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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

JIRIAF: JLAB Integrated Research Infrastructure Acros Facilities

The JIRIAF project aims to combine geographically diverse computing facilities into an integrated science infrastructure. This project starts by dynamically evaluating temporarily unallocated or idled compute resources from multiple providers. These resources are integrated to handle additional workloads without affecting local running jobs. This paper describes our approach to launch best-effort batch tasks which exploit these underutilized resources. Our system measures the real-time behavior of jobs running on a machine and learns to distinguish typical performance from outliers. Unsupervised ML techniques are used to analyze hardware-level performance measures, followed by a real-time cross-correlation analysis to determine which applications cause performance degradation. We then ameliorate bad behavior by throttling these processes. We demonstrate that problematic performance interference can be detected and acted on, which makes it possible to continue to share resources between applications and simultaneously maintain high utilization levels in a computing cluster. We relocate the CLAS12 data processing workflow to a remote data center for a case study, preventing file migration and temporal data persistency.

Lawrence, David↗
DOE OSTI2020

Binary Stars in Upper Scorpius

To address the statistics of binary stars in the 8 Myr old Upper Scorpius (USco) star formation region, we conducted a speckle interferometric survey of 614 association members more massive than 0.4 M{sub ⊙} (spectral types earlier than M3V) based on the list of Luhman et al. (2018). We resolved 187 pairs, 55 of which are new discoveries. Also using the published data and the Gaia DR2, a catalog of 250 physical binaries was produced. We carefully estimated detection limits for each target and studied binary statistics in the separation range from 0.″06 to 20″ (9–2800 au), as well as clustering at larger separations. The frequency of companions with mass ratios q > 0.3 in this separation range is 0.33 ± 0.04 and 0.35 ± 0.04 for early M- and solar-type stars, respectively, larger by 1.62 ± 0.22 and 1.39 ± 0.18 times compared to field stars of similar masses. The excess is produced mostly by pairs closer than 100 au. At separations from 100 to 10{sup 4} au, the separation distribution and companion fraction resemble those of solar-type stars in the field. However, unlike in the field, we see a relative deficit of equal-mass binaries at separations of ∼500 au, compared to smaller and larger separations. The distribution of q depends on the separation, with a preference of larger q and a larger fraction of twins with q > 0.95 at smaller separations. The binary population of USco differs from binaries in the field in several ways and suggests that binary statistics is not universal.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1987

Rotational velocities of low-mass stars in the Hyades

High-resolution echelle spectra have been used to estimate rotational velocities for K and M dwarfs in the Hyades. All of the K dwarfs have rotational velocities less than the instrumental limit of 10 km/s. Most of the M dwarfs with (R - I)K larger than 1.0 have detectable rotational velocities, with v sin i between 10 and 20 km/s. Combining these data with results from the younger Pleiades and Alpha Persei clusters, it is found that G dwarfs spin down from about 100 km/s to about 10 km/s in less than 40 million yr, whereas M dwarfs take an order of magnitude longer to spin down.

Stauffer, John R.↗
NASA NTRS1991

Do clusters of galaxies affect the spectrum of the microwave background?

The distortion, averaged over the sky, due to the Compton scattering of background photons with electrons in the hot gas in clusters of galaxies is calculated. Using an existing sample of X-ray clusters, various values of the density parameter Omega, and plausible models for cluster evolution, Monte Carlo realizations of the microwave sky are generated. The spatial structure of these simulations shows a network of discrete sources whose properties can be a strong function of both evolution and Omega. The amount of spectral distortion in the models is greatest for models characterized by self-similar cluster evolution in an open universe and is within an order of magnitude of the current upper limits. Thus, improved observational sensitivity must inevitably detect some deviation from a blackbody spectrum.

Markevitch, M.↗
NASA NTRS1993

High-resolution X-ray observations of the central region of M31 with the Rosat satellite

A 48,000-sec observation of M31's central 34 arcmin, using the Rosat HRI, has led to the detection of 86 X-ray sources with luminosities above 1.4 x 10 exp 36 ergs/sec; of these, 18 sources are identified with globular clusters and two with SNRs. An extrapolation of the cumulative luminosity distribution to fainter luminosities indicates that only about 15-26 percent of the diffuse X-ray emission in the bulge is attributable to faint unresolved sources from this distribution. The spatial distribution and number density of X-ray sources in M31 appear to be very different from those of our Galaxy.

Primini, F. A.↗
NASA NTRS2001

An XMM-Newton Study of 9SGR and the Lagoon Nebula

We report preliminary results of an XMM-Newton observation of the 04 V star 9 Sgr (= HD 164794). 9 Sgr is one of a few single OB stars that display a non-thermal radio emission attributed to synchrotron emission by relativistic electrons. Inverse Compton scattering of photospheric UV photons by these relativistic electrons is a priori expected to generate a non-thermal power-law tail in the X-ray spectrum. Our EPIC and RGS spectra of 9 Sgr suggest a more complex situation than expected from this 'simple' theoretical picture. Furthermore, soft-band EPIC images of the region around 9 Sgr reveal a number of point sources inside the Lagoon Nebula (M8). Most of these sources have optical counterparts inside the very young open cluster NGC 6530 and several X-ray sources are associated with low and intermediate mass pre-main sequence stars. Finally, we also detect (probably) diffuse X-ray emission from the Hourglass Region that might reveal a hot bubble blown by the stellar wind of Herschel 36, the ionizing star of the HG region.

Rauw, G.↗
NASA NTRS2010

The HST/ACS Coma Cluster Survey. II. Data Description and Source Catalogs

The Coma cluster, Abell 1656, was the target of a HST-ACS Treasury program designed for deep imaging in the F475W and F814W passbands. Although our survey was interrupted by the ACS instrument failure in early 2007, the partially-completed survey still covers approximately 50% of the core high density region in Coma. Observations were performed for twenty-five fields with a total coverage area of 274 aremin(sup 2), and extend over a wide range of cluster-centric radii (approximately 1.75 Mpe or 1 deg). The majority of the fields are located near the core region of Coma (19/25 pointings) with six additional fields in the south-west region of the cluster. In this paper we present SEXTRACTOR source catalogs generated from the processed images, including a detailed description of the methodology used for object detection and photometry, the subtraction of bright galaxies to measure faint underlying objects, and the use of simulations to assess the photometric accuracy and completeness of our catalogs. We also use simulations to perform aperture corrections for the SEXTRACTOR Kron magnitudes based only on the measured source flux and its half-light radius. We have performed photometry for 76,000 objects that consist of roughly equal numbers of extended galaxies and unresolved objects. Approximately two-thirds of all detections are brighter than F814W=26.5 mag (AB), which corresponds to the 10sigma, point-source detection limit. We estimate that Coma members are 5-10% of the source detections, including a large population of compact objects (primarily GCs, but also cEs and UCDs), and a wide variety of extended galaxies from cD galaxies to dwarf low surface brightness galaxies. The initial data release for the HST-ACS Coma Treasury program was made available to the public in August 2008. The images and catalogs described in this study relate to our second data release.

Hammer, Derek↗
NASA NTRS2004

Sensor for Monitoring Nanodevice-Fabrication Plasmas

The term plasma process diagnostics (PPD) refers to a spectroscopic technique and sensing hardware that have been proposed for monitoring plasma processes used to fabricate electronic devices that feature sizes as small as several nanometers. Nanometer dimensions are characteristic of the quantum level of miniaturization, where single impurity atoms or molecules can drastically change the local properties of the nanostructures. Such changes may be purposely used in nanoscale design but may also be extremely damaging or cause improper operation of the fabricated devices. Determination of temperature and densities of reactants near the developing features is important, since the structural synthesis is affected by characteristics of the local microenvironment. Consequently, sensors capable of nonintrusive monitoring with high sensitivity and high resolution are essential for real-time atomistic control of reaction kinetics and minimizing trace contamination in plasma processes used to fabricate electronic nanodevices. Such process-monitoring sensors are required to be compact, multiparametric, and immune to the harsh environments of processing plasmas. PPD is intended to satisfy these requirements. The specific technique used to implement plasma diagnostics with a PPD sensor would be an advanced version of continuous-wave cavity-ringdown spectroscopy (CW-CRDS) capable of profiling spectral line broadenings in order to derive both Doppler and Stark components. CRDS is based on measurements of the rate of absorption of laser light in an optical resonator. The ultimate sensitivity results from a very long absorption path length within the cavity and immunity to variations in incident laser intensity. The proposed version of this technique would involve the use of multiplexing tunable laser diodes and an actively modulated high-reflectivity optical resonator, thus offering a synergistic combination of simplicity, compactness, high sensitivity, and high resolution. The multiplexing capabilities of diode lasers could be utilized to make the PPD sensor a single, simple, compact, and inexpensive tool for the acquisition of multiparametric data. A PPD sensor would be capable of continuous measurement of such physical parameters as gas temperature, gas velocity, electron number density, and absolute densities of reacting chemical species. A laser beam can be easily adjusted to analyze the immediate vicinity of the growing nanostructures (or features etched down) in real time. The absorption enhancement in an optical cavity would afford the sensitivity needed for measurement of the temperature and densities of species at concentrations significantly lower than measurable by other nonintrusive techniques. It is anticipated that fully developed PPD sensors would enable simultaneous measurement of local temperature and determination of plasma species responsible for the synthesis and functionalization of nanodevices. These sensors would also enable tracking the pathways and origins of damaging contaminants, thereby providing feedback for adjustment of processes to optimize them and reduce contamination. The PPD sensors should also be useful for optimization of conventional microelectronics manufacturing plasma processes. Going beyond plasma processes for fabrication of electronic devices, PPD sensors could be used for monitoring of atoms, molecules, ions, radicals, clusters, and particles in a variety of other settings, including outer space. Because of their high sensitivity, such sensors could also prove useful for detecting traces of illegal drugs and explosives.

Bolshakov, Alexander↗
NASA NTRS2013

Direct Imaging Search for Extrasolar Planets in the Pleiades

We carried out an imaging survey for extrasolar planets around stars in the Pleiades (125 Myr, 135 pc) in the H and K(sub S) bands using HiCIAO combined with adaptive optics, AO188, on the Subaru telescope. We found 13 companion candidates fainter than 14.5 mag in the H band around 9 stars. Five of these 13 were confirmed to be background stars by measurement of their proper motion. One was not found in the second epoch observation, and thus was not a background or companion object. One had multi-epoch images, but the precision of its proper motion was not sufficient to conclude whether it was a background object. Four other candidates are waiting for second-epoch observations to determine their proper motion. Finally, the remaining two were confirmed to be 60 M(sub J) brown dwarf companions orbiting around HD 23514 (G0) and HII 1348 (K5), respectively, as had been reported in previous studies. In our observations, the average detection limit for a point source was 20.3 mag in the H band beyond 1.′′ 5 from the central star. On the basis of this detection limit, we calculated the detection efficiency to be 90% for a planet with 6 to 12 Jovian masses and a semi-major axis of 50–1000 AU. For this reason we extrapolated the distribution of the planet mass and the semi-major axis derived from radial velocity observations, and adopted the planet evolution model Baraffe et al. (2003, A&A, 402, 701). Since there was no detection of a planet, we estimated the frequency of such planets to be less than 17.9% (2 sigma) around one star of the Pleiades cluster.

extrasolar planets↗
NASA NTRS1994

The stellar population in the core of M15

The inner core of the globular cluster M15 within approximately 2 sec of the geometrical center has been explored with high-resolution images taken through several broad-band UV filter with the Faint Object Camera (FOC) on board the Hubble Space Telescope (HST). Approximately 210 stars in this region down to a 5 sigma detection limit of m(sub 220) = 21.5 were reliably identified and located on a UV - U color magnitude diagram for the first time. A majority of stars (about 70% of the total) observed this way lie above the expected main-sequence turn-off of this cluster and below the sparsely populated horizontal branch. The extension of the main sequence above the turn-off separates this population in two roughly equal components situated to the right and left of this line. Most of the former must be classical blue stragglers while the rest belong to a new, as yet unidentified, population of very blue stars. Possibilities include, but are not restricted to, well-mixed single stars, subdwarfs, and helium white dwarfs. Similar objects are also found just outside the core out to approximately 6 sec from the center, but the brighter, presumably more massive ones, are sharply confined to the core itself. The measured excess of bright blue stars and the relative deficiency of bright red giants in the core are consistent with the blue inward color gradient measured from the ground and imply that dynamical evolution can significantly affect the stellar population in the very dense central regions of a high-concentration globular cluster like M15.

De Marchi, Guido↗
DOE OSTI2023

Nature of S-States in the Oxygen-Evolving Complex Resolved by High-Energy Resolution Fluorescence Detected X-ray Absorption Spectroscopy

Photosystem II, the water splitting enzyme of photosynthesis, utilizes the energy of sunlight to drive the four-electron oxidation of water to dioxygen at the oxygen-evolving complex (OEC). The OEC harbors a Mn 4 CaO 5 cluster that cycles through five oxidation states S i (i = 0–4). The S 3 state is the last metastable state before the O 2 evolution. Its electronic structure and nature of the S 2 → S 3 transition are key topics of persisting controversy. Most spectroscopic studies suggest that the S 3 state consists of four Mn(IV) ions, compared to the Mn(III)Mn(IV) 3 of the S 2 state. However, recent crystallographic data have received conflicting interpretations, suggesting either metal- or ligand-based oxidation, the latter leading to an oxyl radical or a peroxo moiety in the S 3 state. Herein, we utilize high-energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy to obtain a highly resolved description of the Mn K pre-edge region for all S-states, paying special attention to use chemically unperturbed S 3 state samples. In combination with quantum chemical calculations, we achieve assignment of specific spectroscopic features to geometric and electronic structures for all S-states. These data are used to confidently discriminate between the various suggestions concerning the electronic structure and the nature of oxidation events in all observable catalytic intermediates of the OEC. Our results do not support the presence of either peroxo or oxyl in the active configuration of the S 3 state. This establishes Mn-centered storage of oxidative equivalents in all observable catalytic transitions and constrains the onset of the O–O bond formation until after the final light-driven oxidation event.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1983

The optical identification content of the Einstein Observatory deep X-ray survey of a region in Pavo

Results are presented from the Einstein deep X-ray survey in Pavo, with correlated optical and radio observations of a complete sample of candidate identifications. There are 16 X-ray sources detected with positional accuracy better than 10 arcsec, of which five are identified, with a further seven (and a maximum nine) probable identifications. Of the identified sources, four are QSOs with J-magnitude about 20 (one is an inverted spectrum radio source) and one is associated with extended emission from a pair or cluster of galaxies. Of the probable identifications, one is a galaxy and the rest are a subset of a yellow stellar object population which may also be QSOs. Identifications with QSOs and QSO candidates with J less than 24 account for 60-80 percent of the detected sources.

Griffiths, R. E.↗
DOE OSTI2020

Identifying Different Classes of Seismic Noise Signals Using Unsupervised Learning

Abstract Proper classification of nontectonic seismic signals is critical for detecting microearthquakes and developing an improved understanding of ongoing weak ground motions. We use unsupervised machine learning to label five classes of nonstationary seismic noise common in continuous waveforms. Temporal and spectral features describing the data are clustered to identify separable types of emergent and impulsive waveforms. The trained clustering model is used to classify every 1 s of continuous seismic records from a dense seismic array with 10–30 m station spacing. We show that dominate noise signals can be highly localized and vary on length scales of hundreds of meters. The methodology demonstrates the complexity of weak ground motions and improves the standard of analyzing seismic waveforms with a low signal‐to‐noise ratio. Application of this technique will improve the ability to detect genuine microseismic events in noisy environments where seismic sensors record earthquake‐like signals originating from nontectonic sources.

Johnson, Christopher W.↗
DOE OSTI2021

Segregation behavior and phase instability of Eurofer97 after neutron irradiation to 72 dpa

Here, a reduced activation ferritic/martensitic steel, Eurofer97, was neutron irradiated in the vicinity of 300 °C in the High Flux Isotope Reactor (HFIR) up to 72 dpa. Advanced analytical scanning transmission electron microscopy and conventional transmission electron microscopy were applied to investigate the radiation-induced segregation and phase instability behavior after neutron irradiation. Amorphization was observed in M 23 C 6 carbides. Cr-rich clusters were seen within the matrix, near the lath boundaries and close to the M 23 C 6 carbides. Cr enrichment and Fe depletion were detected at both prior austenite grain boundaries and lath boundaries, despite different segregation magnitude. In addition, the enrichment of Ni, the depletion of V, and tiny cavities (presumably helium bubbles) are also found at lath boundaries. This work interrogates the evolution of microstructures after neutron irradiation, which provides detailed understanding on the microstructural aspects controlling the mechanical integrity of Eurofer97 under high-dose neutron damage.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A scalable variational method for estimating the latent infection-rate field of an outbreak

In this paper, we explore whether the infection-rate of a disease can serve as a robust monitoring variable in epidemiological surveillance algorithms. The infection-rate is dependent on population mixing patterns that do not vary erratically day-to-day; in contrast, daily case-counts used in contemporary surveillance algorithms are corrupted by reporting errors. The technical challenge lies in estimating the latent infection-rate from case-counts. Here we devise a Bayesian method to estimate the infection-rate across multiple adjoining areal units, and then use it, via an anomaly detector, to discern a change in epidemiological dynamics. We extend an existing model for estimating the infection-rate in an areal unit by incorporating a Markov random field model, so that we may estimate infection-rates across multiple areal units, while preserving spatial correlations observed in the epidemiological dynamics. To carry out the high-dimensional Bayesian inverse problem, we develop an implementation of mean-field variational inference specific to the infection model and integrate it with the random field model to incorporate correlations across counties. The method is tested on estimating the COVID-19 infection-rates across all 33 counties in New Mexico using data from the summer of 2020, and then employing them to detect the arrival of the Fall 2020 COVID-19 wave. We perform the detection using a temporal algorithm that is applied county-by-county. We also show how the infection-rate field can be used to cluster counties with similar epidemiological dynamics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

transcriptome↗