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At least 271 records · Page 15

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Abstract Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

Langwig, Marguerite V. (ORCID:0000000202472816)↗

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes ( SOC1 and SVP ) may regulate vegetative development.

59 BASIC BIOLOGICAL SCIENCES↗

Probing nonlinear velocity profiles of shear-thinning, nematic platelet dispersions in Couette flow using x-ray photon correlation spectroscopy

In this study, we report experiments employing x-ray photon correlation spectroscopy (XPCS) to characterize the velocity profiles of complex fluids in Couette flow. The approach involves modeling the XPCS correlation functions obtained with the incident x-ray beam passing tangentially through the Couette cell gap at various distances from the inner wall. We first demonstrate the technique with measurements on a dilute colloidal dispersion in the Newtonian liquid glycerol, where the expected linear velocity profiles are recovered. We then employ the technique to map the shear-rate-dependent velocity profiles of a shear-thinning dispersion of nematically ordered Gibbsite platelets. The nonlinear velocity profiles of the Gibbsite dispersion include a narrow slip region adjacent to the outer wall and a band with a small velocity gradient in the interior of the gap that evolves into a region increasingly resembling plug flow with increasing shear rate. Variations in the velocity profile along the vorticity direction indicate an instability in the interface between this region of small velocity gradient and a region of high velocity gradient near the inner wall. The analysis of the small-angle scattering patterns provides information about the spatial and temporal variations in the nematic order of the Gibbsite dispersion and their coupling to the velocity profile. Additional potential applications of this XPCS-based technique and comparisons with established methods for characterizing velocity profiles are discussed.

42 ENGINEERING↗

Cluster Structures with Machine Learning Support in Neutron Star M-R relations

Neutron stars (NS) are compact objects with strong gravitational fields, and a matter composition subject to extreme physical conditions. The properties of strongly interacting matter at ultra-high densities and temperatures impose a big challenge to our understanding and modelling tools. Some difficulties are critical, since one cannot reproduce such conditions in our laboratories or assess them purely from astronomical observations. The information we have about neutron star interiors are often extracted indirectly, e.g., from the star mass-radius relation. The mass and radius are global quantities and still have a significant uncertainty, which leads to great variability in studying the micro-physics of the neutron star interior. This leaves open many questions in nuclear astrophysics and the suitable equation of state (EoS) of NS. Recently, new observations appear to constrain the mass-radius and consequently has helped to close some open questions. In this work, utilizing modern machine learning techniques, we analyze the NS mass-radius (M-R) relationship for a set of EoS containing a variety of physical models. Our objective is to determine patterns through the M-R data analysis and develop tools to understand the EoS of neutron stars in forthcoming works.

79 ASTRONOMY AND ASTROPHYSICS↗

XPlacer/Tracer

XPlacer/Tracer is a dynamic analysis tool that finds bad memory access patterns in heterogeneous codes. XPlacer/Tracer consists of two components. (1) A configurable ROSE plugin for source code instrumentation of heterogeneous code written in the C/C++ and CUDA programming languages. (2) A sample configuration that instruments memory accesses to dynamic memory in CPU and GPU codes, and a runtime library that tracks these memory accesses at runtime. The collected information is reported in form of a textual summary or as memory map that can be converted to images.

Pirkelbauer, PeterM.↗

Shelter Island, New York, Energy Reliability Assessment and Local Generation Options

Shelter Island's Green Options Committee (GOC), an all-volunteer committee tasked with considering all environmental conservation issues, requested technical assistance under the U.S. Department of Energy (DOE)-funded Energy Technology Innovation Partnership Project (ETIPP). The primary goals of this technical assistance project included: 1. Informing the GOC about energy use trends within the community as well as distributed solar, wind and storage opportunities; 2. Providing additional resources and technical feasibility information for geothermal, agrivoltaics and tidal energy; 3. Supporting the development of a community engagement plan; and 4. Supporting collaboration between the GOC and PSEG in order to find mutually beneficial follow-on projects. Assistance from NLR to help the GOC meet these overall project goals was provided through the following primary tasks: 1. Collaborate with the local utility in order to collect energy use data and inform the community on energy use patterns through a baseline assessment; 2. Technical analysis of distributed renewable and resiliency opportunities (solar, wind and storage) that best align with the community's energy priorities; 3. Provide high level feasibility support for future renewable energy scenarios that include agrivoltaic solutions, tidal energy, and geothermal projects on Shelter Island, and 4. Integrate all findings into a Community Outreach presentation to help the GOC engage with community stakeholders to build support and awareness of chosen resilience strategies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Analyzing the Effects of Atmospheric Turbulent Fluctuations on the Wake Structure of Wind Turbines and Their Blade Vibrational Dynamics

In recent trends, a rising demand for renewable energy has driven wind turbines to larger proportions, where lighter blade designs are often adopted to reduce the costs associated with logistics and production. This causes modern utility-scale wind turbine blades to be inherently more flexible, and their amplified aeroelastic sensitivity results in complex multi-physics reactions to variant atmospheric conditions, including dynamic patterns of aerodynamic loading at the rotor and vortex structure evolutions within the wake. In this paper, we analyze the influence of inflow variance for wind turbines with large, flexible rotors through simulations of the National Rotor Testbed (NRT) turbine, located at Sandia National Labs’ Scaled Wind Farm Technology (SWiFT) facility in Lubbock, Texas. The Common Ordinary Differential Equation Framework (CODEF) modeling suite is used to simulate wind turbine aeroelastic oscillatory behavior and wind farm vortex wake interactions for a range of flexible NRT blade variations, operating in differing conditions of variant atmospheric flow. CODEF solutions of turbine operation in Steady-In-The-Average (SITA) wind conditions are compared to SITA wind conditions featuring a controlled gust-like pulse overimposed, to isolate the effects of typical wind fluctuations. Finally, simulations of realistic time-varying wind conditions from SWiFT meteorological tower measurements are compared to the solutions of SITA wind conditions. These increasingly complex atmospheric inflow variations are tested to show the differing effects evoked by various patterns of spatiotemporal atmospheric flow fluctuations. An analysis is presented for solutions of wind turbine aeroelastic response and vortex wake evolution, to elucidate the consequences of variant inflow, which pertain to wind turbine dynamics at an individual and farm-collective scale. The comparisons of simulated farm flow for SITA and measured fluctuating wind conditions show that certain regions of the wake contain up to a 12% difference in normalized axial velocity, due to the introduction of wind fluctuations. The findings of this study prove valuable for practical applications in wind farm control and optimization strategies, with particular significance for modern utility-scale wind power plants operating in variant atmospheric conditions.

Farrell, Alayna (ORCID:000000023555720X)↗

High-resolution mapping of nitrogen oxide emissions in large US cities from TROPOMI retrievals of tropospheric nitrogen dioxide columns

Satellite-derived spatiotemporal patterns of nitrogen oxide (NOx) emissions can improve accuracy of emission inventories to better support air quality and climate research and policy studies. In this study, we develop a new method by coupling the chemical transport Model-Independent SATellite-derived Emission estimation Algorithm for Mixed-sources (MISATEAM) with a divergence method to map high-resolution NO x emissions across US cities using TROPOspheric Monitoring Instrument (TROPOMI) tropospheric nitrogen dioxide (NO 2 ) retrievals. The accuracy of the coupled method is validated through application to synthetic NO 2 observations from the NASA-Unified Weather Research and Forecasting (NU-WRF) model, with a horizontal spatial resolution of 4 km × 4 km for 33 large and mid-size US cities. Validation reveals excellent agreement between inferred and NU-WRF-provided emission magnitudes (R= 0.99, normalized mean bias, NMB = —0.01) and a consistent spatial pattern when comparing emissions for individual grid cells (R = 0.88 ± 0.06). We then develop a TROPOMI-based database reporting annual emissions for 39 US cities at a horizontal spatial resolution of 0.05° × 0.05° from 2018 to 2021. This database demonstrates a strong correlation (R= 0.90) with the National Emission Inventory (NEI) but reveals some bias (NMB = —0.24). There are noticeable differences in the spatial patterns of emissions in some cities. Our analysis suggests that uncertainties in TROPOMI-based emissions and potential misallocation of emissions and/or missing sources in bottom-up emission inventories both contribute to these differences.

54 ENVIRONMENTAL SCIENCES↗

The effects of storms and a transient sandy veneer on the interannual planform evolution of a low-relief coastal cliff and shore platform at Sargent Beach, Texas, USA

Coastal cliff erosion is alongshore-variable and episodic, with retreat rates that depend upon sediment as either tools of abrasion or protective cover. However, the feedbacks between coastal cliff planform morphology, retreat rate, and sediment cover are poorly quantified. This study investigates Sargent Beach, Texas, USA, at the annual to interannual scale to explore (1) the relationship between temporal and spatial variability in cliff retreat rate, roughness, and sinuosity and (2) the response of retreat rate and roughness to changes in sand and shell hash cover of the underlying mud substrate as well as the impact of major storms using field measurements of sediment cover, erosion, and aerial images to measure shore platform morphology and retreat. A storm event in 2009 increased the planform roughness and sinuosity of the coastal cliff at Sargent Beach. Following the storm, aerial-image-derived shorelines with annual resolution show a decrease in average alongshore erosion rates from 12 to 4 m yr –1 , coincident with a decrease in shoreline roughness and sinuosity (smoothing). Like the previous storm, a storm event in 2017 increased the planform roughness and sinuosity of the cliff. Over shorter timescales, monthly retreat of the sea cliff occurred only when the platform was sparsely covered with sediment cover on the shore platform, indicating that the tools and cover effects can significantly affect short-term erosion rates. The timescale to return to a smooth shoreline following a storm or roughening event, given a steady-state erosion rate, is approximately 24 years, with the long-term rate suggesting a maximum of ~107 years until Sargent Beach breaches, compromising the Gulf Intracoastal Waterway (GIWW) under current conditions and assuming no future storms or intervention. The observed retreat rate varies, both spatially and temporally, with cliff face morphology, demonstrating the importance of multi-scale measurements and analysis for interpretation of coastal processes and patterns of cliff retreat.

58 GEOSCIENCES↗

Machine Intelligence to Detect, Characterise, and Defend against Influence Operations in the Information Environment

Social media has enabled a new era of manipulation in the information and cognitive domains. Deceptive content—misleading, falsified, and fabricated—is routinely created and spread in the modern social media environment with the intent to create confusion and widen political and social divides, and exploit the societal conflict exacerbated by these divides in the real-world (aka physical domain). Such disinformation campaigns demonstrate a threat to the integrity of economic, political, cultural, public health, and national security institutions around the world. In this work we overview our artificial intelligence (AI) capabilities to detect, describe, and defend against information operations on Twitter as an example social platform to understand the influence of misleading and falsified content diffusion and better enable those charged with defending against such manipulation to enable responsive parties to counter it. We first present novel linguistically-informed deep learning (DL) models for misinformation and disinformation detection, and present an in-depth linguistic analysis of psycho-linguistic markers across broad deception categories. We then demonstrate how our models perform in the multilingual and multimodal setting and categorize falsified and misleading content based on the intent to deceive. We also provide a large-scale analysis to describe user behavior and spread patterns while engaging with deceptive content and report novel findings about the immediate diffusion of deceptive content by characterizing the vulnerable sub-populations and their demographics, and explicitly measuring speed and scale of deception spread to uncover who shares deceptive content, how quickly, how much, and how evenly. In addition, we measure audience reactions to misinformation and disinformation at scale, distinguishing the reactions of users identified as bots versus humans. Finally, we take advantage of deep translation and generation models to create unique solutions for real-time defense against digital deception and discuss how to apply causal inference to prescribe and intervene into strategic communications jointly across information, cognitive, and physical domains.

artificial intelligence, deep learning, neural lan↗

Improvements in Reflected Target Non-intrusive Assessment (ReTNA)

Accurate optical surfaces are a primary driver of concentrated solar power plant performance. Errors in pointing and tracking mirrors, the canting of individual mirror facets, and the surface slope of the mirror itself can be caused by errors during assembly, transportation, wind loading, gravity, and many other sources. The tools that exist to measure these error sources today largely rely on fringe deflectometry (SOFAST, QDec, others), or photogrammetry with targets attached to the mirror surface. In 2022, NREL presented a new indoor optical measurement system to measure fully assembled heliostats during development and on the assembly line for quality assurance purposes, which has undergone significant development in the last year, including the installation of a new, larger laboratory setup. This system, called ReTNA (Reflected Target Non-intrusive Assessment), uses a printed pattern as a deflectometry target. Using printed pattern features as deflectometry targets instead of fringes allows the software to measure the surface slope in two dimensions, eliminating the need to for changing, projected targets. In the last year, NREL's ReTNA tool has been adapted to use a tall, thin target, that only spans one dimension of the mirror, and a camera moving on an automatic track system. We will present these new developments, including the new setup, target patterns, software methodology for fast, automatic optical analysis, and important lessons learned throughout the process. ReTNA results will be compared to established tools, to establish the uncertainty of this new method. ReTNA leverages recent improvements in computer vision and photogrammetry to remove as much careful calibration from the setup process as possible, making the tool low cost, simple, and portable. While it will not achieve the resolution of a fringe deflectometry system, its advantages make it well suited for CSP evaluation, and allow it to fill a different industry need.

concentrating solar power↗

Chemical mixture exposure patterns and obesity among U.S. adults in NHANES 2005–2012

The effect of chemical exposure on obesity has raised great concerns. Real-world chemical exposure always imposes mixture impacts, however their exposure patterns and the corresponding associations with obesity have not been fully evaluated. To discover obesity-related mixed chemical exposure patterns in the general U.S. population. Sparse Decompositional Regression (SDR), a model adapted from sparse representation learning technique, was developed to identify exposure patterns of chemical mixtures with exclusion (non-targeted model) and inclusion (targeted model) of health outcomes. We assessed the relationships between the identified chemical mixture patterns and obesity-related indexes. We also conducted a comprehensive evaluation of this SDR model by comparing to the existing models, including generalized linear regression model (GLM), principal component analysis (PCA), and Bayesian kernel machine regression (BKMR). Eight core exposure patterns were identified using the non-targeted SDR model. Patterns of high levels of MEP, high levels of naphthalene metabolites (ΣOH-Nap), and a pattern of high exposure levels of MCOP, MCNP, and MCPP were positively associated with obesity. Patterns of high levels of BP3, and a pattern of higher mixed levels of MPB, PPB, and MEP were found to have negative associations. Associations were strengthened using the targeted SDR model. In the single chemical analysis by GLM, BP3, MBP, PPB, MCOP, and MCNP showed significant associations with obesity or body indexes. The SDR model exceeded the performance of PCA in pattern identification. Both SDR and BKMR identified a positive contribution of ΣOH-Nap and MCOP, as well as a negative contribution of BP3 and PPB to obesity. Our study identified five core exposure patterns of chemical mixtures significantly associated with obesity using the newly developed SDR model. The SDR model could open a new avenue for assessing health effects of environmental mixture contaminants.

54 ENVIRONMENTAL SCIENCES↗

Synoptic Typing of Multiduration, Heavy Precipitation Records in the Northeastern United States: 1895–2017

Much of the previous research on total and heavy precipitation trends across the northeastern United States (herein, the Northeast) used daily precipitation totals over relatively short periods of record, which do not capture the full range of climate variability and change. Less well understood are the characteristics of long-term changes and synoptic patterns in longer-duration heavy precipitation events across the Northeast. A multiduration (1, 2, 3, 7, 14, and 30 days), multi-return-interval (2, 5, 10, and 50 years) precipitation dataset was used to diagnose changes in various types of precipitation events across the Northeast from 1895 to 2017. Increasing trends were found in all duration and return-interval event combinations with the rarest, longest duration events increasing at faster rates than more-frequent, shorter-duration ones. Daily 850-hPa geopotential height patterns associated with precipitation events were extracted from rotated principal component analysis and k -means clustering analysis, which allowed for the main synoptic types present as well as their structure and evolution to be analyzed. The daily synoptic patterns thus identified were found to be similar across all durations and return intervals and included coastal low (Northeasters, tropical cyclones, and predecessor rain events), deep trough, East Coast trough, zonal, and high pressure patterns.

54 ENVIRONMENTAL SCIENCES↗

The maximum extent of the filaments and sheets in the cosmic web: an analysis of the SDSS DR17

Filaments and sheets are striking visual patterns in cosmic web. The maximum extent of these large-scale structures are difficult to determine due to their structural variety and complexity. We construct a volume-limited sample of galaxies in a cubic region from the SDSS, divide it into smaller subcubes and shuffle them around. We quantify the average filamentarity and planarity in the 3D galaxy distribution as a function of the density threshold and compare them with those from the shuffled realizations of the original data. The analysis is repeated for different shuffling lengths by varying the size of the subcubes. The average filamentarity and planarity in the shuffled data show a significant reduction when the shuffling scales are smaller than the maximum size of the genuine filaments and sheets. We observe a statistically significant reduction in these statistical measures even at a shuffling scale of $\sim 130 \, {{\, \rm Mpc}}$, indicating that the filaments and sheets in three dimensions can extend up to this length scale. They may extend to somewhat larger length scales that are missed by our analysis due to the limited size of the SDSS data cube. We expect to determine these length scales by applying this method to deeper and larger surveys in future.

79 ASTRONOMY AND ASTROPHYSICS↗

Connecting Large‐Scale Meteorological Patterns to Extratropical Cyclones in CMIP6 Climate Models Using Self‐Organizing Maps

Abstract Extratropical cyclones (ETCs) are responsible for the majority of cool‐season extreme events in the northeastern United States (NEUS), often leading to high‐impact weather conditions that can have wide‐ranging socioeconomic impacts. Evaluating the ability of climate models to adequately simulate ETC dynamics is essential for improving model performance and increasing confidence in future projections used by stakeholders and policymakers. ETCs are traditionally studied using techniques such as case studies and synoptic typing, however, these approaches can be time‐consuming, require subjective analysis, and do not necessarily identify the coincident large‐scale meteorological patterns (LSMPs). Here, we apply self‐organizing maps (SOMs) as an automated machine‐learning approach to characterize the LSMPs and associated frequency and intensity of discrete ETC events over NEUS. The dominant patterns of geopotential height variability are identified through SOM analysis of five reanalysis products during the last four decades. ETC events are tracked using TempestExtremes and are integrated with SOMs to classify the accumulated cyclone activity (ACA) associated with each pattern. We then evaluate the skill of CMIP6 historical experiments in simulating the LSMPs and ETC events identified in the SOM. Our results identify a robust bias toward more zonal patterns, with models struggling to reproduce the more amplified patterns typically associated with the highest cyclone activity. While model resolution has some impact on simulation credibility, model configuration appears to be more important in LSMP representation. The vast majority of CMIP6 models produce too few ETCs, although model errors are distributed around historical reanalyses when ACA is normalized by storm frequency.

54 ENVIRONMENTAL SCIENCES↗

Operando synchrotron X-ray analysis of melt pool dynamics in an Al-Sn immiscible alloy

The melt flow in an Al-50vol.% Sn immiscible alloy, produced by single-track laser melting of Al and Sn elemental powders, was studied in real time. High-speed synchrotron X-ray imaging was used to track Al and Sn liquids’ movements, and also to examine elemental distributions in the laser tracks, complimented by electron microscopy after solidification. Key aspects, including melt pool geometry, keyhole instability, and flow dynamics (flow pattern and velocity), were examined using digital image analysis. Relatively deeper melt pools formed at 400 W and 300 mm/s exhibited greater stability, with smooth surfaces, consistent outward flow, and minor vortices near the keyhole. In contrast, shallower pools produced at higher scanning speeds (>500 mm/s) demonstrated greater instability with increased surface waviness, and stronger velocity fluctuations, leading to numerous micro-vortices and increased Al-Sn heterogeneity. Velocity scale estimations, supported by experimental observations, examined the roles of vapour pressure, Marangoni effect, buoyancy, inertial, and surface tension forces in the flow. The results revealed that vapour pressure and mechanical waves dominated at high scanning speeds (shallow pools), while Marangoni forces were equally significant in deep pools at lower speeds (300 mm/s). Buoyancy was found to have minimal impact in both cases. Furthermore, the interaction between inertial and surface tension forces played a critical role in determining the degree of waviness of the pools’ surfaces. These findings offer valuable insights into melt pool dynamics during laser processing of immiscible alloys and other metallic systems using elemental powders, and provide guidance for developing high-fidelity computational fluid dynamics models.

immiscible alloys↗

MAPredict: Static Analysis Driven Memory Access Prediction Framework for Modern CPUs

Application memory access patterns are crucial in deciding how much traffic is served by the cache and forwarded to the dynamic random-access memory (DRAM). However, predicting such memory traffic is difficult because of the interplay of prefetchers, compilers, parallel execution, and innovations in manufacturer-specific micro-architectures. This research introduced MAPredict, a static analysis-driven framework that addresses these challenges to predict last-level cache (LLC)-DRAM traffic. By exploring and analyzing the behavior of modern Intel processors, MAPredict formulates cache-aware analytical models. MAPredict invokes these models to predict LLC-DRAM traffic by combining the application model, machine model, and user-provided hints to capture dynamic information. MAPredict successfully predicts LLC-DRAM traffic for different regular access patterns and provides the means to combine static and empirical observations for irregular access patterns. Evaluating 130 workloads from six applications on recent Intel micro-architectures, MAPredict yielded an average accuracy of 99% for streaming, 91% for strided, and 92% for stencil patterns. By coupling static and empirical methods, up to 97% average accuracy was obtained for random access patterns on different micro-architectures.

Monil, M. A. H.↗