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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

WE-E-BRE-11: New Method to Simulate DNA Damage Using Ionization Cross-Sections and a Geometrical Nucleosome Model

Purpose: To obtain probability distributions of various DNA damage types as a function of the incident electron kinetic energy. Methods: Using Geant4-DNA electron ionization cross-sections, we calculated path length distributions for electrons of energies between 10 eV and 1 MeV, defined as the length between two subsequent interactions. These path lengths were then convolved with probability distributions for the creation of same-strand damage, opposite-strand damage, clustered damage, isolated damage, and same DNA strand target damage. These probability distributions of DNA damage were obtained by a Monte Carlo routine calculating probabilities of interaction in DNA targets inside a nucleosome geometrical model. Results represent the probability of a secondary electron, initially created inside a DNA strand target, of undergoing its next interaction: (1) in the opposite strand (DSB), (2) in the same strand (SSB+), (3) in either the opposite or same-strand (clustered), (4) in the same DNA target (multiple-hit) or (5) more than 10 base pairs away (isolated). Results: Electrons with kinetic energy between 50 and 250 eV have a maximal probability of creating DSB, SSB+, clustered damage and multiple-hits in the same target The probabilities for these damage patterns have values of 2.5%, 4.3%, 6.7% and 5.4%, respectively. Isolated damage is most probable between 700 eV to 900 eV with a probability of 0.2%. Conclusion: We obtained DNA damage probability distributions as a function of electron incident energy. We showed that electrons with kinetic energies between 50 and 250 eV have the highest probability of producing complex forms of DNA damage (DSB, SSB+). We also showed that a double ionization within the same DNA target is the most frequent outcome occurring 5% of the time. It is expected that electron slowing down spectra can be convolved with our formalism to calculate source specific DNA damage patterns. Research grants from governments of Canada and Quebec. PP acknowledges partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council (Grant number: 432290)

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2019

Study of serious adverse drug reactions using FDA-approved drug labeling and MedDRA

Background Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP), and Adverse Reactions (AR), where the severity of ADRs are intended to decrease in the order of BW > WP > AR. Several reported studies have extracted ADRs from labeling documents, but most, if not all, did not discriminate the severity of the ADRs by the different labeling sections. Such a practice could overstate or underestimate the impact of certain ADRs to the public health. In this study, we applied the Medical Dictionary for Regulatory Activities (MedDRA) to drug labeling and systematically analyzed and compared the ADRs from the three labeling sections with a specific emphasis on analyzing serious ADRs presented in BW, which is of most drug safety concern. Results This study investigated New Drug Application (NDA) labeling documents for 1164 single-ingredient drugs using Oracle Text search to extract MedDRA terms. We found that only a small portion of MedDRA Preferred Terms (PTs), 3819 out of 21,920 or 17.42%, were observed in a whole set of documents. In detail, 466/3819 (12.0%) PTs were in BW, 2023/3819 (53.0%) were in WP, and 2961/3819 (77.5%) were in AR sections. We also found a higher overlap of top 20 occurring BW PTs with WP sections compared to AR sections. Within the MedDRA System Organ Class levels, serious ADRs (sADRs) from BW were prevalent in Nervous System disorders and Vascular disorders. A Hierarchical Cluster Analysis (HCA) revealed that drugs within the same therapeutic category shared the same ADR patterns in BW (e.g., nervous system drug class is highly associated with drug abuse terms such as dependence, substance abuse, and respiratory depression). Conclusions This study demonstrated that combining MedDRA standard terminologies with data mining techniques facilitated computer-aided ADR analysis of drug labeling. We also highlighted the importance of labeling sections that differ in seriousness and application in drug safety. Using sADRs primarily related to BW sections, we illustrated a prototype approach for computer-aided ADR monitoring and studies which can be applied to other public health documents.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

Mars: Morphology of Southern Hemisphere intracrater dunefields

Viking Orbiter images of intracrater dunefields in the Noachis Terra region were examined in order to study the morphology of these landforms and to assess their relationship to local geological settings. The sizes of the dunefields range from 40 to 3600 sq km and vary directly with crater size. Preliminary studies reveal dunefields of two varieties. The most common type is composed of massed straight to slightly wavy crescentic dunes similar to those described by Breed. Dunefields of this type occupy more than 20% of the area of the crater floor, with the dunefield margins often marked by a large dune wall or rampart. Dune spacing ranges between 0.7 and 1.2 km. The second type of dune accumulation consists of clusters of large, widely spaced straight or curved ridges, which often intersect to create rectilinear patterns. Dunes are typically spaced 1.6 to 4 km apart. Earth terrestrial analogs for these dunes are discussed.

Lancaster, N.↗
NASA NTRS1992

Off-center nuclei in galaxies

The nucleus of a galaxy orbits around the mass centroid. Orbital motions appear overstable in numerical experiments started with a galaxy's nucleus at rest atop its mass centroid. The amplitude doubles in 6-10 orbital periods. Orbits precess, nutate, and change their amplitudes, but they keep fairly constant periods. Orbital periods are in resonance with local particle motions, and amplitudes reach a core radius. This resonance suggests that center motions are a local, rather than a global, phenomenon. The overstability implies that a galaxy cannot be formed in nature with its nucleus at rest atop its mass centroid, and that nuclei orbit the mass centroid in real galaxies. These center motions should show up observationally as a shift of the nucleus away from the center defined by nearby isophotes. Off-center nuclei have been reported in many galaxies (e.g., M33, M101, NGC 3379, NGC 3384). Other kinds of observations confirmed the picture of nonsteady galactic centers as well. Gas trapped in moving nuclear regions of a galaxy should show strange flow patterns with possible shocks. The nuclear regions of galaxies including Milky Way and of globular clusters are not likely to be in a static steady state.

Miller, R. H.↗
NASA NTRS1991

Sensor fusion techniques for predicting thunderstorm evolution using lightning and radar networks

A pattern recognition scheme that is used to generate initial seeds or 'first guess' fields for clustering the discrete lightning discharges into storm cells is presented. The clustering process is critically dependent on the prior accuracy of the lightning location estimates. The generation of subsequent storm life-cycle time series (for extrapolation forecasting) also relies on the cluster analysis procedure assigning the correct number of lightning discharges (objects) to the proper storms (groups). The advantages and limitations of different clustering strategies for storm identification and tracking are examined. Storm identification with lightning data alone is compared to storm identification with radar alone, and some synergies for sensor fusion are explored.

Goodman, Steven J.↗
NASA NTRS1999

X-Ray Fingerprinting Techniques for Recognizing A Hydrological Role in the Formation of Minerals on the Surface of Mars

Previous work has demonstrated the ability of a miniaturized XRD-XRF instrument to perform in-situ analyses without sample preparation or acquisition. Deployment of this instrument on a Martian rover will allow a large number of rapid qualitative analyses, which will maximize the diversity of samples studied and selected for possible return. As a first step in designing a decision tree for recognizing minerals in complex mixtures, d spacings were plotted against intensity for several mineral groups comprising rock and soil types inferred for the surface of Mars (weathered basalt, playa and hydrothermal deposits, clay-rich soils). In all groups, d spacings cluster in a range from about 1-4 angstroms, which can under certain circumstances obscure patterns for individual phases. However, within the silicate family, minerals containing either bound OH- or molecules of H20 (clays, micas, amphiboles, zeolites) are characterized by a shift of peaks to higher d spacings. Large d spacings (greater than about 7 angstroms) thus act as a first-order filter for distinguishing hydrous from anhydrous silicates. The ability to quickly verify the presence of silicates that have interacted with water has important implications for using mineral chemistry and structure to help decipher the hydrologic and atmospheric history of Mars. This represents a beginning for developing more sophisticated methods of pattern recognition. These will combine XRD and XRF analyses with optical data to rapidly7 discern environmentally diagnostic assemblages without the necessity of identifying every peak individual mineral phase.

Metzger, Ellen P.↗
NASA NTRS1992

Origin and early evolution of photosynthesis

Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the earth's history, and that a presumed phase of evolution involving non-oxygen evolving photosynthetic organisms took place even earlier. The evolutionary relationships of the reaction center complexes found in all the classes of currently existing organisms have been analyzed using sequence analysis and biophysical measurements. The results indicate that all reaction centers fall into two basic groups, those with pheophytin and a pair of quinones as early acceptors, and those with iron sulfur clusters as early acceptors. No simple linear branching evolutionary scheme can account for the distribution patterns of reaction centers in existing photosynthetic organisms, and lateral transfer of genetic information is considered as a likely possibility. Possible scenarios for the development of primitive reaction centers into the heterodimeric protein structures found in existing reaction centers and for the development of organisms with two linked photosystems are presented.

NASA Program Exobiology↗
DOE OSTI2015

Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfven timescales. Some ELM events are active for less than 100~microsec, but others persist for up to 1~ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Spring Dust in Colorado Plateau: Transport Pathways and Interannual Variability Derived From Two Decades of MERRA‐2 Reanalysis

Spring dust storms in the U.S. Southwest significantly impact environmental and human systems, yet their climatological patterns and driving mechanisms remain poorly understood. Using two decades of MERRA-2 reanalysis data and self-organizing map clustering, we identified four distinct dust transport pathways from surrounding and remote deserts for the top 10% of spring dust events impacting the Colorado Plateau: (a) intense southwesterly near-surface transport where eastward upward transport is blocked by topography, (b) substantial remote transport plus weaker surface emissions, (c) moderate southwesterly transport with stronger upper-level transport, and (d) rare northwesterly pattern linked to the Great Basin sources, which accounts for 38%, 14%, 37%, and 11% of total events, respectively. The frequency and intensity of these events strongly correlate with large-scale climate variability, with increased dust events during La Niña. Our results provide a robust framework for improving seasonal dust forecasts and understanding future dust dynamics under climate change.

aerosol transport↗
DOE OSTI2013

TWO DISTINCT RED GIANT BRANCH POPULATIONS IN THE GLOBULAR CLUSTER NGC 2419 AS TRACERS OF A MERGER EVENT IN THE MILKY WAY

Recent spectroscopic observations of the outer halo globular cluster (GC) NGC 2419 show that it is unique among GCs, in terms of chemical abundance patterns, and some suggest that it was originated in the nucleus of a dwarf galaxy. Here we show, from the Subaru narrowband photometry employing a calcium filter, that the red giant branch (RGB) of this GC is split into two distinct subpopulations. Comparison with spectroscopy has confirmed that the redder RGB stars in the hk[=(Ca–b) – (b – y)] index are enhanced in [Ca/H] by ∼0.2 dex compared to the bluer RGB stars. Our population model further indicates that the calcium-rich second generation stars are also enhanced in helium abundance by a large amount (ΔY = 0.19). Our photometry, together with the results for other massive GCs (e.g., ω Cen, M22, and NGC 1851), suggests that the discrete distribution of RGB stars in the hk index might be a universal characteristic of this growing group of peculiar GCs. The planned narrowband calcium photometry for the Local Group dwarf galaxies would help to establish an empirical connection between these GCs and the primordial building blocks in the hierarchical merging paradigm of galaxy formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

WEAK GRAVITATIONAL LENSING AS A PROBE OF PHYSICAL PROPERTIES OF SUBSTRUCTURES IN DARK MATTER HALOS

We propose a novel method to select satellite galaxies in outer regions of galaxy groups or clusters using weak gravitational lensing. The method is based on the theoretical expectation that the tangential shear pattern around satellite galaxies would appear with negative values at an offset distance from the center of the main halo. We can thus locate the satellite galaxies statistically with an offset distance of several lensing smoothing scales by using the standard reconstruction of surface mass density maps from weak lensing observation. We test the idea using high-resolution cosmological simulations. We show that subhalos separated from the center of the host halo are successfully located even without assuming the position of the center. For a number of such subhalos, the characteristic mass and offset length can be also estimated on a statistical basis. We perform a Fisher analysis to show how well upcoming weak lensing surveys can constrain the mass density profile of satellite galaxies. In the case of the Large Synoptic Survey Telescope with a sky coverage of 20,000 deg{sup 2}, the mass of the member galaxies in the outer region of galaxy clusters can be constrained with an accuracy of ∼0.1 dex for galaxy clusters with mass 10{sup 14} h {sup –1} M {sub ☉} at z = 0.15. Finally we explore the detectability of tidal stripping features for subhalos having a wide range of masses of 10{sup 11}-10{sup 13} h {sup –1} M {sub ☉}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Sub-10 nm Probing of Ferroelectricity in Heterogeneous Materials by Machine Learning Enabled Contact Kelvin Probe Force Microscopy

Reducing the dimensions of ferroelectric materials down to the nanoscale has strong implications on the ferroelectric polarization pattern and on the ability to switch the polarization. As the size of ferroelectric domains shrinks to the nanometer scale, the heterogeneity of the polarization pattern becomes increasingly pronounced, enabling a large variety of possible polar textures in nanocrystalline and nanocomposite materials. Critical to the understanding of fundamental physics of such materials and hence their applications in electronic nanodevices is the ability to investigate their ferroelectric polarization at the nanoscale in a nondestructive way. We show that contact Kelvin probe force microscopy (cKPFM) combined with a k-means response clustering algorithm enables to measure the ferroelectric response at a mapping resolution of 8 nm. In a BaTiO 3 thin film on silicon composed of tetragonal and hexagonal nanocrystals, we determine a nanoscale lateral distribution of discrete ferroelectric response clusters, fully consistent with the nanostructure determined by transmission electron microscopy. Moreover, we apply this data clustering method to the cKPFM responses measured at different temperatures, which allows us to follow the corresponding change in the polarization pattern as the Curie temperature is approached and across the phase transition. This work opens up perspectives for mapping complex ferroelectric polarization textures such as curled/swirled polar textures that can be stabilized in epitaxial heterostructures and more generally for mapping the polar domain distribution of any spatially highly heterogeneous ferroelectric materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Numerical experiments with model monophyletic and paraphyletic taxa

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

Non-NASA Center↗
NASA NTRS2004

Using Fuzzy Clustering for Real-time Space Flight Safety

To ensure space flight safety, it is necessary to monitor myriad sensor readings on the ground and in flight. Since a space shuttle has many sensors, monitoring data and drawing conclusions from information contained within the data in real time is challenging. The nature of the information can be critical to the success of the mission and safety of the crew and therefore, must be processed with minimal data-processing time. Data analysis algorithms could be used to synthesize sensor readings and compare data associated with normal operation with the data obtained that contain fault patterns to draw conclusions. Detecting abnormal operation during early stages in the transition from safe to unsafe operation requires a large amount of historical data that can be categorized into different classes (non-risk, risk). Even though the 40 years of shuttle flight program has accumulated volumes of historical data, these data don t comprehensively represent all possible fault patterns since fault patterns are usually unknown before the fault occurs. This paper presents a method that uses a similarity measure between fuzzy clusters to detect possible faults in real time. A clustering technique based on a fuzzy equivalence relation is used to characterize temporal data. Data collected during an initial time period are separated into clusters. These clusters are characterized by their centroids. Clusters formed during subsequent time periods are either merged with an existing cluster or added to the cluster list. The resulting list of cluster centroids, called a cluster group, characterizes the behavior of a particular set of temporal data. The degree to which new clusters formed in a subsequent time period are similar to the cluster group is characterized by a similarity measure, q. This method is applied to downlink data from Columbia flights. The results show that this technique can detect an unexpected fault that has not been present in the training data set.

Lee, Charles↗
NASA NTRS2005

Probabilisitc Geobiological Classification Using Elemental Abundance Distributions and Lossless Image Compression in Recent and Modern Organisms

Last year we presented techniques for the detection of fossils during robotic missions to Mars using both structural and chemical signatures[Storrie-Lombardi and Hoover, 2004]. Analyses included lossless compression of photographic images to estimate the relative complexity of a putative fossil compared to the rock matrix [Corsetti and Storrie-Lombardi, 2003] and elemental abundance distributions to provide mineralogical classification of the rock matrix [Storrie-Lombardi and Fisk, 2004]. We presented a classification strategy employing two exploratory classification algorithms (Principal Component Analysis and Hierarchical Cluster Analysis) and non-linear stochastic neural network to produce a Bayesian estimate of classification accuracy. We now present an extension of our previous experiments exploring putative fossil forms morphologically resembling cyanobacteria discovered in the Orgueil meteorite. Elemental abundances (C6, N7, O8, Na11, Mg12, Ai13, Si14, P15, S16, Cl17, K19, Ca20, Fe26) obtained for both extant cyanobacteria and fossil trilobites produce signatures readily distinguishing them from meteorite targets. When compared to elemental abundance signatures for extant cyanobacteria Orgueil structures exhibit decreased abundances for C6, N7, Na11, All3, P15, Cl17, K19, Ca20 and increases in Mg12, S16, Fe26. Diatoms and silicified portions of cyanobacterial sheaths exhibiting high levels of silicon and correspondingly low levels of carbon cluster more closely with terrestrial fossils than with extant cyanobacteria. Compression indices verify that variations in random and redundant textural patterns between perceived forms and the background matrix contribute significantly to morphological visual identification. The results provide a quantitative probabilistic methodology for discriminating putatitive fossils from the surrounding rock matrix and &om extant organisms using both structural and chemical information. The techniques described appear applicable to the geobiological analysis of meteoritic samples or in situ exploration of the Mars regolith. Keywords: cyanobacteria, microfossils, Mars, elemental abundances, complexity analysis, multifactor analysis, principal component analysis, hierarchical cluster analysis, artificial neural networks, paleo-biosignatures

Storrie-Lombardi, Michael C.↗
DOE OSTI2014

Lithium abundances in globular cluster giants: NGC 6218 (M12) and NGC 5904 (M5)

Convergent lines of evidence suggest that globular clusters host multiple stellar populations. It appears that they experience at least two episodes of star formation whereby a fraction of first-generation stars contribute astrated ejecta to form the second generation(s). To identify the polluting progenitors, we require distinguishing chemical signatures such as that provided by lithium. Theoretical models predict that lithium can be synthesized in AGB stars, whereas no net Li production is expected from other candidates. It has been shown that in order to reproduce the abundance pattern found in M4, Li production must occur within the polluters, favoring the AGB scenario. Here, we present Li and Al abundances for a large sample of RGB stars in M12 and M5. These clusters have a very similar metallicity, while demonstrating differences in several cluster properties. Our results indicate that the first-generation and second-generation stars share the same Li content in M12; we recover an abundance pattern similar to that observed in M4. In M5, we find a higher degree of complexity, and a simple dilution model fails in reproducing the majority of the stellar population. In both clusters, we require Li production across the different stellar generations, but production seems to have occurred to different extents. We suggest that such a difference might be related to the cluster mass with the Li production being more efficient in less-massive clusters. This is the first time a statistically significant correlation between the Li spread within a GC and its luminosity has been demonstrated. Finally, although Li-producing polluters are required to account for the observed pattern, other mechanisms, such as MS depletion, might have played a role in contributing to the Li internal variation, though at a relatively low level.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids

Abstract Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Influence of solar forcing, climate variability and modes of low-frequency atmospheric variability on summer floods in Switzerland

The higher frequency of severe flood events in Switzerland in recent decades has given fresh impetus to the study of flood patterns and their possible forcing mechanisms, particularly in mountain environments. This paper presents a new index of summer flood damage that considers severe and catastrophic summer floods in Switzerland between 1800 and 2009, and explores the influence of external forcings on flood frequencies. In addition, links between floods and low-frequency atmospheric variability patterns are examined. The flood damage index provides evidence that the 1817–1851, 1881–1927, 1977–1990 and 2005–present flood clusters occur mostly in phase with palaeoclimate proxies. The cross-spectral analysis documents that the periodicities detected in the coherency and phase spectra of 11 (Schwabe cycle) and 104 years (Gleissberg cycle) are related to a high frequency of flooding and solar activity minima, whereas the 22-year cyclicity detected (Hale cycle) is associated with solar activity maxima and a decrease in flood frequency. The analysis of low-frequency atmospheric variability modes shows that Switzerland lies close to the border of the principal summer mode. The Swiss river catchments situated on the centre and southern flank of the Alps are affected by atmospherically unstable areas defined by the positive phase of the pattern, while those basins located in the northern slope of the Alps are predominantly associated with the negative phase of the pattern. Furthermore, a change in the low-frequency atmospheric variability pattern related to the major floods occurred over the period from 1800 to 2009; the summer principal mode persists in the negative phase during the last cool pulses of the Little Ice Age (1817–1851 and 1881–1927 flood clusters), whereas the positive phases of the mode prevail during the warmer climate of the last 4 decades (flood clusters from 1977 to present).

54 ENVIRONMENTAL SCIENCES↗