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DOE OSTI2017

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

ABSTRACT In this study, strain-resolved metagenomics was used to solve a mystery. A 6.4-Mbp complete closed genome was recovered from a soil metagenome and found to be astonishingly similar to that of Delftia acidovorans SPH-1, which was isolated in Germany a decade ago. It was suspected that this organism was not native to the soil sample because it lacked the diversity that is characteristic of other soil organisms; this suspicion was confirmed when PCR testing failed to detect the bacterium in the original soil samples. D. acidovorans was also identified in 16 previously published metagenomes from multiple environments, but detailed-scale single nucleotide polymorphism analysis grouped these into five distinct clades. All of the strains indicated as contaminants fell into one clade. Fragment length anomalies were identified in paired reads mapping to the contaminant clade genotypes only. This finding was used to establish that the DNA was present in specific size selection reagents used during sequencing. Ultimately, the source of the contaminant was identified as bacterial biofilms growing in tubing. On the basis of direct measurement of the rate of fixation of mutations across the period of time in which contamination was occurring, we estimated the time of separation of the contaminant strain from the genomically sequenced ancestral population within a factor of 2. This research serves as a case study of high-resolution microbial forensics and strain tracking accomplished through metagenomics-based comparative genomics. The specific case reported here is unusual in that the study was conducted in the background of a soil metagenome and the conclusions were confirmed by independent methods. IMPORTANCE It is often important to determine the source of a microbial strain. Examples include tracking a bacterium linked to a disease epidemic, contaminating the food supply, or used in bioterrorism. Strain identification and tracking are generally approached by using cultivation-based or relatively nonspecific gene fingerprinting methods. Genomic methods have the ability to distinguish strains, but this approach typically has been restricted to isolates or relatively low-complexity communities. We demonstrate that strain-resolved metagenomics can be applied to extremely complex soil samples. We genotypically defined a soil-associated bacterium and identified it as a contaminant. By linking together snapshots of the bacterial genome over time, it was possible to estimate how long the contaminant had been diverging from a likely source population. The results are congruent with the derivation of the bacterium from a strain isolated in Germany and sequenced a decade ago and highlight the utility of metagenomics in strain tracking.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Photoelectric observations of Krzeminski's star, the companion of Cen X-3

Centaurus X-3 was the first discovered X-ray source whose intensity is pulsed and eclipsed. Though the X-ray properties of the Cen X-3 system have been intensively studied, the optical properties remained unstudied until Krzeminski's identification of the optical counterpart of Cen X-3. Observations of the X-ray eclipse duration, pulsation frequency variation, and pulse arrival time variation have been used to place limits on the nature of the system and to predict the nature of the optical companion and X-ray sources. An observational determination is presented of the several system parameters based on a preliminary interpretation of the light curve of Krzeminski's star.

Petro, L. D.↗

NASA NTRS1989

Si3N4 emissivity and the unidentified infrared bands

Infrared spectroscopy of warm (about 150 to 750 K), dusty astronomical sources has revealed a structured emission spectrum which can be diagnostic of the composition, temperature, and in some cases, even size and shape of the grains giving rise to the observed emission. The identifications of silicate emission in oxygen rich objects and SiC in carbon rich object are two examples of this type of analysis. Cometary spectra at moderate resolution have similarly revealed silicate emission, tying together interstellar and interplanetary dust. However, Goebel has pointed out that some astronomical sources appear to contain a different type of dust which results in a qualitatively different spectral shape in the 8 to 13 micron region. The spectra shown make it appear unlikely that silicon nitride can be identified as the source of the 8 to 13 micron emission in either NGC 6572 or Nova Aql 1982. The similarity between the general wavelength and shape of the 10 micron emission from some silicates and that from the two forms of silicon nitride reported could allow a mix of cosmic grains which include some silicon nitride if only the 8 to 13 micron data are considered.

Russell, Ray W.↗

DOE OSTI2022

XMM-Newton and SRG/eROSITA observations of the isolated neutron star candidate 4XMM J 022141.5-735632

We report the results of follow-up investigations of a possible new thermally emitting isolated neutron star (INS), 4XMM J022141.5-735632, using observations from XMM-Newton and Spectrum Roentgen Gamma (SRG) eROSITA. The analysis is complemented by Legacy Survey imaging in the optical and near-infrared wavelengths. The X-ray source, the first to be targeted by XMM-Newton in an effort to identify new INS candidates from the fourth generation of the XMM-Newton serendipitous source catalogue Data Release 9 (4XMM-DR9), shows a remarkably soft energy distribution and a lack of catalogued counterparts; the very high X-ray-to-optical flux ratio virtually excludes any other identification than an INS. Within current observational limits, no significant flux variation or change of spectral state is registered over nearly ten years. Future dedicated observations, particularly to search for pulsations, are crucial to shed further light on the nature of the X-ray source and relations to other Galactic neutron stars.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Functional Requirements for the Modeling and Simulation of Advanced (Non-LWR) Reactor Mechanistic Source Term

A number of industry vendors are leading a resurgence in advanced reactor development. As the assurance of public safety from the accidental release of radionuclides to the environment is central to regulatory licensing and the reactor design process, the development of a mechanistic source term (MST) assessment has been identified by the advanced reactor industry as a foremost priority. In contrast to historic light-water reactor (LWR) source term analysis efforts, an MST attempts to realistically model the release and transport of radionuclides from the source to the environment for specific scenarios, while accounting for retention or transmutation phenomena and associated uncertainties. This work seeks to aid in the development of MST modeling and simulation tools by performing a preliminary identification of functional requirements for the major advanced reactor types.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

The Evaluation of Machine Learning Techniques for Isotope Identification Contextualized by Training and Testing Spectral Similarity

Precise gamma-ray spectral analysis is crucial in high-stakes applications, such as nuclear security. Research efforts toward implementing machine learning (ML) approaches for accurate analysis are limited by the resemblance of the training data to the testing scenarios. The underlying spectral shape of synthetic data may not perfectly reflect measured configurations, and measurement campaigns may be limited by resource constraints. Consequently, ML algorithms for isotope identification must maintain accurate classification performance under domain shifts between the training and testing data. To this end, four different classifiers (Ridge, Random Forest, Extreme Gradient Boosting, and Multilayer Perceptron) were trained on the same dataset and evaluated on twelve other datasets with varying standoff distances, shielding, and background configurations. A tailored statistical approach was introduced to quantify the similarity between the training and testing configurations, which was then related to the predictive performance. Wilcoxon signed-rank tests revealed that the OVR-wrapped XGB significantly outperformed the other algorithms, with confidence levels of 99.0% or above for the 133Ba, 60Co, 137Cs, and 152Eu sources. The findings from this work are significant as they outline techniques to promote the development of robust ML-based approaches for isotope identification.

domain adaptation↗

NASA NTRS2011

The Atacama Cosmology Telescope: Extragalactic Sources at 148 GHz in the 2008 Survey

We report on extragalactic sources detected in a 455 square-degree map of the southern sky made with data at a frequency of 148 GHz from the Atacama Cosmology Telescope 2008 observing season. We provide a catalog of 157 sources with flux densities spanning two orders of magnitude: from 15 mJy to 1500 mJy. Comparison to other catalogs shows that 98% of the ACT detections correspond to sources detected at lower radio frequencies. Three of the sources appear to be associated with the brightest cluster galaxies of low redshift X-ray selected galaxy clusters. Estimates of the radio to mm-wave spectral indices and differential counts of the sources further bolster the hypothesis that they are nearly all radio sources, and that their emission is not dominated by re-emission from warm dust. In a bright (> 50 mJy) 148 GHz-selected sample with complete cross-identifications from the Australia Telescope 20 GHz survey, we observe an average steepening of the spectra between .5, 20, and 148 GHz with median spectral indices of alp[ha (sub 5-20) = -0.07 +/- 0.06, alpha (sub 20-148) -0.39 +/- 0.04, and alpha (sub 5-148) = -0.20 +/- 0.03. When the measured spectral indices are taken into account, the 148 GHz differential source counts are consistent with previous measurements at 30 GHz in the context of a source count model dominated by radio sources. Extrapolating with an appropriately rescaled model for the radio source counts, the Poisson contribution to the spatial power spectrum from synchrotron-dominated sources with flux density less than 20 mJy is C(sup Sync) = (2.8 +/- 0.3) x 1O (exp-6) micro K(exp 2).

Marriage, T. A.↗

NASA NTRS1990

Laboratory simulation of interstellar grain chemistry and the production of complex organic molecules

During the past 15 years considerable progress in observational techniques has been achieved in the middle infrared (5000 to 500 cm(-1), 2 to 20 microns m), the spectral region most diagnostic of molecular vibrations. Spectra of many different astronomical infrared sources, some deeply embedded in dark molecular clouds, are now available. These spectra provide a powerful probe, not only for the identification of interstellar molecules in both the gas solid phases, but also of the physical and chemical conditions which prevail in these two very different domains. By comparing these astronomical spectra with the spectra of laboratory ices one can determine the composition and abundance of the icy materials frozen on the cold (10K) dust grains present in the interior of molecular clouds. These grains and their ice mantles may well be the building blocks from which comets are made. As an illustration of the processes which can take place as an ice is irradiated and subsequently warmed, researchers present the infrared spectra of the mixture H2O:CH3OH:CO:NH3:C6H14 (100:50:10:10:10). Apart from the last species, the ratio of these compounds is representative of the simplest ices found in interstellar clouds. The last component was incorporated into this particular experiment as a tracer of the behavior of a non-aromatic hydrocarbon. The change in the composition that results from ultraviolet photolysis of this ice mixture using a UV lamp to simulate the interstellar radiation field is shown. Photolysis produces CO, CO2, CH4, HCO, H2CO, as well as a family of moderately volatile hydrocarbons. Less volatile carbonaceous materials are also produced. The evolution of the infrared spectrum of the ice as the sample is warmed up to room temperature is illustrated. Researchers believe that the changes are similar to those which occur as ice is ejected from a comet and warmed up by solar radiation. The warm-up sequence shows that the nitrile or iso-nitrile bearing compound produced during photolysis evaporates between 200 and 250K, suggesting that it is carried by a small molecular species. These molecules could be similar to the source material in Comet Halley that is ejected in grains into the coma, freed by sublimation, and photolyzed by solar radiation to produce the observed jets.

Allamandola, L. J.↗

DOE OSTI2025

Spectral line identification from a photoionised silicon plasma in emission

Next-generation X-ray satellite telescopes such as XRISM, NewAthena and Lynx will enable observations of exotic astrophysical sources at unprecedented spectral and spatial resolution. Proper interpretation of these data demands that the accuracy of the models is at least within the uncertainty of the observations. One set of quantities that might not currently meet this requirement is transition energies of various astrophysically relevant ions. Current databases are populated with many untested theoretical calculations. Accurate laboratory benchmarks are required to better understand the coming data. We obtained laboratory spectra of X-ray lines from a silicon plasma at an average spectral resolving power of ∼7500 with a spherically bent crystal spectrometer on the Z facility at Sandia National Laboratories. Many of the lines in the data are measured here for the first time. We report measurements of 53 transitions originating from the K-shells of He-like to B-like silicon in the energy range between ∼1795 and 1880 eV (6.6–6.9 Å). The lines were identified by qualitative comparison against a full synthetic spectrum calculated with ATOMIC. The average fractional uncertainty (uncertainty/energy) for all reported lines is ∼5.4 × 10 −5 . We compare the measured quantities against transition energies calculated with RATS and FAC as well as those reported in the NIST ASD and XSTAR’s uaDB. Average absolute differences relative to experimentally measured values are 0.20, 0.32, 0.17 and 0.38 eV, respectively. All calculations/databases show good agreement with the experimental values; NIST ASD shows the closest match overall.

astrophysical plasmas↗

DOE OSTI2017

Blood cadmium concentrations and environmental exposure sources in newcomer South and East Asian women in the Greater Toronto Area, Canada

Background: Immigrant women are often identified as being particularly vulnerable to environmental exposures and health effects. The availability of biomonitoring data on newcomers is limited, thus, presenting a challenge to public health practitioners in the identification of priorities for intervention. Objectives: In fulfillment of data needs, the purpose of this study was to characterize blood concentrations of cadmium (Cd) among newcomer women of reproductive age (19–45 years of age) living in the Greater Toronto Area (GTA), Canada and to assess potential sources of environmental exposures. Methods: A community-based model, engaging peer researchers from the communities of interest, was used for recruitment and follow-up purposes. Blood samples were taken from a total of 211 newcomer women from South and East Asia, representing primary, regional origins of immigrants to the GTA, and environmental exposure sources were assessed via telephone survey. Metal concentrations were measured in blood samples (diluted with 0.5% (v/v) ammonium hydroxide and 0.1% (v/v) octylphenol ethoxylate) using a quadrupole ICP-MS. Survey questions addressed a wide range of environmental exposure sources, including dietary and smoking patterns and use of nutritional supplements, herbal products and cosmetics. Results: A geometric mean (GM) blood Cd concentration of 0.39 µg/L (SD:±2.07 µg/L) was determined for study participants (min/max: <0.045 µg /L (LOD)/2.36 µg/L). Several variables including low educational attainment (Relative Ratio (RR) (adjusted)=1.50; 95% CI 1.17–1.91), milk consumption (RR (adjusted)=0.86; 95% CI 0.76–0.97), and use of zinc supplements (RR (adjusted)=0.76; 95% CI 0.64–0.95) were observed to be significantly associated with blood Cd concentrations in the adjusted regression model. The variable domains socioeconomic status (R{sup 2}{sub adj}=0.11) and country of origin (R{sup 2}{sub adj}=0.236) were the strongest predictors of blood Cd. Conclusion: Blood Cd concentrations fell below those generally considered to be of human health concern. However, negative health effects cannot be entirely excluded, especially for those that fall in the upper percentile range of the distribution, given the mounting evidence for negative health outcomes at low environmental exposure concentrations. - Highlights: • Blood Cd and exposure sources were assessed for 211 newcomer women in Toronto. • Blood Cd was slightly elevated compared to that in Canadian-born populations. • SES and country of origin were the strongest predictors of blood Cd. • Intake of essential micronutrients is a likely important modulator of blood Cd. • Identified need for more research on newcomers as a function of country of origin.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Sensitivity of the GAPS experiment to low-energy cosmic-ray antiprotons

The General Antiparticle Spectrometer (GAPS) is an upcoming balloon mission to measure low-energy cosmic-ray antinuclei during at least three ~35-day Antarctic flights. With its large geometric acceptance and novel exotic atom-based particle identification, GAPS will detect ~500 cosmic antiprotons per flight and produce a precision cosmic antiproton spectrum in the kinetic energy range of ~0.07–0.21 GeV/n at the top of the atmosphere. With these high statistics extending to lower energies than any previous experiment, and with complementary sources of experimental uncertainty compared to traditional magnetic spectrometers, the GAPS antiproton measurement will be sensitive to dark matter, primordial black holes, and cosmic ray propagation. The antiproton measurement will also validate the GAPS antinucleus identification technique for the antideuteron and antihelium rare-event searches. Finally, this analysis demonstrates the GAPS sensitivity to cosmic-ray antiprotons using a full instrument simulation and event reconstruction, and including solar and atmospheric effects.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1992

BATSE observations of gamma-ray bursts

Gamma-ray bursts are being detected with unprecedented sensitivity by the Burst and Transient Source Experiment (BATSE) on the Compton Gamma Ray Observatory since its launch in April, 1991. The experiment is detecting about one gamma-ray burst per day. A brief description is presented of the on-orbit performance of BATSE, the methods of identification of bursts, and examples of the diverse time profiles of the gamma-ray bursts observed. The most significant finding thus far is the apparent isotropy of the bursts together with the observed inhomogeneity of the sources.

Fishman, Gerald J.↗

DOE OSTI2022

Automatically generated model for light alkene combustion

Light alkenes are common combustion intermediates for a variety of fuels. Therefore, understanding their oxidation and pyrolysis chemistry is key to building detailed mechanisms for heavier fuels. This work was focused on the development and evaluation of a detailed kinetic mechanism suitable for the combustion of light alkenes up to C 4 without the use of tuned parameters, instead, the parameter values come from first principles or direct measurements. The generated mechanism accurately estimates the laminar burning velocity (S u ) and ignition delay time (IDT) of light alkenes available in the literature, which represent fundamental combustion properties at a wide range of conditions. Because each parameter is thought to have a physically realistic value, not tuned to these measurements, the new model could be used as a sub-mechanism in models for other applications. The reaction network was generated with the open-source Reaction Mechanism Generator (RMG) software. Sensitivity analyses were performed under wide ranges of temperatures and pressures, allowing for the identification of the most impactful species and reactions. Based on these, a comprehensive thermochemistry database, including calculations on 550 molecules performed in this work at the CBS-QB3 level of theory, and a kinetic library, including theoretically-derived reaction rates retrieved from the literature, were built and used in the mechanism generation. The developed mechanism was compared against several existing detailed kinetic mechanisms for ethene, propene, 1-butene, 2-butene, and isobutene. Here, the newly generated model is the most accurate among the ones analyzed, in terms of fractional bias and normalized mean square error. Hence, this new model was used to analyze the chemistry of alkene combustion. Key rate coefficients were compared, to identify the cause of deviations between the models and possible areas for further improvements.

09 BIOMASS FUELS↗

DOE OSTI2023

WPEC SG50: Developing an Automatically Readable, Comprehensive and Curated Experimental Nuclear Reaction Database

The Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) Working Party on International Nuclear Data Evaluation Co-operation (WPEC) subgroup (SG) 50 was formed in 2020 to develop an automatically readable, comprehensive and curated experimental nuclear reaction database. This database is called MEDUSAL (Machine-readable Experimental Data User Application & Library), and will draw from EXFOR. The EXFOR database preserves experimental nuclear reaction data true to its original documentation and information from the authors of the data. MEDUSAL will deviate from EXFOR by storing additional information from users of the data for their fields of work (evaluation, model development, validation, etc.). This includes expert judgment on the data sets, identification of data points as outliers, renormalization of the data to the newest monitor reactions, and estimations of missing uncertainty sources. The format for MEDUSAL is being developed to enable easy automatic parsing of large amounts of data. Here, we will summarize the use cases, high-level requirements and first steps towards developing the database MEDUSAL and the API to access it.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Characterizing a supernova’s standing accretion shock instability with neutrinos and gravitational waves

Here, we perform a novel multi-messenger analysis for the identification and parameter estimation of the Standing Accretion Shock Instability (SASI) in a core collapse supernova with neutrino and gravitational wave (GW) signals. In the neutrino channel, this method performs a likelihood ratio test for the presence of SASI in the frequency domain. For gravitational wave signals we process an event with a modified constrained likelihood method. Using simulated supernova signals, the properties of the Hyper-Kamiokande neutrino detector, and O3 LIGO Interferometric data, we produce the two-dimensional probability density distribution (PDF) of the SASI activity indicator and calculate the probability of detection P D as well as the false identification probability P FI . We discuss the probability to establish the presence of the SASI as a function of the source distance in each observational channel, as well as jointly. Compared to a single-messenger approach, the joint analysis results in P D (at P FI = 0.1) of SASI activities that is larger by up to ≈ 40% for a distance to the supernova of 5 kpc. We also discuss how accurately the frequency and duration of the SASI activity can be estimated in each channel separately. Our methodology is suitable for implementation in a realistic data analysis and a multi-messenger setting.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development

The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize ( Zea mays , cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at =95 reads per 20 M, and 693 of them at =500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.

09 BIOMASS FUELS↗

DOE OSTI2025

Studies for the selection of fully contained muon neutrino CC events in the ICARUS T600 detector at Fermilab

The ICARUS T600 LAr-TPC detector has started its new physics runs in June 2022 at Fermilab within the SBN program. This detector is recording neutrino interactions from the Booster BNB neutrino beam in order to definitively clarify the open questions related to the possible existence of sterile neutrinos, as suggested by numerous observed experimental anomalies. In addition the neutrinos events recorded from the NuMI off-axis beam are under study in order to perform neutrino-Argon cross section measurements. At Fermilab, ICARUS is facing a challenging experimental condition: the detector is presently installed essentially at Earth surface where cosmic ray particles can become a serious source of background for the neutrino event search. This condition makes it necessary to deploy suitable automatic tools for the identification, selection, and measurement of the neutrino events among the millions of events triggered by cosmics. In this contribution, two automatic selection procedures devoted to the identification of fully contained muon neutrino interactions in the BNB neutrino beam will be presented, together with the first results of their application on simulated and on recently recorded events in the T600 detector.

Farnese, Christian [INFN, Padua] (ORCID:0000000163↗

DOE OSTI2025

Studies for the Selection of Fully Contained Muon Neutrino CC Events in the ICARUS T600 Detector at Fermilab

Farnese, Christian [INFN, Padua]↗