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Results for “Hierarchical clustering”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Integrating Data From In Vitro New Approach Methodologies for Developmental Neurotoxicity

Abstract In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array neuronal network formation assay; and high-content imaging to evaluate proliferation, apoptosis, neurite outgrowth, and synaptogenesis. This work addresses 3 hypotheses: (1) a broad screening battery provides a sensitive marker of DNT bioactivity; (2) selective bioactivity (occurring at noncytotoxic concentrations) may indicate functional processes disrupted; and, (3) a subset of endpoints may optimally classify chemicals with in vivo evidence for DNT. The dataset was comprised of 92 chemicals screened in all 57 assay endpoints sourced from publicly available data, including a set of DNT NAM evaluation chemicals with putative positives (53) and negatives (13). The DNT NAM battery provides a sensitive marker of DNT bioactivity, particularly in cytotoxicity and network connectivity parameters. Hierarchical clustering suggested potency (including cytotoxicity) was important for classifying positive chemicals with high sensitivity (93%) but failed to distinguish patterns of disrupted functional processes. In contrast, clustering of selective values revealed informative patterns of differential activity but demonstrated lower sensitivity (74%). The false negatives were associated with several limitations, such as the maximal concentration tested or gaps in the biology captured by the current battery. This work demonstrates that this multi-dimensional assay suite provides a sensitive biomarker for DNT bioactivity, with selective activity providing possible insight into specific functional processes affected by chemical exposure and a basis for further research.

Carstens, Kelly E.↗

DOE OSTI2022

A Novel Data Segmentation Method for Data-driven Phase Identification

This paper presents a smart meter phase identification algorithm for two cases: meter-phase-label-known and meter-phase-label-unknown. To improve the identification accuracy, a data segmentation method is proposed to exclude data segments that are collected when the voltage correlation between smart meters on the same phase is weakened. Then, using the selected data segments, a hierarchical clustering method is used to calculate the correlation distances and cluster the smart meters. If the phase labels are unknown, a Connected-Triple-based Similarity (CTS) method is adapted to further improve the phase identification accuracy of the ensemble clustering method. The methods are developed and tested on both synthetic and real feeder data sets. Here, simulation results show that the proposed phase identification algorithm outperforms the state-of-the-art methods in both accuracy and robustness.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Structural features of xylan dictate reactivity and functionalization potential for bio-based materials

Plant-based materials have the potential to replace some petroleum-based products, offering compostability and biodegradability as critical advantages. Xylan-rich biomass sources are gaining recognition due to their abundance and underutilization in current industrial applications. Research of potential xylan applications has been complicated by the complex and heterogeneous structure that varies for different xylan feedstocks. Acylation is a broadly used reaction in functionalization of polysaccharides at an industrial scale. However, the efficiency of this reaction varies with the xylan source. To optimize xylan valorization, a systematic understanding of structure–reactivity relationships is essential. This study explores, characterizes, and compares various xylan feedstocks in the acylation process. Xylan feedstocks were analyzed for their chemical composition, degree of polymerization, branching, solubility, and presence of impurities. These features were correlated with xylan glycotypes’ reactivity toward functionalization with succinic anhydride in an optimized DMSO/KOH condition, achieving carboxyl contents of up to 1.46. We used principal component analysis and hierarchical clustering to identify key structural features of xylan that promote its reactivity. Our findings reveal that xylans with higher xylose content and lower degrees of branching exhibit enhanced reactivity, achieving higher carboxyl content and yields. Structural analyses confirmed successful modification, and light scattering analyses showed dramatic changes in the solution properties. Succinylation improves the solubility and film-forming properties of native xylans. This study shows key structure–reactivity relationships in xylan succinylation, establishing that low branching, high xylose content, and reduced lignin impurity enhance chemical functionalization. The results offer a framework for selecting optimal biomass feedstocks and support future efforts in genetic and synthetic biology to design plants with tunable xylan architectures. These findings advance the hemicellulose valorization for applications in coatings and packaging.

Acylation↗

DOE OSTI2024

Using low volume eDNA methods to sample pelagic marine animal assemblages

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Coastal typologies and surface and subsurface characteristics of the Alaskan Beaufort Sea Coast

This dataset was generated to classify the Alaskan Beaufort Sea Coast (ABSC) into a set of distinct coastal typologies, to understand the surface and subsurface characteristics and variability of the ABSC, and to quantify relationships between these characteristics and historical rates of shoreline change. This geospatial dataset contains two csv files of points along the ABSC at a 50 m spacing, one for points sheltered by a barrier island and one for points exposed to the open ocean. Each point has a lat/lon location, and we have attributed to each point average values for elevation, historical long-term shoreline change rates, shoreline orientation, landcover, mean annual ground temperature, geomorphic unit, lithology, geology, ecological landscape unit, maximum thaw settlement potential, massive ice content, and segregated ice content. Each point is also assigned to one of 16 coastal typologies, determined by a hierarchical clustering algorithm on the elevation, shoreline change, orientation, and ground temperature data. There are 9 sheltered typologies and 7 exposed typologies, identified by an integer label in the last column of each csv file. The other two csv files contain the integer IDs and classes for the landcover and geomorphology datasets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Meteorological and hydrological parameters for 17 locations of meteorological stations of the East River Watershed

The Data Package includes a set of csv files of input meteorological parameters for locations of 17 meteorological stations within the East River watershed. These meteorological datasets were downloaded from the (1) PRISM database--monthly precipitation, air temperature (minimum, mean, and maximum), vapor pressure deficit (minimum and maximum), and dewpoint temperature, and (2) NCEP/NCAR Reanalysis database – wind database. The datasets were used for calculations of the Potential Evapotranspiration (ETo), Actual Evapotranspiration (ET), Standard Precipitation Index (SPI) , Standard Evapotranspiration-Precipitation Index (SPEI) for the period from 1966 to 2021. The main research questions addressed are: the evaluation of the long-term temporal trends of climatic parameters, hierarchical clustering, and areal mapping/zonation of the East River watershed. Calculations were conducted in the Rstudio environment. The dataset additionally includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata; and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.The input datasets were downloaded from (a) PRISM database (the Northwest Alliance for Computational Science and Engineering at the Oregon State University), and (b) NCEP/NCAR Reanalysis database.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Remote Sensing and GIS data at 1km-grid over Chesapeake Bay used in “He et al. 2024, Effects of spatial variability in vegetation phenology, climate, landcover, biodiversity, topography, and soil property on soil respiration across a coastal ecosystem”

The package contains the data layers used in “He et al. 2024, Effects of spatial variability in vegetation phenology, climate, landcover, biodiversity, topography, and soil property on soil respiration across a coastal ecosystem”. The study aims to use multi-source remote sensing and GIS datasets to investigate the spatial heterogeneity and identify spatial zones with similar environmental characteristics and understand the primary driving factors affecting soil respiration within sub-ecosystems of the coastal ecosystem. We employed unsupervised hierarchical clustering analysis to identify spatial regions with distinct environmental characteristics, then determined the main driving factors using Random Forest regression and SHapley Additive exPlanations (SHAP). Spatial data layers include soil respiration, kernel Normalized Difference Vegetation Index (kNDVI) computed from Harmonized Landsat 8 and Sentinel-2 time series, climate variables from the Daymet dataset, land cover, biodiversity, topographical metrics, soil property, and tidal elevation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Templates for Risk Informed Assurance with Curvature Embeddings (TRACE)

We investigate recovery of geometric structure from networks embedded in manifolds with spatially varying curvature, extending the constant-curvature framework of Lubold et al. (2023). Our work supports cascade risk assessment in critical infrastructure through the Templates for Risk-informed Assurance with Curvature Embeddings (TRACE) framework. Simulations on a bi-modal Gaussian surface show that constant-curvature methods yield weighted averages shaped by clique patterns, while hierarchical clustering identifies distinct regimes. Localized estimation, however, reveals boundary contamination in transitional regions. To address heterogeneity, we develop distance metrics for graphs with edge and node features, proving their metric validity, and validate them via deterministic graph generation from canonical tilings. We further propose a diffusion-based anomaly detection approach that treats networks as glued manifolds, using curvature discontinuities to detect structural anomalies. Employing the carré-du-champ operator and scalar curvature, we achieve robust anomaly discrimination, demonstrated on the Singapore Water Treatment (SWaT) dataset with joint network-traffic and sensor features. Integration with TRACE reveals how curvature shapes cascade dynamics: positive curvature impedes, while negative curvature accelerates propagation. This geometric perspective provides interpretable risk metrics and visualization tools for critical infrastructure managers. While full validation remains ongoing, our contributions establish a rigorous foundation for geometric analysis of network resilience and cascade vulnerability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Assessing Dynamic Time Warping Techniques for Discriminating Seismic Sources at Local and Regional Distances

Effective monitoring of seismic explosions and hazard assessment relies heavily on the accurate discrimination of underground seismic sources. This study investigates the application of novel nonlinear alignment techniques, specifically Dynamic Time Warping (DTW), for event-type discrimination at regional and local distances. Building on prior research that used DTW and Elastic Shape Analysis (ESA) in discrimination at regional distances, we evaluate the performance of recently developed variants of DTW, including a method that employs Pearson cross-correlation as a measure of warping distance and a time distortion coefficient that quantifies the type and degree of time distortion between signals. By analyzing observational datasets that include different source types, we assess the performance of these approaches for realistic monitoring scenarios. Specifically, we consider a dataset recorded at regional distances in the Korean Peninsula and a local-distance subset from the Unconstrained Utah Event Bulletin catalog to evaluate DTW-based discrimination across multiple distance scales. Additionally, we introduce the maximum cross-correlations of warped waveforms as a similarity metric for event classification. Through hierarchical cluster analysis and dendrogram interpretation, we present our findings, highlighting the strengths and limitations of these techniques in seismic event classification.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A Meta-Analysis of the Protein Components in Rattlesnake Venom

The specificity and potency of venom components give them a unique advantage in developing various pharmaceutical drugs. Though venom is a cocktail of proteins, rarely are the synergy and association between various venom components studied. Understanding the relationship between various components of venom is critical in medical research. Using meta-analysis, we observed underlying patterns and associations in the appearance of the toxin families. For Crotalus, Dis has the most associations with the following toxins: PDE; BPP; CRL; CRiSP; LAAO; SVMP P-I and LAAO; SVMP P-III and LAAO. In Sistrurus venom, CTL and NGF have the most associations. These associations can predict the presence of proteins in novel venom and understand synergies between venom components for enhanced bioactivity. Using this approach, the need to revisit the classification of proteins as major components or minor components is highlighted. The revised classification of venom components is based on ubiquity, bioactivity, the number of associations, and synergies. The revised classification can be expected to trigger increased research on venom components, such as NGF, which have high biomedical significance. Using hierarchical clustering, we observed that the genera’s venom compositions were similar, based on functional characteristics rather than phylogenetic relationships.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Untangling the Galaxy. II. Structure within 3 kpc

We present the results of the hierarchical clustering analysis of the Gaia DR2 data to search for clusters, comoving groups, and other stellar structures. The current paper builds on the sample from the previous work, extending it in distance from 1 to 3 kpc and increasing the number of identified structures up to 8292. To aid in the analysis of the population properties, we developed a neural network called Auriga to robustly estimate the age, extinction, and distance of a stellar group based on the input photometry and parallaxes of the individual members. We apply Auriga to derive the properties of not only the structures found in this paper, but also previously identified open clusters. Through this work, we examine the temporal structure of the spiral arms. Specifically, we find that the Sagittarius Arm has moved by >500 pc in the last 100 Myr and the Perseus Arm has been experiencing a relative lull in star formation activity over the last 25 Myr. We confirm the findings of the previous paper on the transient nature of the spiral arms, with the timescale of transition of a few 100 Myr. Finally, we find a peculiar ~1 Gyr old stream of stars that appears to be heliocentric. Its origin is unclear.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Data for "Divergent urban land trajectories under alternative population projections within the shared socioeconomic pathways"

Datasets supporting findings and visualizations behind McManamay et al. (2024) Divergent urban land trajectories under alternative population projections within the shared socioeconomic pathways. Environmental Research Letters, DOI: 10.1088/1748-9326/ad2eec Using a spatial modeling experiment at high resolution (1-km), this study compared how two alternative US population projections, varying in the spatially explicit nature of demographic patterns and migration, affect urban land dynamics simulated by the Spatially Explicit, Long-term, Empirical City development (SELECT) model for SSP2, SSP3, and SSP5. The numerical experiment, inputs and outputs are fully described in McManamay et al. (2024). The datasets summarize SELECT model simulations within urban areas and rural areas of the conterminous United States. For code to reproduce the results, please refer to https://github.com/IMMM-SFA/mcmanamay_etal_2024_erl Please refer to the README file provided in Files for more details. Descriptions of the datasets are provided below. Dataset(s) Descriptions: Urban_Land_delta_UA_County.csv: Urban land area for original (default) population, updated population, and urban land delta (difference between the two) according to Shared Socioeconomic Pathways (SSPs) and year. Urban land is summarized for U.S. counties (FIPS code) and urban areas (GEOID) as unique areas within various counties. JO_Gao_pop_ufdelta.csv: Comparison of population differences and urban land differences between the origial (default) and updated population projections. City_Case_studies.csv: Differences in urban land areas arising from different population projections summarized for selected cities (Atlanta, Los Angeles, Houston, and New York) and their surrounding rural areas UA_county_FID.zip: Zipped folder of .tiff file depicting unique combination of urban areas and US counties used for summarizing urban land differences in urban and rural areas based on different population projections. ULD_clusters.zip: Zipped folder of .csv files depicting normalized changes in urban land delta (difference in urban land arising from population projections) and the respective Ward's hierarchical clusters, which group urban and rural areas based on similarities in temporal trends. Urban_Percent_change_2100.zip: Zipped folder of .csv files depicting percent changes in urban land area for year 2100 based on differences in the original (default) population and updated population. Each file is for SSPs and urban or rural areas.

Land↗

NASA NTRS1981

Dissipational galaxy formation - Confrontation with observations

An exploration is presented of the hypothesis that a protogalaxy consists of an aggregate of interacting gas clouds which undergo mergers with neighboring systems, as envisaged by both the hierarchical clustering and fragmentation schemes of galaxy formation. Both gaseous dissipation and violet relaxation play fundamental roles in this galaxy formation model, in order to account for such diverse structural and dynamical properties of spheroidal galaxies as velocity anisotropy and metallicity gradients. Protogalaxy mergers during the initial stages of galaxy clustering can account for the observed spatial distribution of spiral, S0, and elliptical galaxies, and galaxy formation can occur slowly and at late epochs, since the time scale for disk formation is less than about 10 to the 10th years.

Silk, J.↗

NASA NTRS1983

From dwarfs to giants - Signposts of galaxy formation

A two-dimensional parametrization of galactic evolution from the primordial state involving mean surface density and velocity dispersion is presented. A dissipation diagram for large-scale structure is presented and its evolutionary significance explored while considering both the pancake and the hierarchical clustering models of galaxy formation. Gaseous dissipation is studied by assuming that individual clouds or turbulent elements of gas interact supersonically, producing strong shocks. It is found that many diverse properties of galaxies can be understood in terms of an evolutionary sequence operative during an early gas-rich protogalactic phase in which dissipation played a key role. Dwarf galaxies may be the fossilized link between primordial fluctuations and the giant galaxies observed today, relics of a past era of prolific galaxy formation.

Silk, J.↗

NASA NTRS1984

Analysis methods for Thematic Mapper data of urban regions

Studies have indicated the difficulty in deriving a detailed land-use/land-cover classification for heterogeneous metropolitan areas with Landsat MSS and TM data. The major methodological issues of digital analysis which possibly have effected the results of classification are examined. In response to these methodological issues, a multichannel hierarchical clustering algorithm has been developed and tested for a more complete analysis of the data for urban areas.

Wang, S. C.↗

NASA NTRS1985

Venus global radar reflectivity and correlations with elevation

A geological analysis of the global radar reflectivity data for Venus is presented. The statistical and map pattern distribution of the radar reflectivity rho is first analyzed in the context of the porosity structure of the surface. Rho is then correlated with elevation in order to examine the degree of topographic control on material properties which could depend on PT-sensitive chemical weathering phenomena. Comparison of the rms slope alpha and rho correlations with elevation demonstrates that there are distinct topographic zones defined on the basis of the rho and alpha trends. Finally, hierarchical clustering analysis is applied to the global rho, alpha, and 100-km baseline regional slope data sets in order to define radar property-related subregions.

Garvin, J. B.↗