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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Background. In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. Results. Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host’s immune system. Conclusions. This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhancing Cluster Identification in Atom Probe Tomography Data Using Transfer Learning

Atom probe tomography (APT) has enabled the direct visualization of solute clusters, providing valuable insights into material structures. This clustering is crucial for understanding the nanoscale composition and behavior of materials, which can significantly influence their mechanical and physical properties. However, the widely used clustering methods in the APT community face challenges such as subjective parametric selection and limited applicability, particularly in dealing with overlapping clusters, nested clusters, and artifacts across different scales, such as precipitates and dislocations. To address these challenges, we present a framework based on density-based cluster analysis that aims to be less dependent on user input, reproducible, and robust.

Density-based clustering↗
DOE OSTI2024

Fungal diversity and function in metagenomes sequenced from extreme environments

Fungi are increasingly recognized as key players in various extreme environments. Here we present an analysis of publicly-sourced metagenomes from global extreme environments, focusing on fungal taxonomy and function. The majority of 855 selected metagenomes contained scaffolds assigned to fungi. Relative abundance of fungi was as high as 10% of protein-coding genes with taxonomic annotation, with up to 289 fungal genera per sample. Despite taxonomic clustering by environment, fungal communities were more dissimilar than archaeal and bacterial communities, both for within- and between-environment comparisons. Relatively abundant fungal classes in extreme environments included Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Saccharomycetes, and Sordariomycetes. Broad generalists and prolific aerial spore formers were the most relatively abundant fungal genera detected in most of the extreme environments, bringing up the question of whether they are actively growing in those environments or just surviving as spores. More specialized fungi were common in some environments, such as zoosporic taxa in cryosphere water and hot springs. Relative abundances of genes involved in adaptation to general, thermal, oxidative, and osmotic stress were greatest in soda lake, acid mine drainage, and cryosphere water samples.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Discovery of correlated electron molecular orbital materials using graph representations

Correlated electron molecular orbital (CEMO) materials host emergent electronic states built from molecular orbitals localized over clusters of transition metal ions yet have historically been discovered sporadically and generally been treated as isolated case studies. Here we establish CEMO materials as a systematically discoverable class and introduce a graph-based framework to identify, classify, and organize transition-metal cluster motifs in inorganic solids. Starting from crystal structures in the Materials Project, we construct transition metal connectivity graphs, extract cluster motifs using a bond-cutting algorithm, and determine cluster point groups, effective cluster sublattice dimensionality, and translational symmetry. Applying this approach in a high-throughput screen of 34,548 compounds yields 5,306 cluster-containing materials, including 2,627 stable or metastable compounds with isolated clusters and 984 materials featuring mixed-metal clusters. The resulting dataset reveals symmetry and element dependent trends in cluster formation. By integrating cluster classification with flat band lattice topology and battery-relevant information, we provide further relevant information to multiple scientific communities. The accompanying open dataset, Cluster Finder software, and interactive web platform enable systematic exploration of cluster driven electronic phenomena and establish a general pathway for discovering correlated quantum materials and functional materials with cluster-based or extended metal-metal bonding in inorganic solids.

Akhond, Md. Rajbanul [Department of Chemistry, 800↗
DOE OSTI2024

Exploring the Landscape of Distributed Graph Clustering on Leadership Supercomputers

The rapid growth of large-scale datasets in fields like biology and social networks has driven the need for advanced graph analytics techniques. Community detection, a fundamental task in graph analytics, identifies closely connected groups of nodes within a network, providing valuable insights across various disciplines. This study focuses on two classic community detection methods, the Louvain algorithm and Markov Clustering (MCL), and evaluates the performance of two prominent distributed community detection algorithms: HiPDPL-GPU, our prior implementation, and HipMCL. We conduct experiments on GPU-accelerated heterogeneous HPC systems, Summit and Frontier, to assess their performance under varying conditions. Our objective is to identify the strengths and weaknesses of these algorithms in terms of scalability, and quality of solutions. We evaluate these algorithms on a diverse set of 70+ networks spanning 13 domains, with sizes ranging up to 4.2 billion edges. Our results demonstrate that HiPDPL-GPU consistently outperforms HipMCL, especially for large-scale networks. HiPDPL-GPU achieves significantly faster runtimes (47x to 1439x), higher modularity scores, and improved scalability. These findings highlight HiPDPL-GPU as a promising solution for efficient and effective large-scale graph analytics in diverse application domains, and provide insights into the feasibility of using MCL-based approaches for certain application domains.

Community detection, graph algorithms↗
NASA NTRS1973

Multispectral scanner imagery for plant community classification.

Optimum channel selection among 12 channels of multispectral scanner imagery identified six as providing the best information for computerized classification of 11 plant communities and two nonvegetation classes. Intensive preprocessing of the spectral data was required to eliminate bidirectional reflectance effects of the spectral imagery caused by scanner view angle and varying geometry of the plant canopy. Generalized plant community types - forest, grassland, and hydrophytic systems - were acceptably classified based on ecological analysis. Serious, but soluble, errors occurred with attempts to classify specific community types within the grassland system. However, special clustering analyses provided for improved classification of specific grassland communities.

Driscoll, R. S.↗
DOE OSTI2020

An Automatic Learning Framework for Smart Residential Communities

Predictability has been foundational to matching supply and demand in the day-to-day operation of the electric power system. Demand predictability is eroding because of the increased use of renewable energy resources and more sophisticated loads, such as electric vehicles and smart appliances. In this paper, an automatic software framework is described which can be used for load forecasting in smart communities. A time-varying clustering-based Markov chain approach is used to predict the energy consumption of residential buildings in a smart community. The training data is based on 1-minute meter data of occupied homes over one month. The data points are first clustered based on the energy consumption and the time of the day. Then, the original data is converted using the Centroids of the clusters. A time-varying Markov chain is subsequently trained to model the energy consumption behavior of residents for each home using the transformed data. The trained model is shown to successfully predict load in 5-minute intervals over a 24 hours period.

Zandi, Helia↗
DOE OSTI2020

On the Robustness of Network Community Structure Under Addition of Edges

Communities represent important functional modules in networked systems. A key goal in preserving such communities is understanding their robustness under perturbations. Previous research has studied the impact of node removals and edge removals on the community structure. However, the impact of edge additions on the robustness of the community structure is relatively unknown. Edge additions or false positive edges may simulate measurement errors or external exceptional events that threaten the functionality of networked systems. Here, we study the impact of edge additions on the community structure using Lancichinetti-Fortunato-Radicchi (LFR) benchmark networks. We show that, for a fixed network size, the impact of edge additions is greater on networks with initially weak community structure than on networks with strongly clustered structures. In addition, we find that the perception of the impact is also dependent on the community detection algorithm used to uncover communities. In particular, we found that modularity-based methods such as Leiden and Louvain are less affected than information-theoretic and message passing-based methods such as Infomap and Label Propagation. Our results demonstrate that edge addition can (a) significantly impact the community structure of networks based on their initial conditions, and (b) the perception of the impact is dependent on the community detection algorithm used. We describe limitations, open challenges, and how this methodology can inform the design of resilient networked systems under edge additions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Topology-Informed Design Rules for Deconstructable Thermoset Copolymer Networks

Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.

coarse-grained molecular dynamics↗
DOE OSTI2020

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Radial Profile of the 3.5 kev Line Out to R200 in the Perseus Cluster

The recent discovery of the unidentified emission line at 3.5 keV in galaxies and clusters has attracted great interest from the community. As the origin of the line remains uncertain, we study the surface brightness distribution of the line in the Perseus cluster since that information can be used to identify its origin. We examine the flux distribution of the 3.5 keV line in the deep Suzaku observations of the Perseus cluster in detail. The 3.5 keV line is observed in three concentric annuli in the central observations, although the observations of the outskirts of the cluster did not reveal such a signal. We establish that these detections and the upper limits from the non-detections are consistent with a dark matter decay origin. However, absence of positive detection in the outskirts is also consistent with some unknown astrophysical origin of the line in the dense gas of the Perseus core, as well as with a dark matter origin with a steeper dependence on mass than the dark matter decay. We also comment on several recently published analyses of the 3.5 keV line.

dark matter – elementary particles – galaxies:↗
NASA NTRS2013

Massively Clustered CubeSats NCPS Demo Mission

Technologies under development for the proposed Nuclear Cryogenic Propulsion Stage (NCPS) will require an un-crewed demonstration mission before they can be flight qualified over distances and time frames representative of a crewed Mars mission. In this paper, we describe a Massively Clustered CubeSats platform, possibly comprising hundreds of CubeSats, as the main payload of the NCPS demo mission. This platform would enable a mechanism for cost savings for the demo mission through shared support between NASA and other government agencies as well as leveraged commercial aerospace and academic community involvement. We believe a Massively Clustered CubeSats platform should be an obvious first choice for the NCPS demo mission when one considers that cost and risk of the payload can be spread across many CubeSat customers and that the NCPS demo mission can capitalize on using CubeSats developed by others for its own instrumentation needs. Moreover, a demo mission of the NCPS offers an unprecedented opportunity to invigorate the public on a global scale through direct individual participation coordinated through a web-based collaboration engine. The platform we describe would be capable of delivering CubeSats at various locations along a trajectory toward the primary mission destination, in this case Mars, permitting a variety of potential CubeSat-specific missions. Cameras on various CubeSats can also be used to provide multiple views of the space environment and the NCPS vehicle for video monitoring as well as allow the public to "ride along" as virtual passengers on the mission. This collaborative approach could even initiate a brand new Science, Technology, Engineering and Math (STEM) program for launching student developed CubeSat payloads beyond Low Earth Orbit (LEO) on future deep space technology qualification missions. Keywords: Nuclear Propulsion, NCPS, SLS, Mars, CubeSat.

Robertson, Glen A.↗
DOE OSTI2022

An overview of the operation architectures and energy management system for multiple microgrid clusters

The emerging novel energy infrastructures, such as energy communities, smart building-based microgrids, electric vehicles enabled mobile energy storage units raise the requirements for a more interconnective and interoperable energy system. It leads to a transition from simple and isolated microgrids to relatively large-scale and complex interconnected microgrid systems named multi-microgrid clusters. In order to efficiently, optimally, and flexibly control multi-microgrid clusters, cross-disciplinary technologies such as power electronics, control theory, optimization algorithms, information and communication technologies, cyber-physical, and big-data analysis are needed. This paper introduces an overview of the relevant aspects for multi-microgrids, including the outstanding features, architectures, typical applications, existing control mechanisms, as well as the challenges.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRSDate not supplied

FAIR-ness Assessment of NASA’s Earth Observation System Data and Information System (EOSDIS)

This presentation addresses the challenge of evaluating a multi-disciplinary institutional network of data repositories in operation since 1994 against the relatively recent criteria that constitute FAIR (Findable, Accessible, Interoperable, Reusable) data. NASA’s Earth Observation System Data and Information System (EOSDIS), with its 12 discipline-based Distributed Active Archive Centers (DAACs), preceded the definition and popularization of FAIR by over two decades. An assessment is very useful to describe how well the FAIR principles are met and to identify any improvements needed. In 2020, A “self-assessment” of EOSDIS and DAACs was performed by the ESDIS Project staff and the DAACs from the points of view of human actionability and machine actionability. More recently, a draft of a Science Mission Directorate (SMP) Program Directive (SPD-41a) has been released by NASA Headquarters for comment, where it is recommended that all SMD-funded data should follow the FAIR principles. This presentation is timely to initiate community discussion within the Information Quality Cluster (IQC) of the Earth Science Information Partners (ESIP) and help strategize and develop implementation guidelines for EOSDIS and DAACs to conform to FAIR principles.

Remote sensing↗
DOE OSTI2025

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change. IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.

Kellom, Matthew↗
DOE OSTI2025

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗
DOE OSTI2025

Geospatial analysis of preterm and small-for-gestational age births in Washington D.C.

Background: This study is based on the recognition that adverse pregnancy outcomes significantly affect maternal and infant health, leading to increased morbidity and mortality. These outcomes are shaped by a complex interplay of individual-level factors—like maternal age and education—and community-level influences, including socio-economic status and access to healthcare. Understanding these determinants is crucial for developing effective public health strategies, especially for marginalized populations, by identifying high-risk areas and informing targeted interventions that address both individual and structural barriers. Methods: We utilized geospatial analysis to explore the association between individual- and community-level factors and adverse pregnancy outcomes, specifically preterm birth (PTB) and small-for-gestational-age (SGA) birthweight in Washington, D.C. We used Empirical Bayes smoothing methods to calculate rates of adverse birth outcomes from 2010 to 2018 at the U.S. Census tract–level. Spatial scan statistics were used to investigate if adverse birth outcomes clustered in specific areas. ANOVA tests were conducted for individual- and community-level factors within identified clusters. Results: Spatial analysis identified significant high-risk clusters for PTB and SGA infants primarily in southeastern Washington, D.C., particularly in Wards 7 and 8. Individuals residing within these clusters experienced a 47% increased risk of PTB (RR = 1.467) and a 56% increased risk of SGA (RR = 1.560) compared to those outside clusters. Space–time analysis revealed temporal variation, with PTB clusters persisting from 2011 to 2014 and SGA clusters extending through 2017. Compared to low-risk clusters, high-risk clusters had younger birthing individuals (mean age ~26.5 vs. ~33 years), lower maternal college degree attainment (~20% vs. ~80%), higher rates of late or no prenatal care (~16% vs. 11%), and increased prevalence of smoking and hypertension (all P < 0.001). Community-level indicators showed lower median household incomes ($\$40,000$ vs. ~$\$105,000$), greater poverty (~16% vs. ~7% below $\$10,000$/year), higher public assistance use (~32% vs. ~5%), and reduced healthcare access (greater distances to emergency and specialty care) in high-risk areas (all P < 0.001). Neighborhood deprivation indices were significantly elevated, commutes were longer, and population density was lower in these clusters. These findings highlight that adverse birth outcomes cluster in neighborhoods with pronounced socioeconomic and health disparities. Conclusion: High-risk birth clusters highlight intertwined factors: individual, socio-economic, and geographic. Addressing these requires comprehensive interventions focusing on social and structural determinants of health.

Birth outcomes↗
NASA NTRS2016

ESIP Information Quality Cluster (IQC)

The Information Quality Cluster (IQC) within the Federation of Earth Science Information Partners (ESIP) was initially formed in 2011 and has evolved significantly over time. The current objectives of the IQC are to: 1. Actively evaluate community data quality best practices and standards; 2. Improve capture, description, discovery, and usability of information about data quality in Earth science data products; 3. Ensure producers of data products are aware of standards and best practices for conveying data quality, and data providers distributors intermediaries establish, improve and evolve mechanisms to assist users in discovering and understanding data quality information; and 4. Consistently provide guidance to data managers and stewards on how best to implement data quality standards and best practices to ensure and improve maturity of their data products. The activities of the IQC include: 1. Identification of additional needs for consistently capturing, describing, and conveying quality information through use case studies with broad and diverse applications; 2. Establishing and providing community-wide guidance on roles and responsibilities of key players and stakeholders including users and management; 3. Prototyping of conveying quality information to users in a more consistent, transparent, and digestible manner; 4. Establishing a baseline of standards and best practices for data quality; 5. Evaluating recommendations from NASA's DQWG in a broader context and proposing possible implementations; and 6. Engaging data providers, data managers, and data user communities as resources to improve our standards and best practices. Following the principles of openness of the ESIP Federation, IQC invites all individuals interested in improving capture, description, discovery, and usability of information about data quality in Earth science data products to participate in its activities.

data products↗