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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 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Enhanced nucleation mechanism in ruthenium atomic layer deposition: Exploring surface termination and precursor ligand effects with RuCpEt(CO)2

Miniaturization of microelectronic devices necessitates atomic precision in manufacturing techniques, particularly in the deposition of thin films. Atomic layer deposition (ALD) is recognized for its precision in controlling film thickness and composition on intricate three-dimensional structures. This study focuses on the ALD nucleation and growth mechanisms of ruthenium (Ru), a metal that has significant future implications for microelectronics. Despite its advantages, the deposition of a high surface-free energy material like Ru on a low surface-free energy material such as an oxide often faces challenges of large nucleation delays and non-uniform growth. To address these challenges, we explored the effectiveness of organometallic surface pretreatments using trimethylaluminum (TMA) or diethylzinc (DEZ) to enhance Ru film nucleation and growth. Our study employed a less-studied Ru precursor, cyclopentadienylethyl(dicarbonyl)ruthenium [RuCpEt(CO)2], which demonstrated promising results in terms of reduced nucleation delay and increased film continuity. Ru ALD was performed on silicon substrates with native oxide, using RuCpEt(CO)2 and O2 as coreactants. Our findings reveal that surface pretreatment significantly improves nucleation density and film thickness within the initial 60 ALD cycles, achieving up to a 3.2-fold increase in Ru surface coverage compared to nonpretreated substrates. Supported by density functional theory calculations, we propose that the enhanced nucleation observed with RuCpEt(CO)2 compared to previously-studied Ru(Cp)2 is due to two key mechanisms: the facilitated removal of CO ligands during deposition, which enhances the reactivity of the precursor, and a hydrogen-abstraction reaction involving the ethyl ligand of RuCpEt(CO)2 and the metal-alkyl groups on the surface. This study not only advances our understanding of Ru ALD processes but also highlights the significant impact of precursor chemistry and surface treatments in optimizing ALD for advanced microelectronic applications.

Materials Science↗
DOE OSTI2020

Adaptive noise canceling for transient absorption microscopy

Significance: Ultrafast fiber lasers are an attractive alternative to bulk lasers for nonlinear optical microscopy for their compactness and low cost. The high relative intensity noise (RIN) of these lasers poses a challenge for pump-probe measurements such as transient absorption and stimulated Raman scattering, along with modalities that provide label-free contrast from the vibrational and electronic structure of molecules. Aim: Digital adaptive filtering was applied to determine the applicability for canceling laser RIN in a transient absorption microscope with an ultrafast fiber laser source. Approach: Digitized signals from the transmitted probe and reference photodetectors were fed to an adaptive filter in MATLAB, running in a noise canceling configuration. This result was then fed to a software lock-in algorithm to demodulate the pump-probe signal. Images were built up one line scan at a time with a 3.5-kHz resonant scanner, with 100× averaging. The imaging target was Bi4Ge3O12, which exhibits nondegenerate two-photon absorption at the pump/probe wavelengths used (530-nm pump and 490-nm probe). Results: Without adaptive noise cancellation, the lock-in output primarily passes the laser RIN within its detection bandwidth, resulting in images that closely follow the linear transmissivity and lack sensitivity to pump-probe time delay. With adaptive noise cancellation in front of the lock-in, the RIN rejection is enough to restore the z-sectioning and sensitivity to pump-probe delay, as expected for transient absorption. Results were limited primarily by noise from the photodetector and analog-to-digital converter. Conclusions: Digital adaptive noise cancellation, even when limited by electronics noise, can recover pump-probe signals by removal of laser RIN, under conditions where averaging alone fails.

42 ENGINEERING↗
DOE OSTI2021

Diffuse energy transport and coda-wave interferometry for resonant transmission between reverberant structures

Approximate analytic and numerical theories are developed with which to model, and compare with laboratory measurements, the diffuse ultrasonic field transmitted from one elastic body to another through a resonant coupling. Particular focus is on the sensitivity of the transmitted field to perturbations in the natural frequency of the coupling, and on the manifestation of such perturbations as time delays in the second body. Immediate application is to measurements of slow dynamic elastic nonlinearity. It is found that the developed approximate theories do a good job of predicting the time dependence of mean square transmitted signal and signal spectra. They also predict the time delays, both their erratic character and their means. Analytic dependence of these time shifts on the fractional frequency perturbation df/f is derived.

42 ENGINEERING↗
DOE OSTI2023

Angularly resolved photoionization dynamics in atoms and molecules combining temporally and spectrally resolved experiments at ATTOLab and Synchrotron SOLEIL

We report results for XUV-IR two-photon ionization of Ar, Ne, NO, and O2, where an XUV attosecond pulse train is superimposed with a synchronized IR pulse, obtained at the ATTOLab laser facility using electron–ion coincidence 3D momentum spectroscopy. Temporally resolved photoelectron angular distributions providing angle-resolved time-delays for np ionization of Ar and Ne, achieved by reconstruction of attosecond beating by interference of two-photon transitions through a unified formalism (Joseph et al. in J Phys B At Mol Opt Phys 53:184007, 2020), are summarized. For inner valence XUV-IR dissociative photoionization of NO and O2 molecules, we report electron–ion kinetic energy correlation diagrams and disentangle the dissociative photoionization processes relying on parallel XUV experiments at Synchrotron SOLEIL. For ionization into the NO+(c3Π) ionic state, extending the formalism developed for single-photon ionization, we focus on photoelectron angular distributions averaged on the delay between the XUV and the IR field in the field frame, molecular frame, and electron frame of reference.

Joseph, J↗
DOE OSTI2021

Evaluating Automated Face Identity-Masking Methods with Human Perception and a Deep Convolutional Neural Network

Face de-identification (or “masking”) algorithms have been developed in response to the prevalent use of video recordings in public places. Here, we evaluated the success of face identity masking for human perceivers and a deep convolutional neural network (DCNN). Eight de-identification algorithms were applied to videos of drivers’ faces, while they actively operated a motor vehicle. These masks were pre-selected to be applicable to low-quality video and to maintain coarse information about facial actions. Humans studied high-resolution images to learn driver identities and were tested on their recognition of active drivers in low-resolution videos. Faces in the videos were either unmasked or were masked by one of the eight algorithms. When participants were tested immediately after learning (Experiment 1), all masks reduced identification, with six of eight masks reducing identification to extremely poor performance. In a second experiment, two of the most effective masks were tested after a delay of 7 or 28 days. The delay did not further reduce identification of the masked faces. In all masked conditions, participants maintained stringent decision criteria, with low confidence in recognition, further indicating the effectiveness of the masks. Next, the DCNN performed an identity-matching task between high-resolution images and masked videos—a task analogous to that done by humans. The pattern of accuracy for the DCNN mirrored some, but not all, aspects of human performance, highlighting the need to test the effectiveness of identity masking for both humans and machines. The DCNN was also tested on its ability to match identity between masked and unmasked versions of the same video, based only on the face. DCNN performance for the eight masks offers insight into the nature of the information in faces that is coded in these networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Timely Reporting of Heavy Hitters Using External Memory

Given an input stream S of size N, a Φ-heavy hitter is an item that occurs at least ΦN times in S. The problem of finding heavy-hitters is extensively studied in the database literature. In this work, we study a real-time heavy-hitters variant in which an element must be reported shortly after we see its T = Φ N-th occurrence (and hence it becomes a heavy hitter). We call this the Timely Event Detection (TED) Problem. The TED problem models the needs of many real-world monitoring systems, which demand accurate (i.e., no false negatives) and timely reporting of all events from large, high-speed streams with a low reporting threshold (high sensitivity). Like the classic heavy-hitters problem, solving the TED problem without false-positives requires large space (Ω (N) words). Thus in-RAM heavy-hitters algorithms typically sacrifice accuracy (i.e., allow false positives), sensitivity, or timeliness (i.e., use multiple passes). We show how to adapt heavy-hitters algorithms to external memory to solve the TED problem on large high-speed streams while guaranteeing accuracy, sensitivity, and timeliness. Our data structures are limited only by I/O-bandwidth (not latency) and support a tunable tradeoff between reporting delay and I/O overhead. With a small bounded reporting delay, our algorithms incur only a logarithmic I/O overhead. We implement and validate our data structures empirically using the Firehose streaming benchmark. Multi-threaded versions of our structures can scale to process 11M observations per second before becoming CPU bound. In comparison, a naive adaptation of the standard heavy-hitters algorithm to external memory would be limited by the storage device’s random I/O throughput, i.e., ≈100K observations per second.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Analytical and Numerical Analysis of Lithium Plating Onset in Single and Bilayer Graphite Electrodes during Fast Charging

Lithium plating is commonly observed in anodes charged at fast rates, and can lead to capacity loss and battery safety issues. The increased risk of plating has been attributed to transport limitations, and architectured electrodes may reduce plating risk. However, while theoretical studies have shown that reaction non-uniformity arises due to interplay of transport limitations, anode open circuit voltage behavior and reaction kinetics, its effect on lithium plating has not been studied. We use analytic and numerical simulations to predict onset of plating in graphite anode half-cells at high C-rates and demonstrate how anodes with layered porosities can delay plating. Simplified analytical models identify trends for plating onset and predictions are calibrated against numerical models. A calibrated numerical model of graphite demonstrates qualitative agreement with analytical model predictions. This reaction inhomogeneity mechanism occurs in the absence of lithium ion depletion, indicating that these mechanisms may contribute to capacity loss independently or simultaneously. A bilayer model of graphite exhibits delayed plating onset, and an optimization procedure is presented. This theoretical work presents quantitative and mechanistic insight on how reaction inhomogenity affects lithium metal plating onset and can be used as a guide to engineer anodes resistant to lithium plating.

Mijailovic, Aleksandar S.↗
DOE OSTI2025

Microstructure Scale Lithium-Ion Battery Modeling: Part III. When and Where Lithium Plating Occurs and its Correlation with the Electrode Microstructure

Li-ion battery performance and degradation are closely related to the cell’s underlying electrode microstructure. Electrode microstructures are typically characterized with volume-averaged properties that neglect the impact of local heterogeneities. However, local heterogeneities create hot spots that can trigger degradation onset. Herein, a microstructure scale electrochemical model is used to investigate the impact of microstructure heterogeneity on lithium plating. The model predicts lithium plating is not uniform, even when considering a relatively small portion of the electrode (a cross-sectional area of 154×144 µm 2 ), preferring to plate on larger particles as compared to smaller particles. While local heterogeneities control where plating occurs, the model predicts that volume-averaged properties control when plating occurs. Additionally, the model predicts that the active material specific surface area has a linear relationship with the plating onset. However, the linear relationship between increased active material surface area and delayed plating response appears to be sensitive to the microstructure feature used to increase the active interface area. Here, a comparative case-study is explored where the specific surface area is increased by either reducing the active material particle diameter, adding open-porosity cracks, or increasing the active material surface roughness. The model predicts that increasing the specific surface area by reducing the active material particle diameter is the most effective strategy for delaying lithium plating. At 6C, reducing particle size is shown to be 3 and 20 times more effective than, respectively, adding open-porosity cracks and increasing surface roughness. A dual-layer electrode architecture combining gradations both for average properties and uniformities is eventually proposed to improve homogeneous material utilization and reduce degradation at high charge rates.

25 ENERGY STORAGE↗
DOE OSTI2024

Inhibition of the eukaryotic initiation factor-2α kinase PERK decreases risk of autoimmune diabetes in mice

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress–responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eukaryotic translation initiation factor-2α (eIF2α). In T1D, maladaptive unfolded protein response (UPR) in insulin-producing β cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PKR-like ER kinase (PERK), a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved β cell mass in T1D-susceptible mice. Single-cell RNA-Seq of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen-processing and presentation pathways in β cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein programmed death-ligand 1 (PD-L1) in β cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-βH1 human β cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity and that inhibition of PERK may offer a strategy for preventing or delaying the development of T1D.

Research & Experimental Medicine↗
DOE OSTI2024

Impacts of stochastic coalescence variability on warm rain initiation using Lagrangian microphysics in box and large-eddy simulations

Various coalescence methods for Lagrangian microphysics schemes are tested in box and large-eddy simulation (LES) models, including the stochastic all-or-nothing super-droplet method (SDM) and a version of SDM (dSDM) that applies a fractional approach similar to the average impact method. In LES, variabilities driven by microphysics and by flow realizations are separated using the “piggybacking” technique. Rain initiation averaged over many realizations of the box model is delayed and rain variability increases as the number of super-drops per collision volume ( N SD ) is decreased using SDM. In contrast, rain initiation time using SDM in LES is insensitive to N SD for 32 ≤ N SD ≤ 512. This is explained through the interaction between LES grid boxes, each acting as a separate collision volume. Variability across the ensemble of LES collision volumes using SDM results in rain quickly initiating in some of the LES grid cells at low N SD and leading to a similar overall timing of rain initiation from the cloud compared to simulations with high N SD . There is a ~20% decrease in the total rain mass and mean rain flux as N SD is increased from 32 to 256, with little additional change as N SD is increased from 256 to 512. The fractional coalescence approach in dSDM leads to reduced microphysical variability and a 15-18 min delay in rain initiation compared to SDM. Finally, an additional LES ensemble with microphysical variability feeding back to the dynamics shows that flow variability dominates the impact of microphysical variability on rain properties. Thus, flow variability must be constrained to isolate impacts of microphysical variability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

The Strength of Coupling to the Southern Ocean Modulates Tropical Eastern Pacific Variability and Forced Response

Despite rising global-mean temperatures, large parts of the Southern Ocean and tropical eastern Pacific Ocean have cooled during the satellite era. These regions may be linked by teleconnections, with Southern Ocean cooling contributing to tropical eastern Pacific cooling. We demonstrate that, on average, state-of-the-art Earth system models (ESMs) underestimate the magnitude of interaction between the Southern Ocean and tropical eastern Pacific Ocean. The strength of the teleconnection is shown to be mediated by the magnitude of the positive cloud–sea surface temperature (SST) feedback in the subtropical eastern Pacific Ocean and the strength of the wind–evaporation–SST (WES) feedback. We link excessive precipitation in the tropical Pacific south of the equator to the strength of the Southern Ocean–eastern Pacific teleconnection. This model bias, known as the double intertropical convergence zone (ITCZ), is shown to be related to erroneous convection south of the equator, weakened cross-equatorial trade winds, and unfavorable meteorological conditions for marine boundary layer subtropical clouds. We postulate there is a two-way interaction, in which a double-ITCZ occurs with weaker cloud–SST and WES feedbacks, which in turn impact local SSTs and amplify the double-ITCZ. Models with a stronger Southern Ocean to tropical Pacific teleconnection tend to exhibit more multidecadal variability in the Walker circulation, ITCZ, and west–east equatorial SST gradient, as well as greater delayed warming in the tropical eastern Pacific Ocean resulting from delayed Southern Ocean warming under greenhouse gas forcing. These results provide insight into why ESMs struggle to replicate observed tropical Pacific temperature trend patterns and point to ITCZ location as a key target for improvement in future model development.

Climate change↗
DOE OSTI2022

Evaluating an Eco-Cooperative Automated Control System

The paper evaluates an Eco-Cooperative Automated Control (Eco-CAC) system on a large-scale network considering a combination of internal combustion engine vehicles (ICEVs), hybrid electric vehicles (HEVs), and battery-only electric vehicles (BEVs) in a microscopic traffic simulation environment. We used a novel integrated control system that: (1) routes ICEVs, HEVs, and BEVs in a fuel/energy-efficient manner; (2) selects vehicle speeds based on anticipated traffic network evolution; (3) minimizes vehicle fuel/energy consumption near signalized intersections; and (4) intelligently modulates the longitudinal motion of vehicles along freeways within a cooperative platoon to minimize fuel/energy consumption. The study tested the system using the INTEGRATION software on the Los Angeles (LA), U.S., downtown network for three different demand levels: no congestion, mild congestion, and heavy congestion. The results demonstrated that the Eco-CAC system effectively reduces vehicle fuel and energy consumption, travel time, total delay, and stopped delay in heavily congested conditions. However, different vehicle compositions produced different results. In particular, the maximum energy consumption savings for BEVs (36.9%) for a current vehicle composition occurred at a 10% market penetration rate (MPR) of connected automated vehicles (CAVs) in mild congestion, while the maximum savings for a future vehicle composition (35.5%) occurred at a 50% CAV MPR in no congestion. The system reduced fuel consumption for ICEVs and HEVs by up to 5.4% and 6.3% at a 25% CAV MPR in heavy congestion for current and future vehicle compositions, respectively. However, the system increased total fuel consumption by up to 4.6% at a 50% CAV MPR in no congestion for a current vehicle composition. The study demonstrates that the effectiveness of the Eco-CAC system depends on traffic conditions, including congestion level, network configuration, CAV MPR, and vehicle composition.

Engineering↗
DOE OSTI2023

Fuel-Based Nash Bargaining Approach for Adaptive Signal Control in an N -Player Cooperative Game

This paper presents a fuel-based game-theoretic approach for adaptive signal control. Our controller applies Nash bargaining (NB) in an n-player cooperative game to identify optimal phasing splits considering future traffic demands. The fuel-based NB controller utilizes an objective function that combines operational measures (delays and stops) with fuel consumption measures at intersections. The proposed controller was encoded in Python and then implemented and evaluated in a VISSIM microscopic traffic simulation model in an intersection with increasing volumes. The performance of the NB controller was compared to a traditional actuated control as the baseline. The results show that the NB controller was able to achieve superior environmental gains with a 17% saving in fuel consumption and a 17% reduction in CO emissions. In addition, the proposed controller was capable of maintaining acceptable operational conditions as it achieved a 20% reduction in delay, 8% reduction in the number of stops, and 8% reduction in queue lengths compared to the actuated controller. Compared to similar studies that applied NB for adaptive signal control, our fuel-based NB controller stands out as a promising approach to significantly improve fuel consumption at signalized intersections.

Engineering↗
DOE OSTI2022

Important powertrain dynamics for developing models for control of connected and automated electrified vehicles

Connected and Automated Vehicles (CAV) technology presents significant opportunities for energy saving in the transportation sector. CAV technology forecasts vehicle and powertrain power needs under various terrain, ambient, and traffic conditions. Integration of the CAV technology in Hybrid Electric Vehicles (HEVs) provides the opportunity for optimal vehicle operation. Indeed, Hybrid Electric Vehicle powertrains present high degrees of flexibility and possibility for choosing optimum powertrain modes based on the predicted traction power needs. In modeling complex CAV powertrain dynamics, the modeler needs to consider short-time scale powertrain dynamics, such as engine transients, and hysteresis of mode-switching for a multi-mode HEV. Therefore, the powertrain dynamics essential for developing powertrain controllers for a class of connected HEVs is presented. To this end, control-oriented powertrain dynamic models for a test vehicle consisting of full electric, hybrid, and conventional engine operating modes are developed. The resulting powertrain model can forecast vehicle traction torque and energy consumption for the specified prediction horizon of the test vehicle. The model considers different operating modes and associated energy penalty terms for mode switching. Thus, the vehicle controller can determine the optimum powertrain mode, torque, and speed for forecasted vehicle operation via utilizing connectivity data. The powertrain model is validated against the experimental data and shows prediction error of less than 5% for predicting vehicle energy consumption. The model is used to create energy penalty maps that can be used for CAV control, for example fuel penalty map for engine torque changes (10–40 Nm) at each engine speed. The results of model-based optimization show optimum switching delays ranging from 0.4 to 1.4 s to avoid hysteresis in mode switching.

Engineering↗
DOE OSTI2021

Impact of low reactivity fuel type on low load combustion, emissions, and cyclic variations of diesel-ignited dual fuel combustion

In this study, cyclic variations in dual fuel combustion with diesel ignition of three different low reactivity fuels (methane, propane, and gasoline) are examined under identical operating conditions. Experiments were performed on a single cylinder research engine (SCRE) at a low load of 3.3 bar brake mean effective pressure (BMEP). The start of injection (SOI) of diesel was varied from 280 to 330 absolute crank angle degrees (CAD). Engine speed, rail pressure, and boost pressure were held constant at 1500 rpm, 500 bar, and 1.5 bar, respectively. The energy substituted by the low reactivity fuel was fixed at 80% of the total energy input. It was found that diesel-methane (DM) and diesel-propane (DP) combustion were affected by diesel mixing to a greater extent than diesel-gasoline (DG) combustion due to the higher reactivity of gasoline. The magnitude of low temperature heat release was greatest for DG combustion followed by DM and DP combustion for all SOIs. The ignition delay for DG combustion was the shortest, followed by DM and DP combustion. DM and DP combustion exhibited more cyclic variations than DG combustion. Cyclic variations decreased for DM and DP combustion when SOI was advanced; however, DG combustion cyclic variations remained essentially constant for all SOIs. Earlier SOIs (280, 290, 300, and 310 CAD) for DM and (280, 290, and 300 CAD) for DP combustion indicated some prior-cycle effects on the combustion and IMEP (i.e. some level of determinism).

Engineering↗
DOE OSTI2021

CFD modeling of pre-spark heat release in a boosted direct-injection spark-ignition engine

Accurate predictions of low-temperature heat release (LTHR) are critical for modeling auto-ignition processes in internal combustion engines. While LTHR is typically obscured by deflagration, extremely late ignition phasing can lead to LTHR prior to the spark, a behavior known as pre-spark heat release (PSHR). In this research, PSHR in a boosted direct-injection spark-ignition engine was studied using 3-D computational fluid dynamics (CFD) and detailed chemical kinetics. The turbulent combustion was modeled via a hybrid approach that incorporates the G-equation model for tracking the turbulent flame front, and the well-stirred reactor model with detailed chemistry for assessing the low-temperature reactions in unburnt gas. Simulations were conducted using Co-Optima alkylate and E30 fuels at operating conditions characterized by different PSHR intensities. The predicted in-cylinder pressure and heat release rate were found to agree well with experiments. It was found the estimate of previous-cycle trapped residuals is of utmost importance for capturing PSHR correctly. A simulation best practice was developed which keeps the detailed chemistry solver active throughout the entire simulation, allowing to track the evolution of intermediate species from one cycle to the next. Following the validation, the dynamics of PSHR were analyzed in detail employing the pressure-temperature (P-T) trajectory framework. It was shown that PSHR correlated with the first-stage ignition delay of the fuel, hence showing close relation to the in-cylinder P-T trajectory and the chemical kinetics. Besides, it was indicated that LTHR is a self-limiting process that has the effect of attenuating the thermal stratification in the combustion chamber. Furthermore, it was observed the occurrence of PSHR caused the P-T trajectory of end-gas to overlap with the negative temperature coefficient region of the fuel’s ignition-delay maps. This effect was more significant in the fuel-rich regions where engine knock tendency would be generally higher, with potential implications on knock control and mitigation.

42 ENGINEERING↗
DOE OSTI2022

Current state and future trends in boundary layer control on lifting surfaces

Successful flow control may bring numerous benefits, such as flow stabilization, flow reattachment, separation delay, drag reduction, lift increase, aerodynamic performance improvement, energy efficiency increase, shock delay or weakening, noise reduction, etc. For these purposes, many different flow control devices, which can be classified as passive, semi-active and active, have been designed and tested. This review paper aims to highlight the most promising and commonly employed boundary layer control methods as well as outline their potential in specific applications in aerospace and energy engineering. Referenced studies, performed on various geometries (flat plates, channels, airfoils, wings, blades, cylinders), are primarily numerical or experimental. Although enhanced aerodynamic performance is achieved in many cases, further research is required to draw general conclusions. This paper aims to demonstrate that, in the future, we may expect further developments of flow control actuators, as well as their increased application.

42 ENGINEERING↗
DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗