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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

Venus: Global radar properties in a geological context

The radar altimetry, roughness (RMS slopes), and reflectivity data acquired for Venus represent the only global radar information available for any of the planets. In addition, the Pioneer Venus radar instrument was able to sound the surface at normal incidence so that it was possible to accurately measure the small-scale surface slopes and reflectivity (dielectric and porosity properties) at the same time as the surface elevation. Analyses of the topography of Venus demonstrate that it differs in its distribution from the Moon, Mars, or the Earth. While the range of topography extends from -2.5 km below the reference level to 11.5 km above, most of Venus falls within 1 km of the mean elevation, this is in sharp contrast to the Earth. The narrow, unimodal nature of the distribution of topography on Venus evidently exerts control on the other radar-derived properties of the surface. When clustering analysis techniques are applied to the Venus radar data sets, the result demonstrates that topographic zones serve as the best criteria for distinguishing regions on Venus which have related radar properties. The individual radar data sets are investigated separately and in conjunction with topography.

Garvin, J. B.↗
DOE OSTI2024

Unveiling Temporal Performance Deviation: Leveraging Clustering in Microservices Performance Analysis

As the market for cloud computing continues to grow, an increasing number of users are deploying applications as microservices. The shift introduces unique challenges in identifying and addressing performance issues, particularly within large and complex infrastructures. To address this challenge, we propose a methodology that unveils temporal performance deviations in microservices by clustering containers based on their performance characteristics at different time intervals. Showcasing our methodology on the Alibaba dataset, we found both stable and dynamic performance patterns, providing a valuable tool for enhancing overall performance and reliability in modern application landscapes.

Clustering↗
NASA NTRS1980

The discovery of an O subdwarf in the globular cluster NGC 6712

Spectral data for C49 in the globular cluster NGC 6712 are examined with reference to evolutionary models for low-mass stars that are contracting into white dwarfs. The spectrum of this star is found to be almost identical to that of the first sdO star found in a globular cluster, star A in NGC 6397. Analysis of the spectral data using nonlocal thermodynamic equilibrium models gives surface parameters T not less than 50,000 K, log g = 5.5 plus or minus 0.5, and N(He)/N(H) approximately equal to 0.1. The results are consistent with the models considered.

Remillard, R. A.↗
DOE OSTI2020

Machine learning analysis of perovskite oxides grown by molecular beam epitaxy

Reflection high-energy electron diffraction (RHEED) is a ubiquitous in situ molecular beam epitaxial (MBE) characterization tool. Although RHEED can be a powerful means for crystal surface structure determination, it is often used as a static qualitative surface characterization method at discrete intervals during a growth. A full analysis of RHEED data collected during the entirety of MBE growths is made possible using principle component analysis (PCA) and $\textit{k}$-means clustering to examine significant boundaries that occur in the temporal clusters grouped from RHEED data and identify statistically significant patterns. This process is applied to data from homoepitaxial SrTiO 3 growths, heteroepitaxial SrTiO 3 grown on scandate substrates, BaSnO 3 films grown on SrTiO 3 substrates, and LaNiO 3 films grown on SrTiO 3 substrates. We report this analysis may provide additional insights into the surface evolution and transitions in growth modes at precise times and depths during growth, and that video archival of an entire RHEED image sequence may be able to provide more insight and control overgrowth processes and film quality.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

ancestral sequence reconstruction↗
DOE OSTI2025

Galaxy cluster matter profiles - I. Self-similarity, mass calibration, and observable-mass relation validation employing cluster mass posteriors

We present a study of the weak lensing inferred matter profiles ΔΣ(R) of 698 South Pole Telescope (SPT) thermal Sunyaev-Zel’dovich effect (tSZE) selected and MCMF optically confirmed galaxy clusters in the redshift range 0.25 < z < 0.94 that have associated weak gravitational lensing shear profiles from the Dark Energy Survey (DES). Rescaling these profiles to account for the mass dependent size and the redshift dependent density produces average rescaled matter profiles ΔΣ(R/R200c)/(ρcritR200c) with a lower dispersion than the unscaled ΔΣ(R) versions, indicating a significant degree of self-similarity. Galaxy clusters from hydrodynamical simulations also exhibit matter profiles that suggest a high degree of self-similarity, with RMS variation among the average rescaled matter profiles with redshift and mass falling by a factor of approximately six and 23, respectively, compared to the unscaled average matter profiles. We employed this regularity in a new Bayesian method for weak lensing mass calibration that employs the so-called cluster mass posterior P(M200|ζ̂, λ̂, z), which describes the individual cluster masses given their tSZE (ζ̂) and optical (λ̂, z) observables. This method enables simultaneous constraints on richness λ-mass and tSZE detection significance ζ-mass relations using average rescaled cluster matter profiles. We validated the method using realistic mock datasets and present observable-mass relation constraints for the SPT×DES sample, where we constrained the amplitude, mass trend, redshift trend, and intrinsic scatter. Our observable-mass relation results are in agreement with the mass calibration derived from the recent cosmological analysis of the SPT×DES data based on a cluster-by-cluster lensing calibration. Our new mass calibration technique offers a higher efficiency when compared to the single cluster calibration technique. We present new validation tests of the observable-mass relation that indicate the underlying power-law form and scatter are adequate to describe the real cluster sample but that also suggest a redshift variation in the intrinsic scatter of the λ-mass relation may offer a better description. In addition, the average rescaled matter profiles offer high signal-to-noise ratio (S/N) constraints on the shape of real cluster matter profiles, which are in good agreement with available hydrodynamical ΛCDM simulations. This high S/N profile contains information about baryon feedback, the collisional nature of dark matter, and potential deviations from general relativity.Key words: gravitational lensing: weak / galaxies: clusters: general / large-scale structure of Universe

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1983

LANDSAT-4 image data quality analysis

Seven heterogeneous areas within the Des Moines, Iowa area test site were selected to define candidate spectral training classes using a clustering algorithm. In addition to the 91 cluster (nonsupervised) classes, three supervised training classes were defined and subsequently included in the training statistics file. The identity of all 94 candidate classes were determined using available reference data. Through analysis of the interclass separabilities, the original 94 candidate training classes were reduced to 42 spectrally separable final classes. The minimum average transformed divergence values for the 42 spectral classes and for the best subsets of TM spectral bands are shown in a table.

Anuta, P. E.↗
NASA NTRS1984

Preliminary Comparisons of the Information Content and Utility of TM Versus MSS Data

Comparisons were made between subscenes from the first TM scene acquired of the Washington, D.C. area and a MSS scene acquired approximately one year earlier. Three types of analyses were conducted to compare TM and MSS data: a water body analysis, a principal components analysis and a spectral clustering analysis. The water body analysis compared the capability of the TM to the MSS for detecting small uniform targets. Of the 59 ponds located on aerial photographs 34 (58%) were detected by the TM with six commission errors (15%) and 13 (22%) were detected by the MSS with three commission errors (19%). The smallest water body detected by the TM was 16 meters; the smallest detected by the MSS was 40 meters. For the principal components analysis, means and covariance matrices were calculated for each subscene, and principal components images generated and characterized. In the spectral clustering comparison each scene was independently clustered and the clusters were assigned to informational classes. The preliminary comparison indicated that TM data provides enhancements over MSS in terms of (1) small target detection and (2) data dimensionality (even with 4-band data). The extra dimension, partially resultant from TM band 1, appears useful for built-up/non-built-up area separation.

Markham, B. L.↗
DOE OSTI2022

Assessment of Outliers in Alloy Datasets Using Unsupervised Techniques

We report advancements in data analytics techniques have enabled complex, disparate datasets to be leveraged for alloy design. Identifying outliers in a dataset can reduce noise, identify erroneous and/or anomalous records, prevent overfitting, and improve model assessment and optimization. In this work, two alloy datasets (9-12% Cr ferritic martensitic steels, and austenitic stainless steels) have been assessed for outliers using unsupervised techniques and supplemented with domain knowledge. Principal component analysis and k-means clustering were applied to the data, and points were assessed as outliers based on their distance away from other points in the cluster and from other points in the dataset. The outlier characteristics were investigated to determine both cluster-specific and overall trends in the properties of the outlier points. The approach demonstrated here is extensible to other alloy datasets for outlier identification and evaluation to improve the reliability of machine learning and modeling predictions for advanced alloy design.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Differentially Private DBSCAN

SAND2022-15185 O Differentially Private DBSCAN is a differential private clustering algorithm used for running experiments and conducting data analysis. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Smith, MichaelReed↗
NASA NTRS1977

Utility of correlation techniques in gravity and magnetic interpretation

Internal correspondence uses Poisson's Theorem in a moving-window linear regression analysis between the anomalous first vertical derivative of gravity and total magnetic field reduced to the pole. The regression parameters provide critical information on source characteristics. The correlation coefficient indicates the strength of the relation between magnetics and gravity. Slope value gives delta j/delta sigma estimates of the anomalous source. The intercept furnishes information on anomaly interference. Cluster analysis consists of the classification of subsets of data into groups of similarity based on correlation of selected characteristics of the anomalies. Model studies are used to illustrate implementation and interpretation procedures of these methods, particularly internal correspondence. Analysis of the results of applying these methods to data from the midcontinent and a transcontinental profile shows they can be useful in identifying crustal provinces, providing information on horizontal and vertical variations of physical properties over province size zones, validating long wavelength anomalies, and isolating geomagnetic field removal problems.

Chandler, V. W.↗
NASA NTRS1985

Applications of Fuzzy Set Theory to Satellite Soundings

The introduction of an appropriate fuzzy setting for satellite soundings and its application to clustering methods via unimodal fuzzy sets in the future is proposed. Methods of hard clustering analysis and fuzzy partitioned clustering were applied on simulated data with very encouraging results. The proposed clustering technique is discussed. The notion of a unimodal fuzzy set was chosen to represent the partition of a data set for two reasons: (1) it detects all the locations in the vector space where highly concentrated clusters of points exist; and (2) the notion is general enough to represent clusters that exhibit quite general distributions of points. The technique detects all of the existing unimodal fuzzy sets and realizes the maximum separation among them. It is economical in memory space and computational time requirements and also detects groups that are fairly generally distributed in the feature space.

Munteanu, M. J.↗
DOE OSTI2026

Constraints on the normal branch of DGP gravity from SPT galaxy clusters with DES and HST weak-lensing mass calibration and from P l a n c k PR4 CMB anisotropies

We present constraints on the normal branch of the Dvali-Gabadadze-Porrati (nDGP) braneworld gravity model from the abundance of massive galaxy clusters. On scales below the nDGP crossover scale r c , the nDGP model features an effective gravitylike fifth force that alters the growth of structure, leading to an enhancement of the halo mass function (HMF) on cluster scales. The enhanced cluster abundance allows for constraints on the nDGP model using cluster samples. We employ the South Pole Telescope (SPT) cluster sample, selected through the thermal Sunyaev-Zel’dovich effect with the SPT and with mass calibration using weak-lensing data from the Dark Energy Survey (DES) and the Hubble Space Telescope (HST). The cluster sample contains 1,005 clusters with redshifts 0.25 < z < 1.78 , which are confirmed with the multicomponent matched filter algorithm using optical and near-infrared data. Weak-lensing data from DES and HST enable a robust mass measurement of the cluster sample. We use DES Year 3 data for 688 clusters with redshifts z < 0.95 , and HST data for 39 clusters with redshifts 0.6 < z < 1.7 . We account for the enhancement in the HMF through a semi-analytic correction factor to the standard cosmology HMF derived from the spherical collapse model in the nDGP model. We then further calibrate this model using N -body simulations. In addition, for the first time, we analyze the primary CMB temperature and polarization anisotropy measurements from Planck PR4 within the nDGP model. We obtain a competitive constraint from the joint analysis of the SPT cluster abundance with the Planck PR4 data, and report an upper bound of 1 / H 0 r c < 1.41 at 95% when assuming a cosmology with massive neutrinos.

Vogt, S. M.L. [Munich U. Observ.; LMU Munich (main↗
DOE OSTI2024

Galaxy Clusters Discovered via the Thermal Sunyaev-Zel’dovich Effect in the 500-square-degree SPTpol Survey

We present a catalog of 689 galaxy cluster candidates detected at significance ξ > 4 via their thermal Sunyaev-Zel’dovich (SZ) effect signature in 95 and 150 GHz data from the 500-square-degree SPTpol survey. We use optical and infrared data from the Dark Energy Camera and the Wide-field Infrared Survey Explorer (WISE) and Spitzer satellites, to confirm 544 of these candidates as clusters with ~ 94% purity. The sample has an approximately redshift-independent mass threshold at redshift z > 0.25. The confirmed sample spans 1.5 × 10 14 < M 500 c < 9 × 10 14 M ⊙ /h 70 and 0.03 < z ≲ 1.6 in mass and redshift, respectively, with a median mass of 2.5×10 14 M ⊙ /h 70 and median redshift z = 0.7; 21% of the confirmed clusters are at z > 1. We use external radio data from the Sydney University Molonglo Sky Survey (SUMSS) to estimate contamination to the SZ signal from synchrotron sources. The contamination reduces the recovered ξ by a median value of 0.032, or ~ 0.8% of the ξ = 4 threshold value, and ~ 7% of candidates have a predicted contamination greater than Δξ = 1. With the exception of a small number of systems (< 1%), an analysis of clusters detected in single-frequency 95 and 150 GHz data shows no significant contamination of the SZ signal by emission from dusty or synchrotron sources. This cluster sample, representing the deepest SZ-selected cluster sample to date, will be a key component in upcoming astrophysical and cosmological analyses of clusters. In addition to the cluster catalog, we also release the millimeter-wave maps and associated data products used to produce this sample. These maps have depths of 5.3 (11.7) µK CMB -arcmin at 150 (95) GHz and an effective angular resolution of 1. '2 (1. '7). The SPTpol products are available at https:// pole.uchicago.edu/public/data/sptpol_500d_clusters/index.html, and the NASA LAMBDA website. An interactive sky server with the SPTpol maps and Dark Energy Survey data release 2 images is also available at NCSA https://skyviewer.ncsa.illinois.edu.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Cluster spin glass correlations and dynamics in Zn 0.5⁢ Mn 0.5⁢ Te

Here, we present a combined magnetometry, muon spin-relaxation (𝜇⁢SR), and neutron-scattering study of the insulating spin glass Zn 0.5 ⁢Mn 0.5 ⁢Te, for which magnetic Mn 2+ and nonmagnetic Zn 2+ ions are randomly distributed on a face-centered cubic lattice. The magnetometry and 𝜇⁢SR results confirm a spin freezing transition around 𝑇 𝑓 ≈ 23 K, with the spin-fluctuation rate decreasing gradually and somewhat inhomogeneously through the sample volume as the temperature decreases toward 𝑇 𝑓 . Characteristic spin-correlation times well above 𝑇 𝑓 are on the order of 10 −10 s, much slower than typically observed in canonical spin glasses but in line with expectations for a cluster spin glass. Using magnetic pair distribution function (mPDF) analysis and reverse Monte Carlo (RMC) modeling of the magnetic diffuse neutron-scattering data, we show that the spin-glass ground state consists of clusters of spins exhibiting short-range-ordered type-III antiferromagnetic correlations with a locally ordered moment of 3.1⁢(1)⁢𝜇 B between nearest-neighbor spins. The type-III correlations decay exponentially as a function of spin separation distance with a correlation length of approximately 5 Å. The diffuse magnetic scattering and corresponding mPDF show no significant changes across 𝑇 𝑓 , indicating that the dynamically fluctuating short-range spin correlations in the paramagnetic state retain the same basic type-III configuration that characterizes the spin-glass state; the only change apparent from the neutron-scattering data is a gradual reduction of the correlation length and locally ordered moment with increasing temperature. Taken together, these results paint a unique and detailed picture of the local magnetic structure and dynamics in Zn 0.5 ⁢Mn 0.5⁢ Te and provide strong evidence that this material is best described as a cluster spin glass. In addition, this work showcases a statistical method for extracting diffuse scattering signals from neutron powder diffraction data, which we developed to facilitate the mPDF and RMC analysis of the neutron data. This method has the potential to be broadly useful for neutron powder diffraction experiments on a variety of materials with short-range atomic or magnetic order.

magnetism↗
DOE OSTI2026

The S-PLUS Fifth Data Release: Over 4500 Square Degrees of the Southern Sky and a Multicolor View of the Hydra and Antlia Galaxy Clusters

Abstract We present the fifth data release (DR5) of the Southern Photometric Local Universe Survey (S-PLUS), covering 4592 deg 2 across 2491 fields. Observations were conducted with the T80-South, a Brazilian robotic telescope equipped with the Javalambre 12-filter system, containing five broadband and seven narrowband filters. Data products feature FITS images and extensive catalogs containing fluxes, magnitudes, and shape parameters for over 113 million detections. In addition, several value-added catalogs are provided, offering photometric redshifts (photo- zs ), object classifications, masks, and extinction coefficients. For the first time, this release includes coverage of 110 deg 2 along the Galactic disk, facilitating new research into Galactic structure and stellar populations. The release also provides full coverage of the Hydra Supercluster and numerous other nearby clusters with improved data reduction and calibration, enhancing photo- z accuracy, which is vital for large-scale structure studies. A preliminary analysis of the Hydra and Antlia galaxy clusters up to 5 × R 200 yields an updated catalog of 1706 cluster members based on both spectroscopic and high-quality photo- zs . Our photometric data shows that both clusters have a similar proportion of galaxies with an H α excess relative to their clustercentric distance, though Hydra has a higher fraction near its center. Additionally, the spatial distribution of all objects in our sample highlights a bridge connecting both clusters. We verify that S-PLUS DR5 provides a solid foundation for future scientific investigations, ranging from solar system studies to cosmology.

Vinicius Rodrigues de Lima, Erik [Universidade de ↗
DOE OSTI2025

Characterization of DESI fiber assignment incompleteness effect on 2-point clustering and mitigation methods for DR1 analysis

We present an in-depth analysis of the fiber assignment incompleteness in the Dark EnergySpectroscopic Instrument (DESI) Data Release 1 (DR1). This incompleteness is caused by therestricted mobility of the robotic fiber positioner in the DESI focal plane, which limits thenumber of galaxies that can be observed at the same time, especially at small angular separations.As a result, the observed clustering amplitude is suppressed in a scale-dependent manner, which,if not addressed, can severely impact the inference of cosmological parameters. We discuss themethods adopted for simulating fiber assignment on mocks and data. In particular, we introducethe fast fiber assignment (FFA) emulator, which was employed to obtain the power spectrumcovariance adopted for the DR1 full-shape analysis. We present the mitigation techniques,organised in two classes: measurement stage and model stage. We then use high fidelity mocks as areference to quantify both the accuracy of the FFA emulator and the effectiveness of the differentmeasurement-stage mitigation techniques. This complements the studies conducted in a parallelpaper for the model-stage techniques, namely the θ-cut approach. We find that pairwiseinverse probability (PIP) weights with angular upweighting recover the “true” clustering in allthe cases considered, in both Fourier and configuration space. Notably, we present the first everpower spectrum measurement with PIP weights from real data.

79 ASTRONOMY AND ASTROPHYSICS↗