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An Introduction to the Benchmarking and Publications for Non-Targeted Analysis Working Group

Non-targeted analysis (NTA) encompasses a rapidly evolving set of mass spectrometry techniques aimed at characterizing the chemical composition of complex samples, identifying unknown compounds, and/or classifying samples, without prior knowledge regarding the chemical content of the samples. Recent advances in NTA are the result of improved and more accessible instrumentation for data generation, and analysis tools for data evaluation and interpretation. As researchers continue to develop NTA approaches in various scientific fields, there is a growing need to identify, disseminate, and adopt community-wide method reporting guidelines. In 2018, NTA researchers formed the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address this need. Consisting of participants from around the world and representing fields ranging from environmental science and food chemistry to ‘omics and toxicology, BP4NTA provides resources addressing a variety of challenges associated with NTA. Furthermore, thus far, BP4NTA group members have aimed to establish consensus on NTA-related terms and concepts, and to create consistency in reporting practices by providing resources on a public website, including consensus definitions, reference content, and lists of available tools. Moving forward, BP4NTA will provide a setting for NTA researchers to continue discussing emerging challenges and contribute to additional harmonization efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗

The cosmological evolution and luminosity function of X-ray selected active galactic nuclei

The cosmological evolution and the X-ray luminosity function of X-ray selected active galactic nuclei (AGNs) are derived and discussed. The sample used consists of 31 AGNs extracted from a fully identified sample of X-ray sources from the Einstein Observatory Medium Sensitivity Survey and is therefore exclusively defined by its X-ray properties. The distribution in space is found to be strongly nonuniform. The amount of cosmological evolution required by the X-ray data is derived in the framework of pure luminosity evolution and is found to be smaller than the amount determined from optically selected samples. The X-ray luminosity function is derived. It can be satisfactorily represented by a single power law only over a limited range of absolute luminosities. Evidence that the luminosity function flattens at low luminosity or steepens at high luminosity, or both, is presented and discussed.

Maccacaro, T.↗

Area estimation using multiyear designs and partial crop identification

Progress is reported for the following areas: (1) estimating the stratum's crop acreage proportion using the multiyear area estimation model; (2) assessment of multiyear sampling designs; and (3) development of statistical methodology for incorporating partially identified sample segments into crop area estimation.

Sielken, R. L., Jr.↗

Askival: An altered feldspathic cumulate sample in Gale crater

Askival is a light-toned, coarsely crystalline float rock, which was identified near the base of Vera Rubin Ridge in Gale crater. We have studied Askival, principally with the ChemCam instrument but also using APXS compositional data and MAHLI images. Askival and an earlier identified sample, Bindi, represent two rare examples of feldspathic cumulate float rocks in Gale crater with >65% relict plagioclase. Bindi appears unaltered whereas Askival shows textural and compositional signatures of silicification, along with alkali remobilization and hydration. Askival likely experienced multiple stages of alteration, occurring first through acidic hydrolysis of metal cations, followed by deposition of silica and possible phyllosilicates at low T and neutral-alkaline pH. Through laser-induced breakdown spectroscopy compositional analyses and normative calculations, we suggest that an assemblage of Fe-Mg silicates including amphibole and pyroxene, Fe phases, and possibly Mg-rich phyllosilicate are present. Thermodynamic modeling of the more pristine Bindi composition predicts that amphibole and feldspar are stable within an upper crustal setting. This is consistent with the presence of amphibole in the parent igneous rocks of Askival and suggests that the paucity of amphiboles in other known Martian samples reflects the lack of representative samples of the Martian crust rather than their absence on Mars.

58 GEOSCIENCES↗

Field Evaluations of Sampling, Interviewing, and Flight Tracking of NASA's Low Boom Flight Demonstrator Aircraft

The first year’s effort identified sampling and interviewing as the principal risks to assessment of prompt reactions to overflights producing low-amplitude sonic booms. It also 1) established the utility of geo-information system-based route planning for LBFD flight missions, 2) developed and demonstrated a prototype of a geographically-distributed, Internet-enabled instrumentation system capable of wide-area tracking of LBFD aircraft in near-real time. The latter system permits synchronizing the conduct of interviews in multiple overflown communities with arrival times of shock waves at interviewing sites; and of measuring, archiving, and processing their acoustic signatures. Means were also recommended for constructing representative, telephone-based samples of eligible respondents living in households within carpet boom corridors adjacent to LBFD flight tracks, and for conducting interviews with cross-sectional (independent) samples of such respondents about their prompt reactions to exposure to low-amplitude sonic booms. A detailed study design was prepared and accepted by NASA for a set of single-contact attempt telephone interviews with a nationally representative sample of households. The study design focused on testing automated and live agent interview completion rates obtainable without callbacks. A minimal (two monitoring station) version of the aircraft tracking system was built and installed near a civil airport in a successful demonstration of the system’s ability to detect and track aircraft movements. The field exercise also demonstrated the ability of the system to capture the acoustic emissions of departing aircraft, and to serve aircraft position and sound level information to remote, geographically-distributed analysts in near-real time. Upon approval of OMB and IRB of the detailed study plan, a stratified, nationally representative sample of landline and wireless telephone-subscribing households was constructed. A total of 12,734 telephone interview contact attempts of the sort required by a straightforward cross-sectional study design were then made. These contact attempts demonstrated the impracticality of conducting a time-critical, cross-sectional study of prompt community response to low-amplitude sonic booms by means of “independent” (single contact attempt per respondent for each LBFD flight mission) telephone samples of respondents. The observed interview completion rates for these single telephone contact attempts were so low (~ 1% to 3% for automated and live agent interviews, respectively) that: 1) the representativeness of collected opinions would be susceptible to intuitive challenge as inadequate, even absent conclusive evidence of non-representativeness. Refuting challenges to representativeness would have to demonstrate that the composition of the actual sample did not differ from that of the target population, a task that is tantamount to proving a negative; 2) the information required to refute allegations of non-representativeness would require a questionnaire considerably lengthier than that required simply to determine the prevalence of boom-induced startle and annoyance. Such a questionnaire would have to inquire about potentially sensitive and intrusive matters, including respondents’ age, gender, education, employment, home ownership, income, ethnicity, family size, and other demographic factors; and 3) unreasonable numbers of attempts would be required to re-contact households with unsuccessful initial contact attempts, given the limited time available for doing so. For example, if about 500 completed interviews were desired in a supersonically overflown community, approximately 50,000 automated interview attempts would have to be made within ten to fifteen minutes of each LBFD overflight. Such large numbers of contact attempts could well exceed the numbers of households available for interview in areas of similar boom exposure levels in some communities near LBFD flight tracks. Such large numbers of interviews could be cost-effectively undertaken only by means of automated (i.e., outgoing interactive voice response) interviewing, a data collection method ill-suited for complex and sensitive questionnaire items. The infeasibility of independent sampling for evaluating prompt responses to LBFD overflights in a cross-sectional study is due in large part to simple non-response: that is, potential respondents – particularly those contacted on wireless telephones – refusing to answer calls with unfamiliar caller IDs. It is also due in part, however, to 1) the lack of time to attempt to contact the same respondent more than once within a few minutes after the arrival of a shock wave at the respondent’s location; and 2) the need to place calls during weekday/daytime hours, when response rates are notably lower than during evenings and weekends. Despite the poor interview completion rates achieved under the above constraints, cross sectional assessments of delayed reactions to LBFD overflights could still be feasible, if multiple attempts could be made to contact respondents during evening and weekend time periods, over extended time periods. Detailed plans for a longitudinal (panel) sample were developed as an alternative to a cross sectional sample design.

Fidell, Sanford↗

Proof-of-concept chemometric approach for environmental forensic sourcing of crude oil samples using SPME-GC-MS

Environmental exposure to crude oil through seepage and spillage poses risks to the immediate environment and the broader ecosystem as areas along the oil distribution path are affected by the influx of crude petroleum as well as the environmental, economic, and civil unrest that accompanies it. There is a large financial burden associated with the lost resources, including the cost of rehabilitation, and the affected sources of revenue for communities affected by oil spills. As such, it is crucial to determine the responsible parties. This work outlines an environmental forensics approach to determining the source of an un-weathered crude oil sample. The researchers employed solid phase microextraction coupled with gas chromatography mass spectrometry (SPME-GC-MS) to capture and analyze the gaseous components emitted by crude oil samples sourced from five locations. Samples were analyzed using Spearman's rank correlation and 3D covariance analysis. Both chemometric approaches yielded optimal performance results with no misclassifications, true positive rate (TPR) = 100 % and false positive rate (FPR) = 0 %. The similarity metrics calculated by each test noted clear delineations between the values of same-source and differently sourced samples. The Spearman's rank correlation test and 3D covariance calculations both demonstrated the ability to correctly identify sample source origin in this dataset. Finally, the authors outline an approach to the future application of these tests and suggest their joint use in future crude oil sourcing endeavors.

3D covariance mapping↗

Characterization of Infrequent Samples from the Concentration, Storage, and Transfer Facility: F-Area Pump Pit 3 (FPP-3) Sump Sample: December 2021 Sample

In December 2021, SRR-E sent an ~185 mL sample identified as FPP-3 from a F-Area pump pit sump to SRNL for analysis. The sample was pale yellow in color and contained a small amount of suspended solids visually estimated to be less than 1% by volume. SRNL analysis indicated that the sample contained 4.4 E+05 dpm/mL Cs-137, 6.2 E+05 dpm/mL total beta activity, 9.3 E+02 dpm/mL beta activity following cesium removal, and below detectable levels of alpha activity following cesium removal. In addition, the sample contained 0.015 M free OH- and 947 μg total organic carbon/mL.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Characterization of Infrequent Samples from the Concentration, Storage, and Transfer Facility: H-Area Diversion Box 7 (HDB-7) Sump Sample: December 2021 Sample

In December 2021, SRR-E sent an ~250 mL sample identified as HDB-7 from an H-Area diversion box sump to SRNL for analysis. The sample was clear and colorless and free from any solids. SRNL analysis indicated that the sample contained 2.97E+05 dpm/mL Cs-137, 3.74E+05 dpm/mL total beta activity, 1.04E+03 dpm/mL beta activity following cesium removal, and below detectable levels of alpha activity and alpha activity following cesium removal. In addition, the pH of the sample was 7.32, free hydroxide concentration was 2.09E-07 M, and the density was 0.991 g/mL.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

IRAS variables as galactic structure tracers - Classification of the bright variables

The characteristics of the 'bright infrared variables' (BIRVs), a sample consisting of the 300 brightest stars in the IRAS Point Source Catalog with IRAS variability index VAR of 98 or greater, are investigated with the purpose of establishing which of IRAS variables are AGB stars (e.g., oxygen-rich Miras and carbon stars, as was assumed by Weinberg (1992)). Results of the analysis of optical, infrared, and microwave spectroscopy of these stars indicate that, out of 88 stars in the BIRV sample identified with cataloged variables, 86 can be classified as Miras. Results of a similar analysis performed for a color-selected sample of stars, using the color limits employed by Habing (1988) to select AGB stars, showed that, out of 52 percent of classified stars, 38 percent are non-AGB stars, including H II regions, planetary nebulae, supergiants, and young stellar objects, indicating that studies using color-selected samples are subject to misinterpretation.

Allen, L. E.↗

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Many animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and could act as reservoirs; however, transmission in free-living animals has not been documented. White-tailed deer, the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 is circulating in deer, 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through January of 2021 were assayed for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 (33.2%) deer samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, following the November 2020 peak of human cases in Iowa, and coinciding with the onset of winter and the peak deer hunting season, SARS-CoV-2 RNA was detected in 80 of 97 (82.5%) RPLN samples collected over a 7-wk period. Whole genome sequencing of all 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%) and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple human-to-deer transmission events followed by subsequent deer-to-deer spread. These discoveries have important implications for the long-term persistence of the SARS-CoV-2 pandemic. Our findings highlight an urgent need for a robust and proactive “One Health” approach to obtain enhanced understanding of the ecology, molecular evolution, and dissemination of SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗

A supercluster catalog

The largest available complete redshift sample of rich clusters of galaxies is used to construct a three-dimensional catalog of superclusters complete to redhsift of about 0.08 or less. The criterion of membership in the catalog is the density enhancement of clusters over the mean density; the catalog is presented for various values of this parameter. The dependence of the identified sample of superclusters on the overdensity is studied, and the sensitivity of the identified superclusters to various quantities and selection procedures is investigated. The validity of the identification procedure is established by comparisons with random catalogs.

Bahcall, N. A.↗

Historic climate, cosmogenic 10Be, denudation-rate, and geospatial datasets from the Pikes Peak region, Colorado, USA

This data package contains geographic information system (GIS) layers and tabular datasets associated with the study of elevation-dependent denudation rates on Pikes Peak in the Front Range of the Rocky Mountains, Colorado, USA. The package includes GIS layers used to produce the study-area map, including sample locations, sample watershed boundaries, the Pikes Peak batholith, Pleistocene glacier extent, weather station locations, and elevation and hillshade rasters, together with comma-separated value (CSV) tables and matching CSV data dictionaries. These mapped layers provide the geographic framework for interpreting denudation patterns across the Pikes Peak region and for relating sample locations to watershed geometry, bedrock setting, glacial history, and nearby climate stations. The first group of tables reports climate and geospatial context for the study area. These files include station-based temperature and precipitation data used to characterize elevational gradients in mean annual climate and monthly climate seasonality, sample locations, denudation-rate and topographic metrics, fixed frost-cracking model parameters, frost-cracking intensity and precipitation-frequency metrics, and stream-power inversion results. Together, these data provide the basis for evaluating how denudation varies with elevation, climate, and landscape form across sampled catchments on Pikes Peak. The second group of tables reports cosmogenic nuclide and erosion-model results used in the denudation analysis. Included files contain accelerator mass spectrometry (AMS) measurements for in situ-produced cosmogenic beryllium-10 (10Be), including sample identifiers, measured 10Be:9Be ratios, analytical uncertainties, carrier mass, quartz mass, blank corrections, blank-group statistics, and calculated 10Be concentrations and uncertainties. Additional tables summarize stream-power-law inversion results for sampled catchments, including optimized model parameters, predicted erosion rates, residual metrics, channel-pixel counts, and convergence status, as well as regression equations and summary statistics used to evaluate relationships among elevation, climate, frost cracking, precipitation forcing, and denudation rate. The package contains GIS files, comma-separated value files (.csv), Microsoft Excel files (.xlsx), CSV data dictionaries, a file-level metadata table, and a readme text file.

10Be cosmogenic nuclides↗

Submillimeter constraints on dust near Lindroos' post T Tauri stars

Young stars from the dynamical sample identified by Lindroos (A&A, 156,223 (1986)) have been observed at 800 micrometers wavelength using the James Clerk Maxwell Telescope on Mauna Kea. The new data are used to constrain the mass of circumstellar dust around these stars. The Lindroos sample is dominated by low-mass stars of age (3-150) x 10(exp 6) yr, intermediate in age between the T Tauri and main-sequence stars. When combined with previous measurements, the present observations are compatible with the depletion of circumstellar dust on a time scale tau approximately 10(exp 7.0) yr. If this dust is present in circumstellar disks, then tau represents the lifetime of these disks.

Jewitt, David C.↗

Binning is Sinning: Redemption for Hubble Diagram Using Photometrically Classified Type Ia Supernovae

Bayesian Estimation Applied to Multiple Species (BEAMS) is implemented in the BEAMS with Bias Corrections (BBC) framework to produce a redshift-binned Hubble diagram (HD) for Type Ia supernovae (SNe Ia). BBC corrects for selection effects and non–SN Ia contamination, and systematic uncertainties are described by a covariance matrix with dimension matching the number of BBC redshift bins. For spectroscopically confirmed SN Ia samples, a recent "Binning is Sinning" article showed that an unbinned HD and covariance matrix reduces the systematic uncertainty by a factor of ~1.5 compared to the binned approach. Here we extend their analysis to obtain an unbinned HD for a photometrically identified sample processed with BBC. To test this new method, we simulate and analyze 50 samples corresponding to the Dark Energy Survey (DES) with a low-redshift anchor; the simulation includes SNe Ia, and contaminants from core-collapse SNe and peculiar SNe Ia. The analysis includes systematic uncertainties for calibration and measures the dark energy equation of state parameter (w). Compared to a redshift-binned HD, the unbinned HD with nearly 2000 events results in a smaller systematic uncertainty, in qualitative agreement with BHS21, and averaging results among the 50 samples we find no evidence for a w-bias. To reduce computation time for fitting an unbinned HD with large samples, we propose an HD-rebinning method that defines the HD in bins of redshift, color, and stretch; the rebinned HD results in similar uncertainty as the unbinned case, and shows no evidence for a w-bias.

79 ASTRONOMY AND ASTROPHYSICS↗

BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes

Secondary metabolites are compounds not essential for an organism’s development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Osmium Isotope Constraints on the Proportion of Bolide Component in Chicxulub Impact Melts

Recent drilling has produced the samples of impact melt breccias examined here. All samples examined here are from the YAX-1 borehole [7]. Two main types of impact breccias have been studied. The first type is a green altered impact meltrock found in the lower portion of the impact sequence. The texture of the rock is microcrystalline and is composed of pyroxene, plagioclase, and alkali feldspars. Its composition is consistent with continental margin rocks. It is generally massive with some flow structure. The rock was brecciated and altered after solidfication and contains small amounts of both shocked and unshocked clasts of the impacted lithologies. These lithologies include lithic quartzite, and isolated feldspar crystals. The compositions of these rocks are similar to those seen in meltrocks sampled by the Yucatan-6 borehole [8-9]. Our study includes samples YAX-1_861.4, YAX-1_863.51, and YAX- 1_876.46, which represent both the top and lower portion of the green impact meltrock. The middle sample in the sequence has the least amount of (mineralogical) alteration [10]. The second type of melt breccia under study is a brown altered impact meltrock. It also has a microcrystalline texture and both shocked and unshocked clasts of the target material. Even though this rock type has been altered, remnant schleiren, metaquartzite, and micritic calcite have been identified. Sample YAX-1_841.32 is representative of this type of rock. It was recovered from a polymict breccia in the middle of the impact sequence.

Gelinas, A.↗

Candidate sample acquisition systems for the Rosetta

The Comet Nucleus Sample Return (CNSR) mission, one of the four cornerstones of the ESA scientific program, is one of the most complex space ventures within the next century, both from technological and deep space exploration point of view. In the Rosetta scenario the sample acquisition phase represents the most critical point for the global mission's success. The proposed paper illustrates the main results obtained in the context of the CNSR-SAS ongoing activity. The main areas covered are related to: (1) sample properties characterization (comet soil model, physical/chemical properties, reference material for testing); (2) concepts identification for coring, shovelling, harpooning and anchoring; (3) preferred concept (trade off among concepts, identification of the preferred configuration); and (4) proposed development activity for gaining the necessary confidence before finalizing the CNSR mission. Particular emphasis will be given to the robotic and flexibility aspects of the identified sample acquisition systems (SAS) configuration, intended as a means for the overall system performance enhancement.

Magnani, P. G.↗