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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Increasing Al-Pair Abundance in SSZ-13 Zeolite via Zeolite Synthesis in the Presence of Alkaline Earth Metal Hydroxide Produces Hydrothermally Stable Co-, Cu- and Pd-SSZ-13 Materials

Replacing alkaline for alkaline-earth metal hydroxide in the synthesis gel during the synthesis of siliceous SSZ-13 zeolite (Si/Al~10) yields SSZ-13 with novel, advantageous properties. Its NH 4 -form ion-exchanges higher amount of isolated divalent M(II) ions than the conventional one: this is the consequence of an increased number of Al pairs in the structure induced by the +2 charge of Sr(II) cations in the synthesis gel that force two charge-compensating AlO 4 – motives to reside closer together. We characterize the +2 state of Co(II) ions in these materials with infra-red spectroscopy and X-ray absorption spectroscopy measurements and show their utility for NOx pollutant adsorption from ambient air: the ones derived from SSZ-13 with higher Al pair content contain more isolated cobalt(II) and, thus, perform better as ambient-air NOx adsorbers. Notably, Co(II)/SSZ-13 with an increased number of Al pairs is significantly more hydrothermally stable than its NaOH-derived analogue. Loading Pd(II) into Co-SSZ-13(Sr) produces an active NOx adsorber (PNA) material that can be used for NOx adsorption from simulated diesel engine exhaust. The critical issue for these applications is hydrothermal stability of Pd-zeolites. Pd/SSZ-13 synthesized in the presence of Sr(OH) 2 does not lose its PNA capacity after extremely harsh aging at 850 and 900 °C (10 h in 10% H 2 O/air flow) and loses only ~55% capacity after hydrothermal aging at 930 °C. This can be extended to other divalent metals for catalytic applications, such as copper: we show that Cu/SSZ-13 catalyst can survive hydrothermal aging at 920 °C without losing its catalytic properties, metal dispersion and crystalline structure. Thus, we provide a new, simple, and scalable strategy for making remarkably (hydro)thermally stable metal-zeolite materials/catalysts with a number of useful applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Quantification of Uncoupled Spin Domains in Spin-Abundant Disordered Solids

Materials often contain minor heterogeneous phases that are difficult to characterize yet nonetheless significantly influence important properties. Here we describe a solid-state NMR strategy for quantifying minor heterogenous sample regions containing dilute, essentially uncoupled nuclei in materials where the remaining nuclei experience heteronuclear dipolar couplings. NMR signals from the coupled nuclei are dephased while NMR signals from the uncoupled nuclei can be amplified by one or two orders of magnitude using Carr-Meiboom-Purcell-Gill (CPMG) acquisition. The signal amplification by CPMG can be estimated allowing the concentration of the uncoupled spin regions to be determined even when direct observation of the uncoupled spin NMR signal in a single pulse experiment would require an impractically long duration of signal averaging. We use this method to quantify residual graphitic carbon using 13 C CPMG NMR in poly(carbon monofluoride) samples synthesized by direct fluorination of carbon from various sources. Our detection limit for graphitic carbon in these materials is better than 0.05 mol%. The accuracy of the method is discussed and comparisons to other methods are drawn.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Plasmonic Core–Shell–Satellites with Abundant Electromagnetic Hotspots for Highly Sensitive and Reproducible SERS Detection

In this work, we develop a Ag@Al2O3@Ag plasmonic core–shell–satellite (PCSS) to achieve highly sensitive and reproducible surface-enhanced Raman spectroscopy (SERS) detection of probe molecules. To fabricate PCSS nanostructures, we employ a simple hierarchical dewetting process of Ag films coupled with an atomic layer deposition (ALD) method for the Al2O3 shell. Compared to bare Ag nanoparticles, several advantages of fabricating PCSS nanostructures are discovered, including high surface roughness, high density of nanogaps between Ag core and Ag satellites, and nanogaps between adjacent Ag satellites. Finite-difference time-domain (FDTD) simulations of the PCSS nanostructure confirm an enhancement in the electromagnetic field intensity (hotspots) in the nanogap between the Ag core and the satellite generated by the Al2O3 shell, due to the strong core–satellite plasmonic coupling. The as-prepared PCSS-based SERS substrate demonstrates an enhancement factor (EF) of 1.7 × 107 and relative standard deviation (RSD) of ~7%, endowing our SERS platform with highly sensitive and reproducible detection of R6G molecules. We think that this method provides a simple approach for the fabrication of PCSS by a solid-state technique and a basis for developing a highly SERS-active substrate for practical applications.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Earth Abundant Oxidation Catalysts for Removal of Contaminants of Emerging Concern from Wastewater: Homogeneous Catalytic Screening of Monomeric Complexes

Twenty novel Mn, Fe, and Cu complexes of ethylene cross-bridged tetraazamacrocycles with potentially copolymerizable allyl and benzyl pendant arms were synthesized and characterized. Multiple X-ray crystal structures demonstrate the cis-folded pseudo-octahedral geometry forced by the rigidifying ethylene cross-bridge and show that two cis coordination cites are available for interaction with substrate and oxidant. The Cu complexes were used to determine kinetic stability under harsh acidic and high-temperature conditions, which revealed that the cyclam-based ligands provide superior stabilization with half-lives of many minutes or even hours in 5 M HCl at 50–90 °C. Cyclic voltammetry studies of the Fe and Mn complexes reveal reversible redox processes indicating stabilization of Fe 2+ /Fe 3+ and Mn 2+ /Mn 3+ /Mn 4+ oxidation states, indicating the likelihood of catalytic oxidation for these complexes. Finally, dye-bleaching experiments with methylene blue, methyl orange, and rhodamine B demonstrate efficient catalytic decolorization and allow selection of the most successful monomeric catalysts for copolymerization to produce future heterogeneous water purification materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

SAGAbg. I. A Near-unity Mass-loading Factor in Low-mass Galaxies via Their Low-redshift Evolution in Stellar Mass, Oxygen Abundance, and Star Formation Rate

Measuring the relation between star formation and galactic winds is observationally difficult. In this work we make an indirect measurement of the mass-loading factor (the ratio between the mass outflow rate and star formation rate) in low-mass galaxies using a differential approach to modeling the low-redshift evolution of the star-forming main sequence and mass–metallicity relation. We use Satellites Around Galactic Analogs (SAGA) background galaxies, i.e., spectra observed by the SAGA Survey that are not associated with the main SAGA host galaxies, to construct a sample of 11,925 spectroscopically confirmed low-mass galaxies from 0.01 ≲ z ≤ 0.21 and measure auroral line metallicities for 120 galaxies. The crux of the method is to use the lowest-redshift galaxies as the boundary condition of our model, and to infer a mass-loading factor for the sample by comparing the expected evolution of the low-redshift reference sample in stellar mass, gas-phase metallicity, and star formation rate against the observed properties of the sample at higher redshift. We infer a mass-loading factor of η m = $0.92^{+1.76}_{-0.74}$, which is in line with direct measurements of the mass-loading factor from the literature despite the drastically different sets of assumptions needed for each approach. While our estimate of the mass-loading factor is in good agreement with recent galaxy simulations that focus on resolving the dynamics of the interstellar medium, it is smaller by over an order of magnitude than the mass-loading factor produced by many contemporary cosmological simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Production of Heavy α -Elements and 44 Ti in Cas A: Comparison to Abundances from 1D Core-collapse Supernova Models and Evidence for Carbon–Oxygen Shell Mergers

The merger between the carbon (C) and oxygen (O) shells hours to days before the collapse of a massive star significantly changes its nucleosynthesis, which is reflected in the elemental ratios observed in supernova remnants (SNRs). We present a nucleosynthesis study of 44 Ti production in core-collapse supernovae (CCSNe), highlighting large silicon (Si), sulfur (S), calcium (Ca), and, most importantly, argon (Ar) to neon (Ne) ratios as diagnostics for carbon–oxygen (C–O) shell mergers. We compare yields from eight different sets of CCSNe models to observations of Cassiopeia A (Cas A), and show that C–O shell mergers are consistently the models that best match X-ray and infrared observations. These models produce high Ar/Ne ratios (≳0.1), due to 20 Ne depletion and production of 36 Ar and 38 Ar, while lower ratios are obtained from nonmerger cases. Based on the Ar/Ne diagnostic, we compare the range of expected 44 Ti produced by C–O shell mergers, which is up to ∼20%–30% of the overall 44 Ti, but expected to be located outside the reverse shock. Based on the sets of models considered, the photon flux expected from the 44 Ti synthesized in the C–O shell merger in Cas A is below the NuSTAR and COSI detection limits, compatible with current limits locating most of the 44 Ti interior to the reverse shock, but might be detectable from proposed missions like ASCENT. Finally, for the SNR of 1987A, a dominant C–O merger origin of the observed 44 Ti is unlikely based on the observed redshift in its 44 Ti line.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Dark Energy Survey Year 3 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Clustering

Galaxy clusters provide a unique probe of the late-time cosmic structure and serve as a powerful independent test of the $\Lambda$CDM model. This work presents the first set of cosmological constraints derived with ~16,000 optically selected redMaPPer clusters across nearly 5,000 $\rm{deg}^2$ using DES Year 3 data sets. Our analysis leverages a consistent modeling framework for galaxy cluster cosmology and DES-Y3 joint analyses of galaxy clustering and weak lensing (3x2pt), ensuring direct comparability with the DES-Y3 3x2pt analysis. We obtain constraints of $S_8 = 0.864 \pm 0.035$ and $\Omega_{\rm{m}} = 0.265^{+0.019}_{-0.031}$ from the cluster-based data vector. We find that cluster constraints and 3x2pt constraints are consistent under the $\Lambda$CDM model with a Posterior Predictive Distribution (PPD) value of $0.53$. The consistency between clusters and 3x2pt provides a stringent test of $\Lambda$CDM across different mass and spatial scales. Jointly analyzing clusters with 3x2pt further improves cosmological constraints, yielding $S_8 = 0.811^{+0.022}_{-0.020}$ and $\Omega_{\rm{m}} = 0.294^{+0.022}_{-0.033}$, a $24\%$ improvement in the $\Omega_{\rm{m}}-S_8$ figure-of-merit over 3x2pt alone. Moreover, we find no significant deviation from the Planck CMB constraints with a probability to exceed (PTE) value of $0.6$, significantly reducing previous $S_8$ tension claims. Finally, combining DES 3x2pt, DES clusters, and Planck CMB places an upper limit on the sum of neutrino masses of $\sum m_\nu < 0.26$ eV at 95% confidence under the $\Lambda$CDM model. These results establish optically selected clusters as a key cosmological probe and pave the way for cluster-based analyses in upcoming Stage-IV surveys such as LSST, Euclid, and Roman.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Atmospheric particle abundance and sea salt aerosol observations in the springtime Arctic: a focus on blowing snow and leads

Abstract. Sea salt aerosols play an important role in the radiation budget and atmospheric composition over the Arctic, where the climate is rapidly changing. Previous observational studies have shown that Arctic sea ice leads are an important source of sea salt aerosols, and modeling efforts have also proposed blowing snow sublimation as a source. In this study, size-resolved atmospheric particle number concentrations and chemical composition were measured at the Arctic coastal tundra site of Utqiaġvik, Alaska, during spring (3 April–7 May 2016). Blowing snow conditions were observed during 25 % of the 5-week study period and were overpredicted by a commonly used blowing snow parameterization based solely on wind speed and temperature. Throughout the study, open leads were present locally. During periods when blowing snow was observed, significant increases in the number concentrations of 0.01–0.06 µm particles (factor of 6, on average) and 0.06–0.3 µm particles (67 %, on average) and a significant decrease (82 %, on average) in 1–4 µm particles were observed compared to low wind speed periods. These size distribution changes were likely caused by the generation of ultrafine particles from leads and/or blowing snow, with scavenging of supermicron particles by blowing snow. At elevated wind speeds, both submicron and supermicron sodium and chloride mass concentrations were enhanced, consistent with wind-dependent local sea salt aerosol production. At moderate wind speeds below the threshold for blowing snow as well as during observed blowing snow, individual sea spray aerosol particles were measured. These individual salt particles were enriched in calcium relative to sodium in seawater due to the binding of this divalent cation with organic matter in the sea surface microlayer and subsequent enrichment during seawater bubble bursting. The chemical composition of the surface snowpack also showed contributions from sea spray aerosol deposition. Overall, these results show the contribution of sea spray aerosol production from leads on both aerosols and the surface snowpack. Therefore, if blowing snow sublimation contributed to the observed sea salt aerosol, the snow being sublimated would have been impacted by sea spray aerosol deposition rather than upward brine migration through the snowpack. Sea spray aerosol production from leads is expected to increase, with thinning and fracturing of sea ice in the rapidly warming Arctic.

54 ENVIRONMENTAL SCIENCES↗