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At least 721 records · Page 40

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Abstract Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of ‘streamlined’ life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

59 BASIC BIOLOGICAL SCIENCES↗

Prevalence and scalable control of localized networks

The ability to control network dynamics is essential for ensuring desirable functionality of many technological, biological, and social systems. Such systems often consist of a large number of network elements, and controlling large-scale networks remains challenging because the computation and communication requirements increase prohibitively fast with network size. Here, we introduce a notion of network locality that can be exploited to make the control of networks scalable, even when the dynamics are nonlinear. We show that network locality is captured by an information metric and is almost universally observed across real and model networks. In localized networks, the optimal control actions and system responses are both shown to be necessarily concentrated in small neighborhoods induced by the information metric. This allows us to develop localized algorithms for determining network controllability and optimizing the placement of driver nodes. This also allows us to develop a localized algorithm for designing local feedback controllers that approach the performance of the corresponding best global controllers, while incurring a computational cost orders-of-magnitude lower. Here, we validate the locality, performance, and efficiency of the algorithms in Kuramoto oscillator networks, as well as three large empirical networks: synchronization dynamics in the Eastern US power grid, epidemic spreading mediated by the global air-transportation network, and Alzheimer’s disease dynamics in a human brain network. Taken together, our results establish that large networks can be controlled with computation and communication costs comparable to those for small networks.

42 ENGINEERING↗

A METHODOLOGY TO SUPPORT THE DEVELOPMENT OF A NEW STATE VISION FOR THE UNITED STATES NUCLEAR INDUSTRY

A new strategy in the way in which the United States nuclear power plants (NPPs) are operated, maintained, and supported is needed. One such strategy is to transform the NPP operating model through a business-driven approach that leverages technology to enable new capabilities that improve performance and reduce cost. This paper presents a methodology for developing an achievable yet transformative new state vision that ensures continued safe and efficient operations of the United States NPP fleet. This work builds on existing guidance and leverages previous research to comprehensively address both bottom-up (i.e., utility needs) and top-down (i.e., first principles) considerations important for developing a new state vision. The proposed methodology is intended to provide industry-wide guidance for developing a new state vision that leverages both the selected vendor’s capabilities in a way that meets the utility’s modernization goals while ensuring state-of-the-art systems engineering and human factors engineering principles are applied that promote overall plant safety, performance, and efficiency.

99 GENERAL AND MISCELLANEOUS↗

Spatiotemporal dynamics of ecosystem fires and biomass burning-induced carbon emissions in China over the past two decades

Fire is a major type of disturbance that has important influences on ecosystem dynamics and carbon cycles. Yet our understanding of ecosystem fires and their carbon cycle consequences is still limited, largely due to the difficulty of large-scale fire monitoring and the complex interactions between fire, vegetation, climate, and anthropogenic factors. Here, using data from satellite-derived fire observations and ecosystem model simulations, we performed a comprehensive investigation of the spatial and temporal dynamics of China's ecosystem fire disturbances and their carbon emissions over the past two decades (1997–2016). Satellite-derived results showed that on average about 3.47 - 4.53 x 10 4 km 2 of the land was burned annually during the past two decades, among which annual burned forest area was about 0.81 - 1.25 × 10 4 km 2 , accounting for 0.33-0.51% of the forest area in China. Biomass burning emitted about 23.02 TgC per year. Compared to satellite products, simulations from the Energy Exascale Earth System Land Model (ELM) strongly overestimated China's burned area and fire-induced carbon emissions. Annual burned area and fire-induced carbon emissions were high for boreal forest in Northeast China's Daxing'anling region and subtropical dry forest in South Yunnan, as revealed by both the satellite product and the model simulations. Our results suggest that climate and anthropogenic factors play critical roles in controlling the spatial and seasonal distribution of China's ecosystem fire disturbances. Our findings highlight the importance of multiple complementary approaches in assessing ecosystem fire disturbance and its carbon consequences. Further studies are required to improve the methods of observing and modelling China's ecosystem fire disturbances, which will provide valuable information for fire management and ecosystem sustainability in an era when both human activities and the natural environment are rapidly changing.

54 ENVIRONMENTAL SCIENCES↗

Transformational Regional-Scale Earthquake Simulations with the DOE EarthQuake SIMulation Exascale Framework

Earthquakes present worldwide risk to economic and human safety. The 2023 earthquakes in Turkiye provided a reminder of the potential for catastrophic consequences with 50,700 deaths and 15.7 million people affected. The ability to predict ground motions and infrastructure damage for earthquakes continues to be a challenging problem for scientists and engineers. Until now, estimates of ground motions have been performed empirically by looking at sparse data from past earthquakes. This approach can provide statistical information on intensity amplitudes but cannot inform site-specific ground motions essential to developing the most effective resilience. Interest has grown in large-scale computational models to simulate earthquakes at regional scale. The U.S. Department of Energy EarthQuake SIMulation (EQSIM) framework was developed for regional-scale earthquake simulations at unprecedented fidelity, taking advantage of emerging GPU-accelerated systems. This article describes the EQSIM workflow and demonstrates regional-scale simulations with the new computational capability available to scientists in their quest to mitigate future disasters.

58 GEOSCIENCES↗

GAAF: Searching Activation Functions for Binary Neural Networks Through Genetic Algorithm

Binary neural networks (BNNs) show promising utilization in cost and power-restricted domains such as edge devices and mobile systems. This is due to its significantly less computation and storage demand, but at the cost of degraded performance. To close the accuracy gap, in this paper we propose to add a complementary activation function (AF) ahead of the sign based binarization, and rely on the genetic algorithm (GA) to automatically search for the ideal AFs. These AFs can help extract extra information from the input data in the forward pass, while allowing improved gradient approximation in the backward pass. Fifteen novel AFs are identified through our GA-based search, while most of them show improved performance (up to 2.54% on ImageNet) when testing on different datasets and network models. Interestingly, periodic functions are identified as a key component for most of the discovered AFs, which rarely exist in human designed AFs. Our method offers a novel approach for designing general and application-specific BNN architecture.

59 BASIC BIOLOGICAL SCIENCES↗

Electricity Subsector Transmission Resilience Maturity Model (TRMM) User Guide

The electric transmission sector is facing a range of threats to its functionality that are either new, more severe than experienced in earlier years, or more well understood. Such threats include more frequent and more severe extreme weather events, wildfires, droughts, and human-caused physical and cyberattacks. They also include geological, electromagnetic, and biological events. The novelty or increasing severity of these threats creates a significant need for transmission owners to implement programs to prevent, prepare for, respond to, and recover from such incidents. The national and economic security of the United States depends on the reliable functioning of the Nation’s critical infrastructure in the face of such threats, and the transmission networks are essential components of that infrastructure. The Electricity Subsector Transmission Resilience Maturity Model (TRMM) is a tool that a transmission organization can use to objectively evaluate and benchmark its currently established transmission resilience strategies, programs, policies, and investments, in order to target and prioritize enhancements where needed. The TRMM was developed to address the unique characteristics of the transmission system. The model can enable users to: • evaluate and benchmark their organization’s resilience capabilities, effectively and consistently • prioritize actions and investments to improve the resilience of their systems • share transmission-related knowledge, best practices, and relevant references within their organization and with business partners as a means to improve resilience capabilities • contribute to increasing the overall resilience of the Nation’s transmission systems. The TRMM provides descriptive rather than prescriptive industry-focused guidance. The model content is presented at a high level of abstraction so that it can be interpreted by transmission organizations of various types, structures, and sizes. The model is designed to an be easy-to-use, self-assessment tool.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Construction of extracellular matrix-based 3D hydrogel and its effects on cardiomyocytes

Highlights: • SOD and Triton X-100 could efficiently decellularize cells to get cardiac ECM. • Main proteins of cECM were fibronectin, collagen, elastin, fibrillin, laminin, etc. • 75% cECM-containing 3D hydrogel promoted cell proliferation and anti-apoptosis. • cECM3DH facilitated the differentiation of ESCs into CMs. • APcECM3DH was more conducive to NCM and ESC-derived CM maturation. Some discoveries resulted from 2-dimensional (2D) cultured cardiac cells have been disqualified in animal testing and later clinical trials. Extracellular matrix (ECM) plays a vital role in cardiac homeostasis, cardiac ECM (cECM)-based 3D cell cultures can mimics the physiological and pathological conditions in vivo closely, it is hopeful of addressing this challenge. Construction of cECM-based 3-dimensional (3D) hydrogel (cECM3DH) and its effects on cell behaviors were studied here. The results indicated that cellular compartments could be efficiently removed from heart tissue via sodium dodecyl sulfonate (SDS)- and Triton X-100-mediated decellularization, remaining the natural fibrous network structure and major proteins. 3D hydrogel consisted of 1 × 10{sup 7} cells/mL cells and 75% cECM could promote the proliferation and anti-apoptosis ability of human embryonic kidney (HEK)-293T cells. 0.25% trypsin or 0.20% collagenase was suitable to retrieve these cells from 3D hydrogel for further researches. Compared with 2D culture system, cECM3DH could significantly increase the proportion of GATA 4{sup +} cardiomyocytes (CMs) derived from heart tissue of neonatal mouse or induced differentiation of embryonic stem cells (ESCs) (P < 0.05) The expression levels of mature genes including cTnT, JCN, CaV1.2, MYL2, CASQ2, NCX1, and Cx43 of these CMs in adult pig cECM-based 3D hydrogel (APcECM3DH) were significantly higher than that in 2D culture system and in newborn piglet cECM-based 3D hydrogel (NPcECM3DH), respectively (P < 0.05). Therefore, cECM3DH supports the generation of primary CMs and ESC-derived CMs, APcECM3DH was more conducive to promoting CM maturation, which contributes to building 3D model for pathogenesis exploration, drug screening, and regenerative medicine of heart diseases.

60 APPLIED LIFE SCIENCES↗

Advanced Computing is at the Forefront of a New “Moonshot” Revolutionizing the North American Power Grid

In the 50+ years since the first humans landed on the moon, computing has grown at breakneck speed. We are faced with another challenge that is just as daunting, and just as important to overcome-modernizing the North American electric power grid-and high-performance computing (HPC) systems with specialized software will be an important element in rising to this challenge. We describe at a high level how software developed in the ExaSGD project addresses this "moonshot" goal by utilizing exascale computing and a novel high performance solver software stack to support the mission of decarbonizing power grid operations in an environment of uncertain weather and climate. To reach the exascale benchmark the team has made a number of first-of-their-kind innovations, including novel method for stochastic optimization, fine grained parallel methods for modeling power systems, and GPU resident sparse numerical linear solvers.

17 WIND ENERGY↗

A Principled Framework to Assess the Information-Theoretic Fitness of Brain Functional Sub-Circuits

In systems and network neuroscience, many common practices in brain connectomic analysis are often not properly scrutinized. One such practice is mapping a predetermined set of sub-circuits, like functional networks (FNs), onto subjects’ functional connectomes (FCs) without adequately assessing the information-theoretic appropriateness of the partition. Another practice that goes unchallenged is thresholding weighted FCs to remove spurious connections without justifying the chosen threshold. This paper leverages recent theoretical advances in Stochastic Block Models (SBMs) to formally define and quantify the information-theoretic fitness (e.g., prominence) of a predetermined set of FNs when mapped to individual FCs under different fMRI task conditions. Our framework allows for evaluating any combination of FC granularity, FN partition, and thresholding strategy, thereby optimizing these choices to preserve the important topological features of the human brain connectomes. By applying to the Human Connectome Project with Schaefer parcellations at multiple levels of granularity, the framework showed that the common thresholding value of 0.25 was indeed information-theoretically valid for group-average FCs, despite its previous lack of justification. Our results pave the way for the proper use of FNs and thresholding methods, and provide insights for future research in individualized parcellations.

Duong-Tran, Duy (ORCID:0009000944967575)↗

Assessment of Electric Grid Transmission System Simulator for Human Factors Research

Over the past decades, various technologies have been developed for electric grid operations to support clean energy, meet rising electricity demands, and address infrastructure concerns. However, the human factors aspect is often overlooked during rapid integration. Questions persist about how these technologies impact human performance. Simulators play a critical role in supporting investigation of human factors design concepts and conducting comprehensive usability testing to evaluate human performance and assess human reliability. This paper aims to address human factors research simulator requirements and conduct a comparative study of six different simulators. A detailed evaluation reveals that the evaluated simulators lack the ability to customize user interfaces. Additionally, their user interface designs do not fulfill the basic human factors design principles, potentially leading to increased response variability and reduced statistical power when conducting controlled experimental research. In the future, it is essential to develop scripting tools to integrate customizable user interfaces and simulation models, ensuring meeting research requirements.

Li, Ruixuan↗

Structural Insights into Mechanisms Underlying Mitochondrial and Bacterial Cytochrome c Synthases

Mitochondrial holocytochrome c synthase (HCCS) is an essential protein in assembling cytochrome c (cyt c) of the electron transport system. HCCS binds heme and covalently attaches the two vinyls of heme to two cysteine thiols of the cyt c CXXCH motif. Human HCCS recognizes both cyt c and cytochrome c1 of complex III (cytochrome bc1). HCCS is mutated in some human diseases and it has been investigated recombinantly by mutational, biochemical, and reconstitution studies in the past decade. Here, we employ structural prediction programs (e.g., AlphaFold 3) on HCCS and its two substrates, heme and cytochrome c. The results, when combined with spectroscopic and functional analyses of HCCS and variants, provide insights into the structural basis for heme binding, apocyt c binding, covalent attachment, and release of the holocyt c product. Results from in vitro reconstitution of purified human HCCS using cyt c and cyt c1 peptides as acceptors are consistent with the structural modeling of substrate binding. Reconstitution of HCCS and cyt c1 provides an approach to studying cyt c1 assembly, which has been refractile to recombinant in vivo reconstitution (unlike HCCS and cyt c). We propose a structural basis for release of the holocyt c product from HCCS based on in vitro studies and on cryoEM structures of the bacterial cyt c synthase (CcsBA) active site. We analyze the kinetoplastid mitochondrial synthase (KCCS), and hypothesize a molecular evolutionary path from mitochondrial endosymbiosis to the current HCCS.

Biochemistry & Molecular Biology↗

Energy-Flow-Environment Linkage Map

Understanding how flexibility in environmental requirements can facilitate co-optimization of hydropower production outcomes and environmental outcomes is critical for future grid decision-making and operations as renewable energy resources increase. The environmental and power system outcomes connectivity linkage maps presented here provide a framework for conceptually and quantitatively linking power system outcomes to environmental outcomes through hydropower flow decisions. The Executive Summary Map serves as a starting for exploring the links between hydropower system performance outcomes and environmental outcomes. The centralized topic is “Flow from Hydropower System,” and connects the hydropower operations through “Flow through turbines” and “Non-turbine flows”, and to environmental outcomes through Reservoir elevation” and “Flow downstream of the hydropower system”. To the left of these central topics, “Hydro-mechanical operations” are linked through “Hydro-electrical operations” to “Hydropower performance outcomes” (“Reliability”, “Resilience”, “Revenue”, “Emissions”). On the right, environmental outcomes are grouped together by their physical location: “Upstream Outcomes” (“Upstream geomorphology”, “Upstream recreation”, “Upstream habitat”, “Upstream biota and biodiversity”, “Upstream water quality and greenhouse gas”), Outcomes relevant to both “Upstream/downstream or dam interface” (“Navigation”, “Dam safety and maintenance", “Human health”, “Water supply”, “Flood control”, ”Fish passage”), and “Downstream outcomes“ (e.g., “Downstream geomorphology”, “Downstream recreations”, “Downstream habitat”, “Downstream biota and biodiversity”, “Downstream water quality and greenhouse gas”). Each of these subtopics (e.g., “Hydro-mechanical operations”, “Hydro-electrical operations”, “Upstream geomorphology”, “Upstream recreation”) is further explored through their corresponding submaps. The “Read Me” file provides more detail information on map navigation. The “Models and tools database” file provides detailed information of models and tools presented in the maps.

13 HYDRO ENERGY↗

Potential of water quality wetlands to mitigate habitat losses from agricultural drainage modernization

Given widespread biodiversity declines, a growing global human population, and demands to improve water quality, there is an immediate need to explore land management solutions that support multiple ecosystem services. Agricultural water quality wetlands designed to provide both water quality benefits and wetland and grassland habitat are an emerging restoration solution that may reverse habitat declines in intensive agricultural areas. Installation of water quality wetlands in the Upper Midwest, USA, when considered alongside the repair and modification of aging agricultural tile drainage infrastructure, is a likely scenario that may mitigate nutrient pollution exported from agricultural systems and improve crop yields. The capacity of water quality wetlands to provide habitat within the wetland pool and the surrounding grassland is not well-studied, particularly with respect to potential habitat changes resulting from drainage infrastructure upgrades. For the current study, we produced spatially explicit models of 37 catchments distributed throughout an important region for agriculture and biodiversity, the Des Moines Lobe of Iowa. Four scenarios were considered - with and without improved drainage and with and without water quality wetlands - to estimate the net potential habitat implications of these scenarios for amphibians, grassland birds, and wild bees. Model results indicate that drainage modification alone will likely result in moderate direct losses of suitable amphibian habitat and large declines in overall habitat quality. However, inclusion of water quality wetlands at the catchment scale may mitigate these amphibian habitat losses while also increasing grassland bird and pollinator habitat. In conclusion, the impacts of water quality wetlands and drainage modernization on waterfowl in the region require additional study.

54 ENVIRONMENTAL SCIENCES↗

Automated, Unmanned Detection and Quantification of Fugitive Methane Emissions

Compressor stations used to move natural gas are one of the largest sources of fugitive methane emissions in the midstream sector, accounting for approximately 50% of all fugitive emissions (Zimmerle et al., 2015). This problem is most widespread at reciprocating compressors (Subramanian et al., 2015) where faulty seals are a key contributor to methane emissions (Johnson et al., 2015). As such, there is a significant need for a robust technology that could provide an early indication of an unexpected emission. Equally important, the technology needs to be able to account for biogenic versus anthropogenic sources of methane. One means of indirectly making this determination, is to leverage optical technologies that can autonomously pinpoint the source of such leaks. This presentation discusses recent work funded by the U.S. Department of Energy (DOE) National Energy Technology Laboratory (NETL), focused on the development of an innovative remote sensing technology that can reliably and autonomously detect fugitive methane emissions in near real-time, using computer vision and deep learning. The technology called the Smart Methane Leak Detection (SLED/M) system was initially developed to monitor facilities such as compressor stations in a stationary, pan-tilt-zoom configuration. The system has recently been adapted to monitor facilities from an unmanned aerial system (UAS). The speed and maneuverability of UAS platforms are attractive to leak detection and repair program operators, but introduce several challenges. Many existing methane detection algorithms rely on mostly static backgrounds becoming unusable with motion. In addition, top-down views of fugitive methane emissions present differently in Optical Gas Imagers (OGI) compared to looking across the plume. Our work has focused on overcoming these challenges, enhancing the operators ability to detect methane emissions, and pinpoint their sources. Another recent adaptation to SLED/M is the ability to quantify methane emissions using passive sensors (OGI, thermal camera), environmental conditions, plume modeling, and deep learning. SLED/M advances the state-of-the-art for methane emission detection and quantification by focusing on three key critical criteria for effective methane emission mitigation: (1) autonomy (no need for a human to be in the loop), (2) high reliability (low false alarm rates), and (3) real-time performance. Results from this work will be presented.

03 NATURAL GAS↗

Data-Driven Forgetting and Discount Factors for Vehicle Speed Forecasting in Ecological Adaptive Cruise Control

Abstract This paper investigates temporal correlations in human driving behavior using real-world driving to improve speed forecasting accuracy. These correlations can point to a measurement weighting function with two parameters: a forgetting factor for past speed measurements that the vehicle itself drove with, and a discount factor for the speeds of vehicles ahead based on information from vehicle-to-vehicle communication. The developed weighting approach is applied to a vehicle speed predictor using polynomial regression, a prediction method well-known in the literature. The performance of the developed approach is then assessed in both real-world and simulated traffic scenarios for accuracy and robustness. The new weighting method is applied to an ecological adaptive cruise control system, and its influence is analyzed on the prediction accuracy and the performance of the ecological adaptive cruise control in an electric vehicle powertrain model. The results show that the new prediction method improves energy saving from the eco-driving by up to 4.7% compared to a baseline least-square-based polynomial regression. This is a 10% improvement over the constant speed/acceleration model, a conventional speed predictor.

Automation & Control Systems↗

Radsource Mr: Mixed Reality Planning Tool For Radioactive Recovery

The RadSource MR system leverages Meta Quest 3's advanced mixed reality capabilities to create a comprehensive spatial planning platform for end-of-life sealed radioactive source recovery operations. The application utilizes the Quest 3's high-resolution passthrough cameras and spatial mapping algorithms to generate accurate 3D environmental models. Core technical components include: (1) Real-time spatial measurement algorithms calculating distances, angles, slopes, and surface areas with sub-centimeter accuracy; (2) Virtual object placement system allowing users to position digital representations of recovery equipment (trailers, containment vessels, protective barriers) within the real environment; (3) Voice recording and annotation system for hands-free documentation in protective equipment; (4) 3D mesh capture and storage capabilities for post-operation analysis and regulatory documentation. (5) Procedure documentation is available for viewing in Mixed Reality, providing an innovative and convenient way to access the information during pre-visit and inspection activities. (6) Support for screen capture for the view for real world and virtual objects together to use it later for planning. The system integrates computer vision techniques for environmental understanding, spatial mathematics for precise measurements, and human-computer interaction principles optimized for hazardous environment operations. Data persistence allows teams to save and share planning sessions across multiple stakeholders while maintaining operational security requirements.

Khadka, Rajiv [Idaho National Laboratory (INL), Id↗

Predictability and empirical dynamics of fisheries time series in the North Pacific

Previous studies have documented a strong relationship between marine ecosystems and large-scale modes of sea surface height (SSH) and sea surface temperature (SST) variability in the North Pacific such as the Pacific Decadal Oscillation and the North Pacific Gyre Oscillation. In the central and western North Pacific along the Kuroshio-Oyashio Extension (KOE), the expression of these modes in SSH and SST is linked to the propagation of long oceanic Rossby waves, which extend the predictability of the climate system to ~3 years. Using a multivariate physical-biological linear inverse model (LIM) we explore the extent to which this physical predictability leads to multi-year prediction of dominant fishery indicators inferred from three datasets (i.e., estimated biomasses, landings, and catches). We find that despite the strong autocorrelation in the fish indicators, the LIM adds dynamical forecast skill beyond persistence up to 5-6 years. By performing a sensitivity analysis of the LIM forecast model, we find that two main factors are essential for extending the dynamical predictability of the fishery indicators beyond persistence. The first is the interaction of the fishery indicators with the SST/SSH of the North and tropical Pacific. The second is the empirical relationship among the fisheries time series. This latter component reflects stock-stock interactions as well as common technological and human socioeconomic factors that may influence multiple fisheries and are captured in the training of the LIM. These results suggest that empirical dynamical models and machine learning algorithms, such as the LIM, provide an alternative and promising approach for forecasting key ecological indicators beyond the skill of persistence.

60 APPLIED LIFE SCIENCES↗