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At least 253 records · Page 14

Legacy surface change analyses of the 1993 Rock Valley earthquake sequence for direct comparison to planned NA-22 underground conventional high-explosive experiments (Source Physics Experiment 3 (SPE3) - RV/DC Task 1.3 FY22 Final Report)

Recent work under two previous phases of the NNSA NA-22 Source Physics Experiment (SPE) have shown that underground chemical high-explosive experiments can produce detectable surface changes that differ in spatial extent and vertical magnitude depending on the geologic media at the site (Schultz-Fellenz et al., 2018; 2020; Crawford et al., 2021). Neither of these two prior phases of SPE identified natural earthquake-related surface effects in the same region that occurred at a similar depth as the explosive experiments for direct comparison. While earthquakes can also produce surface changes that are detectable using remote sensing data analyses, it is expected that the pattern and spatial extent of surface changes would vary between earthquakes and explosions. However, no direct-observed surface-change signature comparison between earthquakes and explosions has ever been performed. The SPE Phase 3 Rock Valley/Direct Comparison (RV/DC) program presents a unique opportunity to investigate and characterize co-occurrence of both earthquakes and explosions. In this project, we worked to address five tasks in a workflow, as follows: 1. Identify and obtain existing high-resolution legacy satellite and aerial imagery as close in time before and after the 1993 Rock Valley earthquake sequence to temporally constrain the analyses. 2. Transform these pre-earthquake and post-earthquake datasets into digital elevation models (DEMs) using geospatial analysis software packages (e.g., ArcGIS, Agisoft Metashape, and Google Earth Engine). 3. Perform DEM differencing analyses to assess and quantify earthquake-related changes from the 1993 sequence, and develop map products that visualize these analyses. 4. Use the analyses from (3) to: (a) assess spatial distribution and magnitude of surface changes due to the 1993 Rock Valley earthquake sequence, and (b) determine parameters of forthcoming, planned explosion-related surface change data collection from sensors mounted on unmanned aerial vehicles (UAVs) (e.g., spatial extent of collection, design and density of survey control, sensors to deploy, forward speed and line spacing of UAV flight lines, flight altitude). 5. Develop a summary report on the analyses, including how the analyses define parameters and identify focus areas for any future surface change analytical field campaigns related to the explosive experiment. Analyzing these legacy data and identifying whether they can detect any surface changes related to the earthquake sequence facilitates opportunities for direct signature comparison of surface change from explosions at one location, which has never previously been performed. Comparing the surface change signatures from a co-located and depth-equivalent earthquake and an explosion could help to advance remote sensing event discrimination techniques. This report summarizes the work completed toward this ambitious goal.

42 ENGINEERING↗

Searching for Active Low-mass Stars in the CMa Star-forming Region: Multi-band Photometry with T80S

An exotic environment surrounds the young stellar groups associated with the Canis Major (CMa) OB1/R1 region, which probably was formed under feedback from at least three supernova events having occurred a few million years ago. We use astrometric data from the Gaia-DR2 to confirm the membership of the stars in CMa R1, based on proper motion and parallax, which revealed 514 new members and candidates. The mean age of 5 Myr estimated from the color–magnitude diagram characterizes the sources as likely pre-main-sequence candidates. In total, a sample of 694 stars detected with the T80-South telescope was analyzed according to different color–color diagrams, which were compared with theoretical colors from evolutionary models, aiming to reveal the objects that exhibit color excess due to accretion processes. Accretion and magnetic activity were also explored on the basis of empirical flux–flux relation, such as F {sub 660} and F {sub 861} that are related to Hα and Ca ii triplet emission, respectively. A low fraction (∼3 percent) of the sample have Hα excess and other colors expected for stars exhibiting chromospheric activity. The number of Class I and Class II objects, identified by the infrared (Wide-field Infrared Survey Explorer) colors, indicates a disk fraction of ∼6 percent, which is lower than that expected for stellar clusters with a similar age. Such a large sample of objects associated with CMa R1 without evidences of circumstellar accretion can be interpreted as a lack of disk-bearing stars, unusual for young star-forming regions. However, this may be explained as the result of supernova events.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Planet Occurrence Rate Correlated to Stellar Dynamical History: Evidence from Kepler and Gaia

The dynamical history of stars influences the formation and evolution of planets significantly. To explore the influence of dynamical history on the planet formation and evolution using observations, we assume stars that experienced significantly different dynamical histories tend to have different relative velocities. Utilizing the accurate Gaia–Kepler Stellar Properties Catalog, we select single main-sequence stars and divide these stars into three groups according to their relative velocities, i.e., high-V, medium-V, and low-V stars. After considering the known biases from Kepler data and adopting prior and posterior correction to minimize the influence of stellar properties on planet occurrence rate, we find that high-V stars have a lower occurrence rate of super-Earths and sub-Neptunes (1–4 R {sub ⊕}, P < 100 days) and a higher occurrence rate of sub-Earth (0.5–1 R {sub ⊕}, P < 30 days) than low-V stars. Additionally, high-V stars have a lower occurrence rate of hot Jupiter-sized planets (4–20 R {sub ⊕}, P < 10 days) and a slightly higher occurrence rate of warm or cold Jupiter-sized planets (4–20 R {sub ⊕}, 10 < P < 400 days). After investigating multiplicity and eccentricity, we find that high-V planet hosts prefer a higher fraction of multiplanet systems and lower average eccentricity, which are consistent with the eccentricity–multiplicity dichotomy of Kepler planetary systems. All of these statistical results favor the scenario that high-V stars with large relative velocity may experience fewer gravitational events, while low-V stars may be influenced by stellar clustering significantly.

79 ASTRONOMY AND ASTROPHYSICS↗

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids

Abstract The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNATyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.

Bhattacharjee, Ananda S.↗

Evolution-inspired design of multicolored photoswitches from a single cyanobacteriochrome scaffold

Significance Cyanobacteriochromes (CBCRs) are small cyanobacterial photoreceptors which are highly diversified and categorized into many lineages based on their primary sequences. In this study, we identified an atypical CBCR exhibiting an orange/green reversible photocycle. Step-by-step site-directed mutagenesis was performed on this native CBCR, and seven new photoconvertible variants were created. During this process, we identified residues crucial for each color tuning event. These seven molecules covering the shorter-wavelength blue-to-orange region would contribute to the future development of multicolored optogenetic tools and are complementary to recently developed molecules sensing longer wavelengths of light.

59 BASIC BIOLOGICAL SCIENCES↗

Brassica rapa Domestication: Untangling Wild and Feral Forms and Convergence of Crop Morphotypes

The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild Brassica rapa into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in B. rapa have been limited due to a lack of clarity about the wild or feral status of conspecific noncrop relatives. To address this gap and reconstruct the domestication history of B. rapa, we analyzed 68,468 genotyping-by-sequencing-derived single nucleotide polymorphisms for 416 samples in the largest diversity panel of domesticated and weedy B. rapa to date. To further understand the center of origin, we modeled the potential range of wild B. rapa during the mid-Holocene. Our analyses of genetic diversity across B. rapa morphotypes suggest that noncrop samples from the Caucasus, Siberia, and Italy may be truly wild, whereas those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for B. rapa, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for Brassica crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life

Agent-based models (ABMs) simulate activity and travel decisions at the disaggregate level of households, and individuals. To do this, ABMs require detailed information pertaining to socioeconomic and demographic characteristics of individuals. Various synthetic population generators (SPGs) have been proposed to address this need. However, most of the SPGs currently in practice are cross-sectional in nature, and do not account for the interrelationships among household's or individual's life progression. This is a major shortcoming of SPGs as literature has shown that transportation decisions are impacted by lifecycle events that unfold over a span of time. While some demographic evolution simulators have been proposed to address this shortcoming, they: i) are developed using cross-sectional data, ii) do not capture the full spectrum of lifecycle events and their interdependency. Overcoming these drawbacks, this paper proposes a Demographic Microsimulator (DEMOS) which captures the 'continuum of life' by accounting for a range of household-, and individual-level lifecycle events. DEMOS is developed using the Panel Survey of Income Dynamics, which is one of the world's longest running longitudinal surveys. DEMOS sub-models consider key lifecycle events which are influenced by a host of demographic variables. The whole framework is applied to evolve the population of San Francisco Bay Area over a 9-year horizon. Results indicate that the household and individual evolution are tightly connected, and that the structural framework (i.e., model sequencing) is a key element in capturing the population trend accurately.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

Utilities Perspective on Protection Challenges with High IBR Penetration

Utilities have seen rapid increase in Solar, Wind, and Battery Energy Storage Resources that interconnect to their electric system through Inverters. Inverter-Based Resources (IBRs) have fault current characteristics that are unlike the fault current response of traditional rotating-machine-based generators, which is well known and repeatable. IBR’s non-traditional fault current behavior is due to the IBR control scheme, which is configured to provide a clean AC output but also protect the inverter’s sensitive power electronics devices from damage, one source of which is overcurrent. This results in low fault current magnitude, low or no negative sequence current injection, the variability of sequence component currents, the variability of voltage with respect to current angles, and the lack of inertia. The control scheme also results in a fault current response that can vary between manufactures and between models of the same manufacturer. High penetration of IBRs can adversely affect the protection schemes applied in areas with high penetration of IBRs. With the proliferation of IBRs, utilities are finding out that conventional protection schemes are not adequately equipped to protect the electric systems. This is mainly because the existing protection elements and practices have been designed based on the fault current response of conventional rotating machines. In several cases, the available literature does not provide any clear solution for the issues when the protection scheme does not operate properly near IBRs. This presentation identifies various protection challenges due to IBRs that industry is facing, from the utility perspective. Instead of facing on one issue, we are looking broadly on all the challenges that system protection has experienced with high penetration of IBRs. Based on the IBR response from various utilities during real fault events and gathering perspective from different utility SMEs via questionnaire, the presentation summarizes on gathered data and internal experiences.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Sequence-Based Anomaly Detection in Critical Infrastructure Networks

United States critical infrastructure faces new cyber threats from adversarial nation-state actors in the form of malware-free attacks. Traditional cybersecurity techniques use rules-based methods to identify indicators of compromise on networks, often missing these sophisticated attacks. Our approach leverages multiple state of the art machine learning models in a pipeline to identify abnormal network events through sequential analysis. We combine both device and packet-level information into individual events to characterize anomalous network actions. The model is trained and tested on real network traffic from the Idaho National Lab High Performance Computing (HPC) with greater than 98% precision. It is capable of flagging malicious tactics used by adversaries in malware-free attacks, severe changes to the network, and abnormal user activity by network devices.

99 - GENERAL AND MISCELLANEOUS↗

Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States

Abstract Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E ( mcyE ) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis . Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

59 BASIC BIOLOGICAL SCIENCES↗

Cyclic Injection Leads to Larger and More Frequent Induced Earthquakes under Volume-Controlled Conditions

As carbon storage technologies advance globally, methods to understand and mitigate induced earthquakes become increasingly important. Although the physical processes that relate increased subsurface pore pressure changes to induced earthquakes have long been known, reliable methods to forecast and control induced seismic sequences remain elusive. Suggested reservoir engineering scenarios for mitigating induced earthquakes typically involve modulation of the injection rate. Some operators have implemented periodic shutdowns (i.e., effective cycling of injection rates) to allow reservoir pressures to equilibrate (e.g., Paradox Valley) or shut-in wells after the occurrence of an event of concern (e.g., Basel, Switzerland). Other proposed scenarios include altering injection rates, actively managing pressures through coproduction of fluids, and preinjection brine extraction. Here, in this work, we use 3D physics-based earthquake simulations to understand the effects of different injection scenarios on induced earthquake rates, maximum event magnitudes, and postinjection seismicity. For comparability, the modeled injection considers the same cumulative volume over the project’s operational life but varies the schedule and rates of fluid injected. Simulation results show that cyclic injection leads to more frequent and larger events than constant injection. Furthermore, with intermittent injection scenario, a significant number of events are shown to occur during pauses in injection, and the seismicity rate remains elevated for longer into the postinjection phase compared to the constant injection scenario.

58 GEOSCIENCES↗

Validation of Maui PSCAD Model: Motivation, Methodology, and Lessons Learned: Preprint

As power systems become increasingly dependent on inverter-based resources, the dominant physical and control interactions that determine system stability may no longer be accurately captured in positive sequence dynamic simulation tools; electromagnetic transient (EMT) simulations may be needed. This paper describes the process of creating and validating an EMT model of the entire Maui island transmission system in PSCAD software. The model is validated against the utility's PSSE model and against field data for an event that consisted of a single-phase fault followed by a generation trip. The methodology and lessons learned are summarized here.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗

SDSS-IV MaNGA: The MaNGA Dwarf Galaxy Sample Presentation

We present the MaNGA Dwarf galaxy (MaNDala) Value Added Catalog (VAC), from the final release of the Sloan Digital Sky Survey-IV program. MaNDala consists of 136 randomly selected bright dwarf galaxies with M * < 10 9.1 M ⊙ and M g > -18.5, making it the largest integral field spectroscopy homogeneous sample of dwarf galaxies. We release a photometric analysis of the g, r, and z broadband imaging based on the DESI Legacy Imaging Surveys, as well as a spectroscopic analysis based on the Pipe3D SDSS-IV VAC. Our release includes the surface brightness (SB), geometric parameters, and color profiles, Sérsic fits as well as stellar population properties (such as stellar ages, metallicities, and star formation histories), and emission lines' fluxes within the FOV and the effective radii of the galaxies. We find that the majority of the MaNDala galaxies are star-forming late-type galaxies with $\langle$n Sersic,r $\rangle$ ~ 1.6 that are centrals (central/satellite dichotomy). MaNDala covers a large range of SB values (we find 11 candidate ultra-diffuse galaxies and three compact ones), filling the gap between classical dwarfs and low-mass galaxies in the Kormendy Diagram and in the size–mass/luminosity relation, which seems to flatten at 10 8 < M * /M ⊙ < 10 9 with $\langle$R e,r $\rangle$ ~ 2.7 kpc. A large fraction of MaNDala galaxies formed from an early low-metallicity burst of SF, but also from late SF events from more metal-enriched gas: half of the MaNDala galaxies assembled 50% of their mass at $\langle$z$\rangle$ > 2, while the last 20% was at $\langle$z$\rangle$ < 0.3. Finally, a bending of the sSFR-M * relation at M * ~ 10 9 M ⊙ for the main-sequence galaxies seems to be supported by MaNDala.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network

Abstract Single-cell RNA sequencing (scRNA-seq) permits researchers to study the complex mechanisms of cell heterogeneity and diversity. Unsupervised clustering is of central importance for the analysis of the scRNA-seq data, as it can be used to identify putative cell types. However, due to noise impacts, high dimensionality and pervasive dropout events, clustering analysis of scRNA-seq data remains a computational challenge. Here, we propose a new deep structural clustering method for scRNA-seq data, named scDSC, which integrate the structural information into deep clustering of single cells. The proposed scDSC consists of a Zero-Inflated Negative Binomial (ZINB) model-based autoencoder, a graph neural network (GNN) module and a mutual-supervised module. To learn the data representation from the sparse and zero-inflated scRNA-seq data, we add a ZINB model to the basic autoencoder. The GNN module is introduced to capture the structural information among cells. By joining the ZINB-based autoencoder with the GNN module, the model transfers the data representation learned by autoencoder to the corresponding GNN layer. Furthermore, we adopt a mutual supervised strategy to unify these two different deep neural architectures and to guide the clustering task. Extensive experimental results on six real scRNA-seq datasets demonstrate that scDSC outperforms state-of-the-art methods in terms of clustering accuracy and scalability. Our method scDSC is implemented in Python using the Pytorch machine-learning library, and it is freely available at https://github.com/DHUDBlab/scDSC.

Gan, Yanglan↗

Ultracompact hybrid stars consistent with multimessenger astrophysics

In this work, we consider the consequences of phase transition in dense QCD on the properties of compact stars and implications for the observational program in gravitational wave and x-ray astrophysics. The key underlying assumption of our modeling is a strong first-order phase transition past the point where the hadronic branch of compact stars reaches the two-solar mass limit. Furthermore, our analysis predicts ultracompact stars with very small radii—in the range of 6–9 km—living on compact star sequences that are entirely consistent with the current multimessenger data. We show that sequences featuring two-solar mass hadronic stars consistent with radio-pulsar observations are also consistent with the inferences of large radii for massive neutron stars by NICER x-ray observations of neutron stars and the small radii predicted by gravitational waves analysis of the binary neutron star inspiral event GW170817 for our models that feature a strong first-order QCD phase transition.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗