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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina

The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Spatial inventory integrating raster databases and point sample data

A timber inventory of the Eldorado National Forest, located in east-central California, provides an example of the use of a Geographic Information System (GIS) to stratify large areas of land for sampling and the collection of statistical data. The raster-based GIS format of the VICAR/IBIS software system allows simple and rapid tabulation of areas, and facilitates the selection of random locations for ground sampling. Algorithms that simplify the complex spatial pattern of raster-based information, and convert raster format data to strings of coordinate vectors, provide a link to conventional vector-based geographic information systems.

Strahler, A. H.↗
NASA NTRS1987

Characterization of fault recovery through fault injection on FTMP

The development of fault-injection procedures and statistical analysis techniques to characterize the fault recovery of fault-tolerant systems is described. Pin-level fault-injection was conducted on a fault-tolerant microprocessor computer in order to generate data to assess the utility of current fault-injection sampling methods. The validity of common reliability-modeling assumptions concerning the statistical distribution of recovery times is investigated. A multiple comparison analysis for detecting behavior variations, and a distribution fitting for determining the best fit for the data were conducted. It is observed that the detection behavior is not homogeneous across all data sets, and that none of the factors under experimental control can account for the observed groupings of behavior. It is determined that no single distribution fits all the data sets, and that stratified random sampling and statistically robust parameter-estimation techniques are required to characterize fault detection time.

Finelli, George B.↗
DOE OSTI2019

Synchrotron X-Ray Microdiffraction Investigation of Scaling Effects on Reliability for Through-Silicon Vias for 3-D Integration

Synchrotron x-ray microdiffraction has been applied to TSV characterization in various studies for nondestructive inspection with submicron resolution due to its high beam intensity and penetration depth. Here, the application of this technique to TSV investigations is examined and the correlation of the plastic deformation to the microstructure and extrusion behavior along with the effect of TSV dimensional scaling is examined. It is shown that the variability of the copper microstructure and resulting TSV behavior requires a larger number of samples in order to report statistically significant observations. The role of the microstructure in creating statistical scatter is demonstrated through microdiffraction measurements of grain orientation correlated with the observed peak widening, which shows that degraded TSV reliability is largely due to the high elastic anisotropy of copper. After taking the statistical variations into account, the scaling effect was clearly observed, with larger plastic deformation in 2μm diameter TSVs than in 5μm diameter TSVs consistent with microstructure variations. This is confirmed by TSV extrusion measurements, which show that the magnitude and statistical spread of the via extrusion for the 2μm diameter TSVs is higher than that of the 5μm diameter TSVs. These findings, confirmed by thermomechanical simulation, demonstrate first that large sample sizes are required in copper TSV investigations due to high variability, which is not improved with scaling.

36 MATERIALS SCIENCE↗
DOE OSTI2018

A Ricin Forensic Profiling Approach Based on a Complex Set of Biomarkers

A forensic method for the retrospective determination of preparation methods used for illicit ricin toxin production was developed. The method was based on a complex set of biomarkers, including carbohydrates, fatty acids, seed storage proteins, in combination with data on ricin and Ricinus communis agglutinin. The analyses were performed on samples prepared from four castor bean plant ( Ricinus communis ) cultivars by four different sample preparation methods (PM1 – PM4) ranging from simple disintegration of the castor beans to multi-step preparation methods including different protein precipitation methods. Comprehensive analytical data was collected by use of a range of analytical methods and robust orthogonal partial least squares-discriminant analysis- models (OPLS-DA) were constructed based on the calibration set. By the use of a decision tree and two OPLS-DA models, the sample preparation methods of a test set of ricin preparations were determined. The model statistics of the two models were good and a 100% rate of correct predictions of the test set was achieved.

Fredriksson, Sten-Åke (ORCID:0000000237131990)↗
DOE OSTI2015

Defining window-boundaries for genomic analyses using smoothing spline techniques

High-density genomic data is often analyzed by combining information over windows of adjacent markers. Interpretation of data grouped in windows versus at individual locations may increase statistical power, simplify computation, reduce sampling noise, and reduce the total number of tests performed. However, use of adjacent marker information can result in over- or under-smoothing, undesirable window boundary specifications, or highly correlated test statistics. We introduce a method for defining windows based on statistically guided breakpoints in the data, as a foundation for the analysis of multiple adjacent data points. This method involves first fitting a cubic smoothing spline to the data and then identifying the inflection points of the fitted spline, which serve as the boundaries of adjacent windows. This technique does not require prior knowledge of linkage disequilibrium, and therefore can be applied to data collected from individual or pooled sequencing experiments. Moreover, in contrast to existing methods, an arbitrary choice of window size is not necessary, since these are determined empirically and allowed to vary along the genome.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

A new method for simulating atmospheric turbulence for rotorcraft applications

Simulation of atmospheric turbulence as seen by a rotating blade element involves treatment of cyclostationary processes. Conventional filtering techniques do not lend themselves well to the generation of such turbulence sample functions as are required in rotorcraft flight dynamics simulation codes. A method to generate sample functions containing second order statistics of mean and covariance is presented. Compared to ensemble averaging involving excessive computer time, the novelty is to exploit cycloergodicity and thereby, replace ensemble averaging by averaging over a single path sample function of long duration. The method is validated by comparing its covariance results with the analytical and ensemble averaged results for a widely used 1-D turbulence approximation.

J. Riaz↗
NASA NTRS2011

Multi-Sensor Aerosol Products Sampling System

Global and local properties of atmospheric aerosols have been extensively observed and measured using both spaceborne and ground-based instruments, especially during the last decade. Unique properties retrieved by the different instruments contribute to an unprecedented availability of the most complete set of complimentary aerosol measurements ever acquired. However, some of these measurements remain underutilized, largely due to the complexities involved in analyzing them synergistically. To characterize the inconsistencies and bridge the gap that exists between the sensors, we have established a Multi-sensor Aerosol Products Sampling System (MAPSS), which consistently samples and generates the spatial statistics (mean, standard deviation, direction and rate of spatial variation, and spatial correlation coefficient) of aerosol products from multiple spacebome sensors, including MODIS (on Terra and Aqua), MISR, OMI, POLDER, CALIOP, and SeaWiFS. Samples of satellite aerosol products are extracted over Aerosol Robotic Network (AERONET) locations as well as over other locations of interest such as those with available ground-based aerosol observations. In this way, MAPSS enables a direct cross-characterization and data integration between Level-2 aerosol observations from multiple sensors. In addition, the available well-characterized co-located ground-based data provides the basis for the integrated validation of these products. This paper explains the sampling methodology and concepts used in MAPSS, and demonstrates specific examples of using MAPSS for an integrated analysis of multiple aerosol products.

Petrenko, M.↗
DOE OSTI2015

Statistical scaling of geometric characteristics in stochastically generated pore microstructures

In this study, we analyze the statistical scaling of structural attributes of virtual porous microstructures that are stochastically generated by thresholding Gaussian random fields. Characterization of the extent at which randomly generated pore spaces can be considered as representative of a particular rock sample depends on the metrics employed to compare the virtual sample against its physical counterpart. Typically, comparisons against features and/patterns of geometric observables, e.g., porosity and specific surface area, flow-related macroscopic parameters, e.g., permeability, or autocorrelation functions are used to assess the representativeness of a virtual sample, and thereby the quality of the generation method. Here, we rely on manifestations of statistical scaling of geometric observables which were recently observed in real millimeter scale rock samples [13] as additional relevant metrics by which to characterize a virtual sample. We explore the statistical scaling of two geometric observables, namely porosity (Φ) and specific surface area (SSA), of porous microstructures generated using the method of Smolarkiewicz and Winter [42] and Hyman and Winter [22]. Our results suggest that the method can produce virtual pore space samples displaying the symptoms of statistical scaling observed in real rock samples. Order q sample structure functions (statistical moments of absolute increments) of Φ and SSA scale as a power of the separation distance (lag) over a range of lags, and extended self-similarity (linear relationship between log structure functions of successive orders) appears to be an intrinsic property of the generated media. The width of the range of lags where power-law scaling is observed and the Hurst coefficient associated with the variables we consider can be controlled by the generation parameters of the method.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Priors on red galaxy stochasticity from hybrid effective field theory

ABSTRACT We investigate the stochastic properties of typical red galaxy samples in a controlled numerical environment. We use halo occupation distribution (HOD) modelling to create mock realizations of three separate bright red galaxy samples consistent with data sets used for clustering and lensing analyses in modern galaxy surveys. Second-order Hybrid Effective Field Theory (HEFT) is used as a field-level forward model to describe the full statistical distribution of these tracer samples, and their stochastic power spectra are directly measured and compared to the Poisson shot-noise prediction. While all of the galaxy samples we consider are hosted within haloes with sub-Poisson stochasticity, we observe that the galaxy samples themselves possess stochasticities that range from sub-Poisson to super-Poisson, in agreement with predictions from the halo model. As an application of our methodology, we place priors on the expected degree of non-Poisson stochasticity in cosmological analyses using such samples. We expect these priors will be useful in reducing the complexity of the full parameter space for future analyses using second-order Lagrangian bias models. More generally, the techniques outlined here present the first application of HEFT methods to characterize models of the galaxy–halo connection at the field level, revealing new connections between once-disparate modelling frameworks.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

THE SWIFT AGN AND CLUSTER SURVEY. II. CLUSTER CONFIRMATION WITH SDSS DATA

We study 203 (of 442) Swift AGN and Cluster Survey extended X-ray sources located in the SDSS DR8 footprint to search for galaxy over-densities in three-dimensional space using SDSS galaxy photometric redshifts and positions near the Swift cluster candidates. We find 104 Swift clusters with a >3σ galaxy over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmation as galaxy clusters. We present a series of cluster properties including the redshift, brightest cluster galaxy (BCG) magnitude, BCG-to-X-ray center offset, optical richness, and X-ray luminosity. We also detect red sequences in ∼85% of the 104 confirmed clusters. The X-ray luminosity and optical richness for the SDSS confirmed Swift clusters are correlated and follow previously established relations. The distribution of the separations between the X-ray centroids and the most likely BCG is also consistent with expectation. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≲ 0.3 and is still 80% complete up to z ≃ 0.4, consistent with the SDSS survey depth. These analysis results suggest that our Swift cluster selection algorithm has yielded a statistically well-defined cluster sample for further study of cluster evolution and cosmology. We also match our SDSS confirmed Swift clusters to existing cluster catalogs, and find 42, 23, and 1 matches in optical, X-ray, and Sunyaev–Zel’dovich catalogs, respectively, and so the majority of these clusters are new detections.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks

Studies of microbial communities by targeted sequencing of rRNA genes lead to recovering numerous rare low-abundance taxa with unknown biological roles. We propose to study associations of such rare organisms with their environments by a computational framework based on transformation of the data into qualitative variables. Namely, we analyze the sparse table of putative species or OTUs (operational taxonomic units) and samples generated in such studies, also known as an OTU table, by collecting statistics on co-occurrences of the species and on shared species richness across samples. Based on the statistics we built two association networks, of the rare putative species and of the samples respectively, using a known computational technique, Association networks (Anets) developed for analysis of qualitative data. Clusters of samples and clusters of OTUs are then integrated and combined with metadata of the study to produce a map of associated putative species in their environments. We tested and validated the framework on two types of microbiomes, of human body sites and that of the Populus tree root systems. We show that in both studies the associations of OTUs can separate samples according to environmental or physiological characteristics of the studied systems.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1989

Chi-squared and C statistic minimization for low count per bin data

Results are presented from a computer simulation comparing two statistical fitting techniques on data samples with large and small counts per bin; the results are then related specifically to X-ray astronomy. The Marquardt and Powell minimization techniques are compared by using both to minimize the chi-squared statistic. In addition, Cash's C statistic is applied, with Powell's method, and it is shown that the C statistic produces better fits in the low-count regime than chi-squared.

Nousek, John A.↗
DOE OSTI2020

CCCP and MENeaCS: (updated) weak-lensing masses for 100 galaxy clusters

ABSTRACT Large area surveys continue to increase the samples of galaxy clusters that can be used to constrain cosmological parameters, provided that the masses of the clusters are measured robustly. To improve the calibration of cluster masses using weak gravitational lensing we present new results for 48 clusters at 0.05 < z < 0.15, observed as part of the Multi Epoch Nearby Cluster Survey, and re-evaluate the mass estimates for 52 clusters from the Canadian Cluster Comparison Project. Updated high-fidelity photometric redshift catalogues of reference deep fields are used in combination with advances in shape measurements and state-of-the-art cluster simulations, yielding an average systematic uncertainty in the lensing signal below 5 per cent, similar to the statistical uncertainty for our cluster sample. We derive a scaling relation with Planck measurements for the full sample and find a bias in the Planck masses of 1 − b = 0.84 ± 0.04 (stat) ±0.05 (syst). We find no statistically significant trend of the mass bias with redshift or cluster mass, but find that different selections could change the bias by up to 0.07. We find a gas fraction of 0.139 ± 0.014 (stat) for eight relaxed clusters in our sample, which can also be used to infer cosmological parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRSDate not supplied

Impact Real World System Validation

Introduction NASA has developed a new evidence-based data-driven probabilistic risk assessment and tradespace analysis tool as a successor to the Integrated Medical Model. This updated decision support tool is known as IMPACT (Informing Mission Planning via Analysis of Complex Tradespaces). IMPACT estimates the frequency and consequences of medical conditions that might arise during exploration missions. A validation analysis of IMPACT was performed with respect to a set of International Space Station (ISS) and Shuttle Transportation System (STS) real world system (RWS) referent data due to the limited referent data available from exploration missions. Methods Observed mission and crew characteristics from STS and ISS missions were used as model inputs within MEDPRAT (Medical Extensible Dynamic Probabilistic Risk Assessment Tool). For each mission, two hundred thousand simulations were generated. For each mission, model outputs included occurrence counts for each condition, total medical events (TME), and the probability of loss of crew life (LOCL). These simulated model outputs were compared to the RWS referent data. Results The predicted number of total medical events exceeded the total RWS medical events for ISS missions and combined ISS and STS missions and fell within the 90% confidence interval for STS missions. For the 32 ISS missions simulated by IMPACT, the number of total medical events was overpredicted for 19 missions and fell within the 90% confidence interval for 13 missions. For the 21 STS missions, the total number of medical events was overpredicted for 3 missions, fell within the 90% confidence interval for 16 missions, and was underpredicted for 2 missions. Combined, 29 missions were in range, 22 were overpredicted, and 2 were underpredicted. The predicted LOCL probability for the 32 ISS missions, the 21 STS missions, and the combined ISS and STS missions was consistent with the zero LOCL events observed in the RWS referent data. The validation analysis included a comparison of the number of medical events predicted by IMPACT and the number of medical events observed in the RWS data on a condition-by-condition basis. For ISS missions, 50 conditions were in range, 52 conditions were statistically underpowered (not enough observed sample to draw any conclusions on precision), 8 conditions were overpredicted, and 9 conditions were underpredicted. Overall, only 14% (17/119) of conditions were out of range for STS missions, 40 conditions were in range, 59 conditions were statistically underpowered, 10 conditions were overpredicted, and 10 conditions were underpredicted. Overall, only 17% (20/119) of conditions were out of range. For combined ISS and STS missions, 11 conditions were overpredicted, and 11 conditions were underpredicted. Overall, only 18% (22/119) of conditions were out of range. For combined ISS and STS missions, 49 conditions were in range, 46 conditions were statistically underpowered, 18 conditions were overpredicted, and 8 conditions were underpredicted. Overall, 21% (26/121) of conditions were out of range. Conclusion The results of this validation analysis should not be interpreted as a pass/fail test of the validity of IMPACT. Instead, this validation analysis should be used to assess some of the IMPACT outcomes in terms of consistencies and inconsistencies with the ISS and STS RWS referent data.

L. Boley↗
DOE OSTI2012

CORRELATION ANALYSIS OF A LARGE SAMPLE OF NARROW-LINE SEYFERT 1 GALAXIES: LINKING CENTRAL ENGINE AND HOST PROPERTIES

We present a statistical study of a large, homogeneously analyzed sample of narrow-line Seyfert 1 (NLS1) galaxies, accompanied by a comparison sample of broad-line Seyfert 1 (BLS1) galaxies. Optical emission-line and continuum properties are subjected to correlation analyses, in order to identify the main drivers of the correlation space of active galactic nuclei (AGNs), and of NLS1 galaxies in particular. For the first time, we have established the density of the narrow-line region as a key parameter in Eigenvector 1 space, as important as the Eddington ratio L/L{sub Edd}. This is important because it links the properties of the central engine with the properties of the host galaxy, i.e., the interstellar medium (ISM). We also confirm previously found correlations involving the line width of H{beta} and the strength of the Fe II and [O III] {lambda}5007 emission lines, and we confirm the important role played by L/L{sub Edd} in driving the properties of NLS1 galaxies. A spatial correlation analysis shows that large-scale environments of the BLS1 and NLS1 galaxies of our sample are similar. If mergers are rare in our sample, accretion-driven winds, on the one hand, or bar-driven inflows, on the other hand, may account for the strong dependence of Eigenvector 1 on ISM density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

MEASURING X-RAY VARIABILITY IN FAINT/SPARSELY SAMPLED ACTIVE GALACTIC NUCLEI

We study the statistical properties of the normalized excess variance of variability process characterized by a ''red-noise'' power spectral density (PSD), as in the case of active galactic nuclei (AGNs). We perform Monte Carlo simulations of light curves, assuming both a continuous and a sparse sampling pattern and various signal-to-noise ratios (S/Ns). We show that the normalized excess variance is a biased estimate of the variance even in the case of continuously sampled light curves. The bias depends on the PSD slope and on the sampling pattern, but not on the S/N. We provide a simple formula to account for the bias, which yields unbiased estimates with an accuracy better than 15%. We show that the normalized excess variance estimates based on single light curves (especially for sparse sampling and S/N < 3) are highly uncertain (even if corrected for bias) and we propose instead the use of an ''ensemble estimate'', based on multiple light curves of the same object, or on the use of light curves of many objects. These estimates have symmetric distributions, known errors, and can also be corrected for biases. We use our results to estimate the ability to measure the intrinsic source variability in current data, and show that they could also be useful in the planning of the observing strategy of future surveys such as those provided by X-ray missions studying distant and/or faint AGN populations and, more in general, in the estimation of the variability amplitude of sources that will result from future surveys such as Pan-STARRS and LSST.

79 ASTRONOMY AND ASTROPHYSICS↗