementary information into the process of validating nuclear data compared to experiments that are traditionally used for this purpose—such as critical assemblies. To be more specific, the 14-MeV D+T LLNL pulsed-sphere neutron-leakage spectra enable to validate scattering and fission nuclear data up to 15 MeV (compared to approximately up to 5 MeV when using criticality experiments) and employ to this end simple compound targets containing only few isotopes. In this work, sensitivity profiles of the spectra to nuclear data are calculated in order to understand in detail which isotopes, observables, and energy ranges of nuclear data contribute significantly to their simulation. These profiles are presented for a few selected spheres containing 16 O, 12 C, 56 Fe, and 239 Pu. It is shown that the neutron-leakage spectra of spheres containing light elements are mostly sensitive to elastic- and inelastic-scattering cross sections on discrete levels and corresponding angular distributions. Spheres of structural materials are sensitive to elastic- and inelastic-scattering cross sections, including scattering on discrete levels and the continuum, and double-differential cross sections. Actinide spheres are also strongly sensitive to the fission observables, in particular to the total-fission neutron spectrum. Thin spheres (in which neutrons experience on average less than one scatter) are mostly sensitive to data near the elastic peak, in the energy range from 12–15 MeV, while thicker ones can be sensitive to data at lower incident-neutron energies due to multiple-scattering effects. This information is brought together with simulations of 71 pulsed-sphere neutron-leakage spectra using the ENDF/B-VII.1 and ENDF/B-VIII.0 nuclear-data libraries. This analysis highlights ENDF/B-VIII.0 data that could be further investigated for potential shortcomings ( 6 Li, 12 C, 16 O, 24-26 Mg, 27 Al, 48 Ti, 56 Fe, and 208 Pb) or are likely reliable ( 1,2 H, 7 Li, 9 Be, 14 N, 235,238 U, and 239 Pu) as indicated by validating with LLNL pulsed-sphere experiments.

14-MeV D+T LLNL pulsed-sphere neutron-leakage spec↗
DOE OSTI2020

Iron Heterogeneity in Early Active Multiple Sclerosis Lesions

Objective: Multiple sclerosis (MS) is a heterogeneous inflammatory demyelinating disease. Iron distribution is altered in MS patients' brains, suggesting iron liberation within active lesions amplifies demyelination and neurodegeneration. Whether the amount and distribution of iron are similar or different among different MS immunopatterns is currently unknown. Methods: We used synchrotron X-ray fluorescence imaging, histology, and immunohistochemistry to compare the iron quantity and distribution between immunopattern II and III early active MS lesions. We analyzed archival autopsy and biopsy tissue from 21 MS patients. Results: Immunopattern II early active lesions contain 64% more iron (95% confidence interval [CI] = 17-127, p = 0.004) than immunopattern III lesions, and 30% more iron than the surrounding periplaque white matter (95% CI = 3–64%, p = 0.03). Iron in immunopattern III lesions is 28% lower than in the periplaque white matter (95% CI = -40 to -14%, p < 0.001). When normalizing the iron content of early active lesions to that of surrounding periplaque white matter, the ratio is significantly higher in immunopattern II (p < 0.001). Microfocused X-ray fluorescence imaging shows that iron in immunopattern II lesions localizes to macrophages, whereas macrophages in immunopattern III lesions contain little iron. Interpretation: Iron distribution and content are heterogeneous in early active MS lesions. Iron accumulates in macrophages in immunopattern II, but not immunopattern III lesions. This heterogeneity in the two most common MS immunopatterns may be explained by different macrophage polarization, origin, or different demyelination mechanisms, and paves the way for developing new or using existing iron-sensitive magnetic resonance imaging techniques to differentiate among immunopatterns in the general nonbiopsied MS patient population.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Addressing the sensitivity of signals from solid/liquid ambient pressure XPS (APXPS) measurement

Ambient pressure XPS has demonstrated its great potential in probing the solid/liquid interface, which is a central piece in electrocatalytic, corrosion, and energy storage systems. Additionally, despite the advantage of ambient pressure XPS being a surface sensitive characterization technique, the ability of differentiating the surface adsorbed species (~Å scale) and bulk electrolyte (~10 nm scale) in the spectrum depends on the delicate balance between bulk solution concentration (C), surface coverage (θ), bulk liquid layer thickness (L), and inelastic mean free path (λ) as a function of photon energy. By investigating a model system of gold dissolving in a bromide solution, the connection between theoretical prediction at the atomic resolution and macroscopic observable spectrum is established.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Performance evaluation of neutron noise analysis in detecting special nuclear materials

Reliable and rapid inspection techniques play a vital role in preventing illicit trafficking of special nuclear materials. Active interrogation systems using neutrons produced by portable, high-flux deuterium-deuterium or deuterium-tritium neutron generators are being actively developed as a secondary scanning tool for this purpose. In this study, a neutron noise analysis-based approach for detecting unshielded and shielded special nuclear materials by using a pulsed deuterium-tritium neutron generator was evaluated. Here, this approach analyzes the fluctuation of neutron counts. Its performance was quantified with regard to time-to-detection to achieve a minimum probability of detection of 99% and a probability of false alarm of less than 1% considering various amounts of special nuclear materials and different shielding configurations. It was demonstrated that this approach could detect 17 uranium slugs in 5 s given a neutron generator yield of 8.1 × 10 7 n/s. These slugs could be detected within a reasonable time frame (200 s) when they were shielded by 10.16 cm of high-density polyethylene. The results obtained using the neutron noise analysis approach were compared with those obtained using the commonly used differential die-away analysis technique, a sensitive technique for detecting the presence of fissile materials by utilizing the prompt fission neutrons produced when the source neutrons from a neutron generator are completely diminished. For example, the time to detect 2 unshielded uranium slugs was 2.1 s when using the differential die-away analysis technique; it increased to 93 s for the neutron noise analysis approach. Although the noise analysis-based approach exhibits an overall performance which is not as good as that of differential die-away, neutron noise provides an alternative method for effective detection of special nuclear materials.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

GEAR-MC and Differential-Operator Methods Applied to Electron-Photon Transport in the Integrated TIGER Series

The sensitivity analysis algorithms that have been developed by the radiation transport community in multiple neutron transport codes, such as MCNP and SCALE, are extensively used by fields such as the nuclear criticality community. However, these techniques have seldom been considered for electron transport applications. In the past, the differential-operator method with the single scatter capability has been implemented in Sandia National Laboratories’ Integrated TIGER Series (ITS) coupled electron-photon transport code. This work is meant to extend the available sensitivity estimation techniques in ITS by implementing an adjoint-based sensitivity method, GEAR-MC, to strengthen its sensitivity analysis capabilities. To ensure the accuracy of this method being extended to coupled electron-photon transport, it is compared against the central-difference and differential-operator methodologies to estimate sensitivity coefficients for an experiment performed by McLaughlin and Hussman. Energy deposition sensitivities were calculated using all three methods, and the comparison between them has provided confidence in the accuracy of the newly implemented method. Unlike the current implementation of the differential-operator method in ITS, the GEAR-MC method was implemented with the option to calculate the energy-dependent energy deposition sensitivities, which are the sensitivity coefficients for energy deposition tallies to energy-dependent cross sections. The energy-dependent cross sections could be the cross sections for the material, elements in the material, or reactions of interest for the element. Further, these sensitivities were compared to the energy-integrated sensitivity coefficients and exhibited a maximum percentage difference of 2.15%.

42 ENGINEERING↗
DOE OSTI2021

Multifrequency radar observations of clouds and precipitation including the G-band

Abstract. Observations collected during the 25 February 2020 deployment of the Vapor In-Cloud Profiling Radar at the Stony Brook Radar Observatory clearly demonstrate the potential of G-band radars for cloud and precipitation research, something that until now was only discussed in theory. The field experiment, which coordinated an X-, Ka-, W- and G-band radar, revealed that the Ka–G pairing can generate differential reflectivity signal several decibels larger than the traditional Ka–W pairing underpinning an increased sensitivity to smaller amounts of liquid and ice water mass and sizes. The observations also showed that G-band signals experience non-Rayleigh scattering in regions where Ka- and W-band signal do not, thus demonstrating the potential of G-band radars for sizing sub-millimeter ice crystals and droplets. Observed peculiar radar reflectivity patterns also suggest that G-band radars could be used to gain insight into the melting behavior of small ice crystals. G-band signal interpretation is challenging, because attenuation and non-Rayleigh effects are typically intertwined. An ideal liquid-free period allowed us to use triple-frequency Ka–W–G observations to test existing ice scattering libraries, and the results raise questions on their comprehensiveness. Overall, this work reinforces the importance of deploying radars (1) with sensitivity sufficient enough to detect small Rayleigh scatters at cloud top in order to derive estimates of path-integrated hydrometeor attenuation, a key constraint for microphysical retrievals; (2) with sensitivity sufficient enough to overcome liquid attenuation, to reveal the larger differential signals generated from using the G-band as part of a multifrequency deployment; and (3) capable of monitoring atmospheric gases to reduce related uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Report on Depth-Dependent Q from Frequency-Dependent Lg Q

As a phase that travels through the crustal waveguide, Lg samples the velocity and attenuation structure of the crust. We have developed methods (Pasyanos et al., 2009a; Pasyanos et al., 2009b) to estimate Qp and Qs of the crust and upper mantle from the amplitudes of regional phases, and have applied it to a number of regions around the world, and over a broad frequency band (0.5 - 10 Hz). In prior attenuation modeling, Lg phase amplitudes are able to effectively distinguish the high Q (low attenuation) of old stable cratonic crust from the low Q (high attenuation) of more recently active tectonic regions. For a variety of purposes (e.g. waveform modeling, seismic hazard, etc.), it is useful to have more information on the depth-dependence of the Q structure in the crust. One obvious candidate for doing this is using the frequency-dependence information of Lg Q, in the manner of surface waves. Unfortunately, however, Lg samples the whole of the crust without much differentiation with respect to frequency that is characteristic of fundamental mode surface waves. Lg is generally thought to be the sum of supercritically reflected S-waves trapped in the crustal waveguide (e.g. Xie and Lay, 1994). The phase can also be modeled as a superposition of surface waves. At lower frequencies, it is primarily composed of fundamental and low-order surface waves, while at higher frequencies, it is comprised purely of many high-order surface waves. The low-order surface waves that comprise Lg in low frequency bands (< 1 Hz) are preferentially sensitive to shallow earth structure, such as sedimentary basins and upper crust, while high-order surface waves have a more homogenized sensitivity to the whole crust. Furthermore, at the lower frequencies, we might expect to see some differentiation in the sensitivity between early Lg (herein referred to as Lg1) and late Lg (referred to as Lg2) where the latter is comprised of lower-order surface waves and, hence, shallower structure. Therefore, we might expect to see the signature of shallow features, primarily the lower Q of sediments as compared to crystalline crust, at lower frequencies and in later arriving Lg amplitudes.

58 GEOSCIENCES↗
DOE OSTI2025

Hypercomplex Automatic Differentiation in the Eulerian Hydrocode PAGOSA

Enabling the computation of partial derivatives or sensitivities in production hydrocodes is beneficial for design, optimization, sensitivity analysis, and uncertainty quantification. Traditional finite difference approximations of these sensitivities are inefficient since convergence studies of the step size is required for each parameter of interest. For these reasons, HYPercomplex Automatic Differentiation (HYPAD) was implemented in the Eulerian hydrocode PAGOSA. HYPAD is analogous to forward-mode automatic differentiation except hypercomplex numbers (numbers with multiple imaginary parts) are used instead of dual numbers. Accurate partial derivatives can be computed of all state variables with respect to multiple input variables in a single run. The method was implemented using operator overloading to handle hypercomplex algebra. HYPAD was demonstrated and verified on Sod’s shock tube problem to compute derivatives of the state variables with respect to a material parameter, initial conditions, and geometry.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

First Measurement of Differential Charged Current Quasielastic-like $\nu_\mu$–Argon Scattering Cross Sections In Kinematic Imbalance Variables With The MicroBooNE Detector

We report the first measurement of flux-integrated multi-differential cross sections for charged-current events with muon neutrinos scattering on argon with solely a muon and a single proton in the final state as a function of kinematic imbalance variables. The measurement was carried out using the Booster Neutrino Beam at Fermi National Accelerator Laboratory within the MicroBooNE Liquid Argon Time Projection Chamber detector with an exposure of 6.79 × 10 20 protons on target. Events were selected to enhance the contribution of charged-current mesonless interactions with one proton detected in the final state. The data discussed here are reported in terms of multidifferential cross sections in kinematic imbalance variables, which are generally sensitive to nuclear effects. The double-differential results in these variables can provide an excellent handle to disentagle specific nuclear aspects not easily isolated via single differential cross sections. Our results pave a path towards identifying regions of the phase-space where future interaction modeling development and Monte Carlo neutrino generator tuning efforts should concentrate. EVENT SELECTION Neutrino oscillation measurements aim to extract neutrino mixing angles, mass differences, the value of the chargeparity violating phase in the lepton sector, and to search for new physics beyond the Standard Model [1, 2]. For that to be achieved, an unprecedented understanding of neutrino-argon interactions is of utmost importance since a growing number of neutrino oscillation experiments employ Liquid Argon Time Projector Chamber (LArTPC) neutrino detectors [3–6]. The accuracy to which these experiments can extract neutrino oscillation parameters requires a good understanding of the neutrino energy. Experimentally, this energy is deduced from the measured kinetic energies of particles that are emitted following the neutrino interaction in the detector. The kinematic properties of such finalstate particles reflect complex dynamics due to nuclear and initial-state effects of the interaction [7]. However, certain categories of nuclear effects can be isolated by variables built specifically to characterize the degeneracy between such effects [8–10]. This note reports cross sections in kinematic variables sensitive to nuclear effects using events with one detected muon with momentum 0.1 < pµ < 1.2 GeV/c, and exactly one proton with 0.3 < pp < 1 GeV/c. This signal definition includes events with any number of protons below 300 MeV/c, neutrons at any momenta, and charged pions with momentum lower than 70 MeV/c. This choice is guided by the fact that their experimental signature of correlated muon-proton pairs is fairly straightforward to reconstruct [11–22]. Such events primarily originate from chargedcurrent (CC) neutrino-nucleon quasielastic (QE) scattering interactions where the neutrino removes a single intact nucleon from the nucleus without producing any additional particles. This definition can also include contributions from interactions that lead to the production of additional particles that are absent from the final state due to nuclear effects, such as pion absorption, or have momenta that are below the experimental detection threshold.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Roadmap and Benchmarking: Privacy in Federated Load Forecasting

Data-driven techniques for energy demand forecasting continue to emerge with promising impacts on distribution grid planning. However, the development of robust and generalizable machine learning models requires that representative high quality training data are available. Distributed energy resources have begun to embed intelligence, gathering large amounts of data on customer demand, behavior, and household devices that are connected to the grid. Though utilities aggregate meter-level demand data for load shaping, demand response, outage management, reliability planning, and billing applications, there lies an inherent privacy concern in sharing consumption data that may identify individual consumer behavioral patterns. Hence, while sharing the data is crucial, the private sensitive customer data must be safeguarded from being exposed or manipulated. In this study, we propose a roadmap for implementing a based privacy preserving framework to support the advancement of data-driven analytics in data-sensitive distributed energy resources environments. The roadmap incorporates federated learning–a distributed training framework, differential privacy–a statistical framework that provides guarantees to safeguard the leakage of sensitive data, secure multiparty computation and homomorphic encryption– techniques for encrypting model gradients and applying secure aggregation on the server. Moreover, we perform baseline experiments on the federated short-term load forecasting (STLF) task using open-source residential load profile datasets, offering insights into the challenges of integrating differential privacy into federated learning.

Abebe, Waqwoya [Oak Ridge National Laboratory (ORN↗
DOE OSTI2023

Mediating Photochemical Reaction Rates at Lewis Acidic Rare Earths by Selective Energy Loss to 4f-Electron States

Manifesting chemical differences in individual rare earth (RE) element complexes is challenging due to the similar sizes of the tripositive cations and the corelike 4f shell. In this work, we disclose a new strategy for differentiating between similarly sized Dy 3+ and Y 3+ ions through a tailored photochemical reaction of their isostructural complexes in which the f-electron states of Dy 3+ act as an energy sink. Complexes RE(hfac) 3 (NMMO) 2 (RE = Dy (2-Dy) and Y (2-Y), hfac = hexafluoroacetylacetonate, and NMMO = N-methylmorpholine-N-oxide) showed variable rates of oxygen atom transfer (OAT) to triphenylphosphine under ultraviolet (UV) irradiation, as monitored by 1 H and 19 F NMR spectroscopies. Ultrafast transient absorption spectroscopy (TAS) identified the excited state(s) responsible for the photochemical OAT reaction or lack thereof. Competing sensitization pathways leading to excited-state deactivation in 2-Dy through energy transfer to the 4f electron manifold ultimately slows the OAT reaction at this metal cation. The measured rate differences between the open-shell Dy 3+ and closed-shell Y 3+ complexes demonstrate that using established principles of 4f ion sensitization may deliver new, selective modalities for differentiating the RE elements that do not depend on cation size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 hours post-fertilization after exposure to eight retene concentrations. The concentrations were selected to produce effects ranging from no phenotype to mortality and malformations in 100% of animals at 5 days post-fertilization. We identified a concentration-response relationship between retene teratogenicity and differential gene expression in both number of DEGs and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of AHR-dependent teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-ß (TGF-ß) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module 7 genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module 7 genes are largely responsible for retene toxicity.

Toxin, Zebrafish, Retene, Transcriptomics, network↗