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At least 775 records · Page 43

Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates

The prevalence of the Omicron subvariant BA.2.75 rapidly increased in India and Nepal during the summer of 2022, and spread globally. However, the virological features of BA.2.75 are largely unknown. Here, we evaluated the replicative ability and pathogenicity of BA.2.75 clinical isolates in Syrian hamsters. Although we found no substantial differences in weight change among hamsters infected with BA.2, BA.5, or BA.2.75, the replicative ability of BA.2.75 in the lungs is higher than that of BA.2 and BA.5. Of note, BA.2.75 causes focal viral pneumonia in hamsters, characterized by patchy inflammation interspersed in alveolar regions, which is not observed in BA.5-infected hamsters. Moreover, in competition assays, BA.2.75 replicates better than BA.5 in the lungs of hamsters. These results suggest that BA.2.75 can cause more severe respiratory disease than BA.5 and BA.2 in a hamster model and should be closely monitored.

59 BASIC BIOLOGICAL SCIENCES↗

Multiple-carrier-lifetime model for carrier dynamics in InGaN/GaN LEDs with a non-uniform carrier distribution

Here we introduce a multiple-carrier-lifetime model (MCLM) for light-emitting diodes (LEDs) with non-uniform carrier distribution, such as in multiple-quantum-well (MQW) structures. By employing the MCLM, we successfully explain the modulation response of V-pit engineered MQW LEDs, which exhibit an S 21 roll-off slower than –20 dB/decade. Using the proposed model and employing a gradient descent method, we extract effective recombination and escape lifetimes by averaging the carrier behavior across the quantum wells. Our results reveal slower effective carrier recombination and escape in MQW LEDs compared with LEDs emitting from a single QW, indicating the advantages of lower carrier density achieved through V-pit engineering. Notably, the effective carrier recombination time is more than one order of magnitude lower than the effective escape lifetime, suggesting that most carriers in the quantum wells recombine, while the escape process remains weak. To ensure the reliability and robustness of the MCLM, we subject it to a comprehensive threefold validation process. This work confirms the positive impact of spreading carriers into several quantum wells through V-pit engineering. In addition, the MCLM is applicable to other LEDs with a non-uniform carrier distribution, such as micro-LEDs with significant surface recombination and non-uniform lateral carrier profiles.

42 ENGINEERING↗

Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire

Forests mitigate climate change by sequestering massive amounts of carbon, but recent increases in wildfire activity are threatening carbon storage. Currently, our understanding of wildfire impacts on forest resilience and the mechanisms controlling post-fire recovery remains unresolved due to a lack of empirical data on mature trees in natural settings. Here, we quantify the physiological mechanisms controlling carbon uptake immediately following wildfire in mature individuals of ponderosa pine (Pinus ponderosa), a wide-spread and canopy-dominant tree species in fire-prone forests. While photosynthetic capacity was lower in burned than unburned trees due to an overall depletion of resources, we show that within the burned trees, photosynthetic capacity increases with the severity of damage. Our data reveal that boosts in the efficiency of carbon uptake at the leaf-level may compensate for whole-tree damage, including the loss of leaf area and roots. We further show that heightened photosynthetic capacity in remaining needles on burned trees may be linked with reduced water stress and leaf nitrogen content, providing pivotal information about post-fire physiological processes. Our results have implications for Earth system modeling efforts because measurements of species-level physiological parameters are used in models to predict ecosystem and landscape-level carbon trajectories. Finally, current land management practices do not account for physiological resilience and recovery of severely burned trees. Our results suggest premature harvest may remove individuals that may otherwise survive, irrevocably altering forest carbon balance.

54 ENVIRONMENTAL SCIENCES↗

Improving Seasonal Forecast Using Probabilistic Deep Learning

The path toward realizing the potential of seasonal forecasting and its socioeconomic benefits relies on improving general circulation model (GCM) based dynamical forecast systems. To improve dynamical seasonal forecasts, it is crucial to set up forecast benchmarks, and clarify forecast limitations posed by model initialization errors, formulation deficiencies, and internal climate variability. With huge costs in generating large forecast ensembles, and limited observations for forecast verification, the seasonal forecast benchmarking and diagnosing task proves challenging. Here, we develop a probabilistic deep learning-based statistical forecast methodology, drawing on a wealth of climate simulations to enhance seasonal forecast capability and forecast diagnosis. By explicitly modeling the internal climate variability and GCM formulation differences, the proposed Conditional Generative Forecasting (CGF) methodology enables bypassing crucial barriers in dynamical forecast, and offers a top-down viewpoint to examine how complicated GCMs encode the seasonal predictability information. We apply the CGF methodology for global seasonal forecast of precipitation and 2 m air temperature, based on a unique data set consisting 52,201 years of climate simulation. Results show that the CGF methodology can faithfully represent the seasonal predictability information encoded in GCMs. We successfully apply this learned relationship in real-world seasonal forecast, achieving competitive performance compared to dynamical forecasts. Using this CGF as benchmark, we reveal the impact of insufficient forecast spread sampling that limits the skill of the considered dynamical forecast system. Finally, we introduce different strategies for composing ensembles using the CGF methodology, highlighting the potential for leveraging the strengths of multiple GCMs to achieve advantgeous seasonal forecast.

54 ENVIRONMENTAL SCIENCES↗

0D Modeling of Reactor Networks Within Zuzax

We report on progress in developing macroscopic balance equations for combustion and electrochemistry systems. A steady state solution capability is described for the macroscopic reactor network, with an associated steady state continuation method and solution storage capability added in. An example is provided of continuation of a hydrogen flame versus the equivalence ratio. The reactor modeling capability is extended to charged fluid systems, with a description of the new ChargedFluidReactor, SubstrateElement, and MetalCurrentElement reactor classes and novel setup of unknowns within these reactors that preserve charge neutrality. Zuzax's setup for electrochemistry is explained including the specification of the electron chemical potential and the adherence to the SHE Reference electrode specification. The description of the different ways to enter electrochemical reaction rates are described, contrasted, and their derivations with respect to one another are derived. An example of using the ChargedFluidReactor within corrosion problems is provided. We present a description of calculations to understand the phenomena of corrosion of copper from a micron sized droplet of NaCl water droplet, where secondary spreading occurs. An analysis of the discrepancies with experiment is carried out, demonstrating that macroscopic balances can be an important tool for understanding what major factors need to be addressed for a better understanding of a physical system.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Mitigation of the Brighter-fatter Effect in the LSST Camera

Abstract Thick, fully depleted charge-coupled devices are known to exhibit nonlinear behavior at high signal levels due to the dynamic behavior of charges collecting in the potential wells of pixels, called the brighter-fatter effect (BFE). The effect results in distorted images of bright calibration stars, creating a flux-dependent point-spread function that if left unmitigated, could make up a large fraction of the error budget in Stage IV weak-lensing (WL) surveys such as the Legacy Survey of Space and Time (LSST). In this paper, we analyze image measurements of flat fields and artificial stars taken at different illumination levels with the LSST Camera (LSSTCam) at SLAC National Accelerator Laboratory in order to quantify this effect in the LSSTCam before and after a previously introduced correction technique. We observe that the BFE evolves anisotropically as a function of flux due to higher-order BFEs, which violates the fundamental assumption of this correction method. We then introduce a new method based on a physically motivated model to account for these higher-order terms in the correction, and then we test the modified correction on both data sets. We find that the new method corrects the effect in flat fields better than it corrects the effect in artificial stars, which we suggest is the result of sub-pixel physics not included in this correction model. We use these results to define a new metric for the full-well capacity of our sensors and advise image processing strategies to further limit the impact of the effect on LSST WL science pathways.

47 OTHER INSTRUMENTATION↗

Image Deconvolution and Point-spread Function Reconstruction with STARRED: A Wavelet-based Two-channel Method Optimized for Light-curve Extraction

We present starred, a point-spread function (PSF) reconstruction, two-channel deconvolution, and light-curve extraction method designed for high-precision photometric measurements in imaging time series. An improved resolution of the data is targeted rather than an infinite one, thereby minimizing deconvolution artifacts. In addition, starred performs a joint deconvolution of all available data, accounting for epoch-to-epoch variations of the PSF and decomposing the resulting deconvolved image into a point source and an extended source channel. The output is a high-signal-to-noise-ratio, high-resolution frame combining all data and the photometry of all point sources in the field of view as a function of time. Of note, starred also provides exquisite PSF models for each data frame. We showcase three applications of starred in the context of the imminent LSST survey and of JWST imaging: (i) the extraction of supernovae light curves and the scene representation of their host galaxy; (ii) the extraction of lensed quasar light curves for time-delay cosmography; and (iii) the measurement of the spectral energy distribution of globular clusters in the "Sparkler," a galaxy at redshift z = 1.378 strongly lensed by the galaxy cluster SMACS J0723.3-7327. starred is implemented in jax, leveraging automatic differentiation and graphics processing unit acceleration. This enables the rapid processing of large time-domain data sets, positioning the method as a powerful tool for extracting light curves from the multitude of lensed or unlensed variable and transient objects in the Rubin-LSST data, even when blended with intervening objects.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep Learning Approach for High-accuracy Electron Counting of Monolithic Active Pixel Sensor-type Direct Electron Detectors at Increased Electron Dose

Abstract Electron counting can be performed algorithmically for monolithic active pixel sensor direct electron detectors to eliminate readout noise and Landau noise arising from the variability in the amount of deposited energy for each electron. Errors in existing counting algorithms include mistakenly counting a multielectron strike as a single electron event, and inaccurately locating the incident position of the electron due to lateral spread of deposited energy and dark noise. Here, we report a supervised deep learning (DL) approach based on Faster region-based convolutional neural network (R-CNN) to recognize single electron events at varying electron doses and voltages. The DL approach shows high accuracy according to the near-ideal modulation transfer function (MTF) and detector quantum efficiency for sparse images. It predicts, on average, 0.47 pixel deviation from the incident positions for 200 kV electrons versus 0.59 pixel using the conventional counting method. The DL approach also shows better robustness against coincidence loss as the electron dose increases, maintaining the MTF at half Nyquist frequency above 0.83 as the electron density increases to 0.06 e−/pixel. Thus, the DL model extends the advantages of counting analysis to higher dose rates than conventional methods.

Materials Science↗

Onset of Scrambling as a Dynamical Transition in Tunable-Range Quantum Circuits

In a fast-scrambling many-body quantum system, information is spread and entanglement is built up on a time scale that grows logarithmically with the system size. This is of fundamental interest in understanding the dynamics of many-body systems, as well as in efficiently producing entangled resource states and error-correcting codes. In this work, we identify a dynamical transition marking the onset of scrambling in quantum circuits with different levels of long-range connectivity. In particular, we show that as a function of the interaction range for circuits of different structures, the tripartite mutual information exhibits a scaling collapse around a critical point between two clearly defined regimes of different dynamical behavior. We study this transition analytically in a related long-range Brownian-circuit model and show how the transition can be mapped onto the statistical mechanics of a long-range Ising model in a particular region of parameter space. This mapping predicts mean-field critical exponents v=–1/(1 + s c ), which are consistent with the critical exponents extracted from Clifford-circuit numerics. In addition to systems with conventional power-law interactions, we identify the same phenomenon in deterministic sparse circuits that can be realized in experiments with neutral-atom arrays.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Characterizing the Spread of COVID-19 from Human Mobility Patterns and SocioDemographic Indicators

Mobility is an indicator of human movement through space and time. With the increasing availability of geolocated data (from GPS, accelerometers, etc.), it is now possible to examine individual as well as group human mobility patterns. Human mobility is influenced by both intrinsic (i.e. personal motivations) and extrinsic (i.e., events like natural hazards or a pandemic like the COVID-19) factors. However, the intricate relationships between human mobility patterns and sociodemographic characteristics in the context of a pandemic are yet to be fully explored. Our goal is to overcome this gap by using human mobility data at the census block group level from mobile phones and combining those with social vulnerability indicators to examine the overall spread of COVID-19 at local spatial scales. We used 585,878 weekly visits to 37,871 points of interests (POIs) from Safegraph to quantify mobility indices and social distancing metrics in 2,820 census block groups in the city of Los Angeles (LA) - before and during lockdown as well as during the phase1 and phase 2 reopening. Finally, using supervised machine learning algorithms, we classified the census block groups in LA into High, Medium and Low categories that represented the vulnerability of these block groups based on the cumulative number of occurrences of COVID-19 cases till July 24, 2020. Our results indicate that the tree-based classifiers performed well in comparison to the Support Vector Machines and Multinomial Logit models. Gradient Boosting had the highest classification accuracy of 97.4% COVID-19 with an AUC score of 0.987. The block groups with high COVID-19 cases also had a high concentration of socially vulnerable populations, high human mobility index and a low social distancing index.

Roy, Avipsa↗

More is definitely different: the zebrafish as witness: Comment on ”Structure and function in artificial, zebrafish and human neural networks” by Peng Ji et al.

We report half a century ago, in his foundation paper More is different, Anderson stated the relevance of including multiple scales of interaction, instead of trying to reduce everything to fundamental principles. By doing so, one may witness phenomena that were not expected by looking at each individual components separately. This idea finds indeed numerous realizations such as the synchronization phenomenon, where a multitude of dynamical systems suddenly start to behave coherently together, or the spreading of diseases over entire populations, to name only two examples. But if one would have to give a single example of a system where the multiplicity of interaction scales is of utmost importance, it would probably be the brain. In their review, Ji et al. give a comprehensive overview of the multiple scales of science required in the investigation of structural and functional brain networks, as well as their interplay.

59 BASIC BIOLOGICAL SCIENCES↗

Addressing Experimental Challenges in Probing Dark Energy with Accuracy and Precision with the Rubin Observatory Legacy Survey of Space & Time (LSST)

With support from this award, the Stanford group under the leadership of PI Patricia Burchat focused on pixel-level algorithms that are key to the investigation of dark energy with the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). The work was carried out through strong engagement in the DOE-supported LSST Dark Energy Science Collaboration (DESC), for which the PI served as Deputy Spokesperson (07/2019 - 07/2021) and Technical Coordinator (07/2021 - 07/2023). Members of the Burchat group are Full DESC members and are among scientists who have been accepted to join the Rubin Observatory System Integration, Test, and Commissioning (SIT-Com) effort. The specific intellectual focus of the group was the optimization of gravitational lensing as a probe of the evolution of the distribution of dark matter in space and time to learn about the nature of dark energy. The Stanford group pursued an integrated research program to understand in detail, and then remediate or calibrate, systematic effects that could limit the sensitivity of the LSST to cosmic shear as a dark energy probe -- particularly those related to our understanding of the atmospheric point spread function (PSF), challenges associated with blended galaxy images, and impacts of residual camera artifacts. Key to this work was developing, enhancing, and validating the fidelity of simulations that play a key role in the development of our understanding of subtle systematic biases and then using these simulations to develop techniques to characterize and mitigate biases, and associated algorithms for implementation in the LSST or DESC science pipelines. The group’s work included contributions to the open-source GalSim simulation package, which is widely used in the community; simulations and studies of spatial correlations of atmospheric PSFs; studies of temporal correlations of the atmospheric PSF; impacts of chromatic PSFs on cosmic shear calibration; continued studies of anisotropic Gaussian process interpolation of PSF models across the focal plane; and measuring and mitigating impacts of residual camera artifacts on cosmic shear. A primary impact of this work is that it increases the scientific discovery potential of the DOE and NSF investments in the Rubin Observatory Legacy Survey of Space \& Time, by addressing challenges in interpreting astronomical images through more accurate descriptions of the blurring of images due to the atmosphere. Specifically, this work impacts our ability to understand the fundamental nature of dark energy.

Burchat, Patricia Rose↗

Characterization of two affinity matured Anti-Yersinia pestis F1 human antibodies with medical countermeasure potential

Yersinia pestis , the causative agent of plague and a biological threat agent, presents an urgent need for novel medical countermeasures due to documented cases of naturally acquired antibiotic resistance and potential person-to-person spread during a pneumonic infection. Immunotherapy has been proposed as a way to circumvent current and future antibiotic resistance. Here, we describe the development and characterization of two affinity matured human antibodies (αF1Ig AM2 and αF1Ig AM8) that promote survival of mice after exposure to aerosolized Y . pestis . We share details of the error prone PCR and yeast display technology-based affinity maturation process that we used. The resultant matured antibodies have nanomolar affinity for Y . pestis F1 antigen, are produced in high yield, and are resilient to 37°C stress for up to 6 months. Importantly, in vitro assays using a murine macrophage cell line demonstrated that αF1Ig AM2 and αF1Ig AM8 are opsonic. Even more importantly, in vivo studies using pneumonic plague mouse models showed that 100% of the mice receiving 500 μg of IgGs αF1Ig AM2 and αF1Ig AM8 survived lethal challenge with aerosolized Y . pestis CO92. Combined, these results provide evidence of the quality and robustness of αF1Ig AM2 and αF1Ig AM8 and support their development as potential medical countermeasures against plague.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of Materials Used as Face Coverings for Respiratory Protection

Use of masks is a primary tool to prevent the spread of the novel COVID-19 virus resulting from unintentional close contact with infected individuals. However, detailed characterization of the chemical properties and physical structure of common mask materials is lacking in the current literature. In this study, a series of commercial masks and potential mask materials, including 3M Particulate Respirator 8210 N95, a material provided by Oak Ridge National Laboratory Carbon Fiber Technology Facility (ORNL/CFTF), and a Filti Face Mask Material, were characterized by a suite of techniques, including scanning electron microscopy, X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy. Wetting properties of the mask materials were quantified by measurements of contact angle with a saliva substitute. Mask pass-through experiments were performed using a dispersed metal oxide nanoparticle suspension to model the SARS-CoV-2 virus, with quantification via spatially resolved X-ray fluorescence mapping. Notably, all mask materials tested provided a strong barrier against respiratory droplet breakthrough. The comparisons and characterizations provided in this study provide useful information when evaluating mask materials for respiratory protection.

36 MATERIALS SCIENCE↗

Shattered pellet penetration in low and high energy plasmas on DIII-D

Shattered Pellet Injection (SPI) was previously adopted as the baseline disruption mitigation system for ITER, as the radiative payload penetration into DIII-D plasmas from SPI is superior to those using the Massive Gas Injection (MGI) method. Because of the substantial differences in the energy content of ITER plasma and those in present experiments, reliable 3d MHD modeling, benchmarked against present experiments is needed to project to ITER plasmas. On account of these needs, the depth of SPI fragment penetration in DIII-D plasmas was investigated by injecting SPI into two discharges with vastly different energy content and pedestal height. 400 Torr-L pure Ne fragmented pellets at a velocity of about 200 m s -1 were injected into a 0.2 MJ L-mode discharge and a 2 MJ super H-mode discharge. Results show deep penetration of SPI fragments into low-energy plasmas in DIII-D. SPI fragment penetration is reduced as the plasma energy content increases, with some discharges exhibiting penetration that is confined to the outer regions of the plasma. The injected SPI fragments are also spread out over a distance of about 20 cm, which results in some fragments arriving near the end of or after the thermal quench is over.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

WhiteWind: White Etching Crack (WEC) Bearing Failures in Wind Turbine: Cooperative Research and Development, CRADA Number CRD-18-00758 (Final Report)

A WEC is a particularly aggressive, unpredictable and wide spread rolling element bearing failure mode that is common for large multi-megawatt (MW) wind turbines. WEC is considered the single most expensive failure mode for all wind turbine components, and there is currently no commercial solution. The Technical University of Denmark (DTU) is leading the WhiteWind project to investigate WECs through funding provided by the Innovation Fund Denmark. Other project partners include Vestas, SKF, Expanite, Rheinisch-Westfalische Technische Hochschule Aachen University (RWTH Aachen), and Argonne National Laboratory. The objective of the overall project is to develop a new surface engineered WEC-resistant bearing material using novel surface engineering techniques that shall provide a commercially competitive alternative to existing wind turbine bearings. NREL will support the project by providing existing measured bearing loads and validating models of drivetrain loads.

17 WIND ENERGY↗

Shattered pellet penetration in low and high energy plasmas on DIII-D

Shattered pellet injection (SPI) has been adopted as the baseline disruption mitigation system for ITER, as the radiative payload penetration into DIII-D plasmas from SPI is superior to those using the massive gas injection (MGI) method. Because of the substantial differences in the energy content of ITER plasma and those in present experiments, reliable 3D MHD modeling, benchmarked against present experiments is needed to project to ITER plasmas. In support of these needs, the depth of SPI fragment penetration in DIII-D plasmas was investigated by injecting SPI into two discharges with vastly different energy content and pedestal height. 400 Torr-L pure Ne fragmented pellets at a velocity of about 200 m s−1 were injected into a 0.2 MJ L-mode discharge and a 2 MJ super H-mode discharge. Results show deep penetration of SPI fragments into low-energy plasmas in DIII-D. SPI fragment penetration is reduced as the plasma energy content increases, with some discharges exhibiting penetration that is confined to the outer regions of the plasma. The injected SPI fragments are also spread out over a distance of about 20 cm, which results in some fragments arriving near the end of or after the thermal quench is over.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗