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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Proteomic-based stable isotope probing reveals taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

Heterotrophic marine bacterioplankton are a critical component of the carbon cycle, processing nearly a quarter of annual global primary production, yet defining how substrate utilization preferences and resource partitioning structure these microbial communities remains a challenge. In this study, we utilized proteomics-based stable isotope probing (proteomic SIP) to characterize the assimilation of amino acids by coastal marine bacterioplankton populations. We incubated microcosms of seawater collected from Newport, OR and Monterey Bay, CA with 1 M 13 C-amino acids for 15 and 32 hours. Subsequent analysis of 13 C incorporation into protein biomass quantified the frequency and extent of isotope enrichment for identified proteins. Using these metrics we tested whether amino acid assimilation patterns were different for specific bacterioplankton populations. Proteins associated with Rhodobacterales and Alteromonadales tended to have a significantly high number of tandem mass spectra from 13 C-enriched peptides, while Flavobacteriales and SAR11 proteins generally had significantly low numbers of 13 C-enriched spectra. Rhodobacterales proteins associated with amino acid transport and metabolism had an increased frequency of 13 C-enriched spectra at time-point 2, while Alteromonadales ribosomal proteins were 13 C- enriched across time-points. Overall, proteomic SIP facilitated quantitative comparisons of dissolved free amino acids assimilation by specific taxa, both between sympatric populations and between protein functional groups within discrete populations, allowing an unprecedented examination of population-level metabolic responses to resource acquisition in complex microbial communities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

5-Bromosalicylalcohol was prepared by the interaction of NaBH{sub 4} and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, {sup 1}H NMR, {sup 13}C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Spectroscopy and Regge trajectories of heavy quarkonia in the relativistic quark model

The mass spectra of charmonia and bottomonia are calculated in the framework of the relativistic quark model up to high orbital and radial excitations. The Regge trajectories of heavy quarkonia are constructed both in the (J,M{sup 2}) and (n{sub r},M{sup 2}) planes, where J is the total angular momentum and nr is the radial quantum number. All daughter trajectories turn out to be almost linear and parallel, while parent trajectories exhibit some nonlinearity. Such nonlinearity occurs only in the vicinity of ground states and few lowest excitations and is more pronounced for bottomonia, while it is only marginal for charmonia. The obtained results are compared with available experimental data, and a possible interpretation of the new charmonium-like states above open charm production threshold is discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

New Cluster Secondary Ions for Quantitative Analysis of the Concentration of Boron Atoms in Diamond by Time-of-Flight Secondary-Ion Mass Spectrometry

A new approach to quantitative analysis of the concentration of boron atoms in diamond using secondary- ion mass spectrometers with time-of-flight mass analyzers is proposed. Along with the known boron-containing lines (B, BC, BC{sub 2}), many lines related to cluster secondary ions BC{sub N} have been found in the mass spectrum; their intensity increases by one or two orders of magnitude when Bi{sub 3} probe ions are used. Lines BC{sub 4}, BC{sub 6}, BC{sub 2}, and BC{sub 8} have the highest intensity (in the descending order); when they are summed, the sensitivity increases by an order of magnitude in comparison with the known mode of detecting BC{sub 2}. The parameters of the boron δ-layer in single-crystal diamond films grown under optimal conditions have been measured to be unprecedented: the δ-layer width is about 2 nm, and the concentration is 6.4 × 10{sup 20} cm{sup –3} (the boron concentrations for doped and undoped diamonds differ by four orders of magnitude).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Supersymmetry in Light of 1/fb of LHC Data

We update previous frequentist analyses of the CMSSM and NUHM1 parameter spaces to include the public results of searches for supersymmetric signals using ~1 /fb of LHC data recorded by ATLAS and CMS and ~0.3/fb of data recorded by LHCb in addition to electroweak precision and B-physics observables. We also include the constraints imposed by the cosmological dark matter density and the XENON100 search for spin-independent dark matter scattering. The LHC data set includes ATLAS and CMS searches for jets + missing ET events and for the heavier MSSM Higgs bosons, and the upper limits on B_s to mu^+ mu^- from LHCb and CMS. The absences of jets + missing ET signals in the LHC data favour heavier mass spectra than in our previous analyses of the CMSSM and NUHM1, which may be reconciled with (g-2)_mu if tan beta ~ 40, a possibility that is however under pressure from heavy Higgs searches and the upper limits on B_s to mu^+ mu^-. As a result, the p-value for the CMSSM fit is reduced to ~ 15 (38)%, and that for the NUHM1 to ~ 16 (38)%, to be compared with ~ 9 (49)% for the Standard Model limit of the CMSSM for the same set of observables (dropping (g-2)_mu), ignoring the dark matter relic density in both cases. We discuss the sensitivities of the fits to the (g-2)_mu and b to s gamma constraints, contrasting fits with and without the (g-2)_mu constraint, and combining the theoretical and experimental errors for b to s gamma linearly or in quadrature. We present predictions for m_gluino, B_s to mu^+ mu^-, M_h and M_A, and update predictions for spin-independent dark matter scattering, stressing again the importance of taking into account the uncertainty in the pi-nucleon sigma term, Sigma_{pi N}. Finally, we present predictions based on our fits for the likely thresholds for sparticle pair production in e^+e^- collisions in the CMSSM and NUHM1.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Measurement of $\phi $ meson production in $p + p$ interactions at 40, 80 and $158 \, \hbox {GeV}/c$ with the NA61/SHINE spectrometer at the CERN SPS

Results on $\phi$ meson production in inelastic p+p collisions at CERN SPS energies are presented. They are derived from data collected by the NA61/SHINE fixed target experiment, by means of invariant mass spectra fits in the $\phi \to K^+K^-$ decay channel. They include the first ever measured double differential spectra of $\phi$ mesons as a function of rapidity $y$ and transverse momentum $p_T$ for proton beam momenta of 80 GeV/c and 158 GeV/c, as well as single differential spectra of $y$ or $p_T$ for beam momentum of 40 GeV/c. The corresponding total $\phi$ yields per inelastic p+p event are obtained. These results are compared with existing data on $\phi$ meson production in p+p collisions. The comparison shows consistency but superior accuracy of the present measurements. The emission of $\phi$ mesons in p+p reactions is confronted with that occurring in Pb+Pb collisions, and the experimental results are compared with model predictions. It appears that none of the considered models can properly describe all the experimental observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Heavy-light mesons on the light front

Abstract We study the heavy-light mesons within basis light-front quantization. The resulting mass spectra of D , $$D_s$$ D s , B , and $$B_s$$ B s agree reasonably well with experiments. We also predict states which could be measured in the near future. In the light-front formalism, we calculate the light-front wave functions and additional experimental observables, such as parton distribution functions, distribution amplitudes, and decay constants by means of integrations over light-front wave functions. We also provide ratios of decay constants for selected pseudoscalar meson decays ( $$D_s$$ D s to D and $$B_s$$ B s to B ) as they may prove to be theoretically more robust and more reliably determined in experiments. We find that our ratios are systematically smaller than existing experiments and other approaches by 5–18%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

New insights into the doubly charmed exotic mesons

Abstract Using effective Lagrangians constrained by the heavy quark spin symmetry and chiral symmetry, for the light quarks, we analyze the $$D^0 D^0\pi ^+,$$ D 0 D 0 π + , $$\bar{D}^0D^0\pi ^0$$ D ¯ 0 D 0 π 0 and $$D^0\bar{D}^{*0}$$ D 0 D ¯ ∗ 0 invariant mass spectra. Performing a simultaneous analysis of the doubly charmed and charm-anti-charm states gives further insights into the nature of the $$T^+_{cc}$$ T cc + and $$\chi ^0_{c1}(3872),$$ χ c 1 0 ( 3872 ) , exotic hadrons. It is confirmed that both states should lie below their respective $$DD^*$$ D D ∗ / $$D\bar{D}^*$$ D D ¯ ∗ thresholds. Also, the contributions of the triangle and box diagrams are negligible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Enhancing the hunt for new phenomena in dijet final states using anomaly detection filters at the high-luminosity large Hadron Collider

In the realm of dijet searches in high-energy physics, a significant challenge has emerged: with experiments producing more and more data, the traditional methods of using analytic functions to describe dijet mass spectra start to fail. Here, to address this, we suggest the application of an anomaly detection approach to eliminate less interesting background events based on event final states. This method not only bypasses the limitations of conventional background models but also significantly enhances our ability to detect potential signals of new physics. Through simulations that mimic the conditions of the upcoming high-luminosity large Hadron collider, we demonstrate the strength and efficiency of this approach in dealing with large data volumes. The integration of unsupervised machine learning into our experimental framework paves the way for a promising avenue to unveil hidden physics discoveries within the overwhelming influx of data.

47 OTHER INSTRUMENTATION↗
DOE OSTI2012

ATS Spotted MSI Analysis with Matlab

Samples are placed on a surface using an acoustic transfer system (ATS). This results in one ore more small droplets on a surface. Typically there are hundreds to thousands of these droplets arrayed in a regular coordinate system. The surface is analyzed using mass spectrometry imaging (MSI) and at each position, one or more mass spectra are recorded. The purpose of the software is to help the user assign locations to the spots and build a report for each spot.

Bowen, Benjamin↗
DOE OSTI2023

QC-GN2OMS2

The QC-GN2OMS2 neural network was designed to predict mass spectra better than currently available approaches. Fundamentally the neural net is designed to input the structure of a molecule and collision energy value then output a spectra datafile for the end user. This software is able to make predictions orders of magnitude faster (milliseconds) than QC methods and with 50-60% greater accuracy than rules approaches.

Overstreet, Richard↗
DOE OSTI2021

BLINK v1

We introduce the Binned Large Interval Network Kernel approach for scoring fragmentation mass spectra similarity which takes advantage of sparse matrix multiplication. This enables BLINK to perform 100 million comparisons while maintaining 98% accuracy in 2.2 seconds making it over 1,000 times faster than the current implementations.

Bowen, Benjamin↗
DOE OSTI2013

Laboratory Studies of the Reactive Chemistry and Changing CCN Properties of Secondary Organic Aerosol, Including Model Development

The chemical evolution of secondary-organic-aerosol (SOA) particles and how this evolution alters their cloud-nucleating properties were studied. Simplified forms of full Koehler theory were targeted, specifically forms that contain only those aspects essential to describing the laboratory observations, because of the requirement to minimize computational burden for use in integrated climate and chemistry models. The associated data analysis and interpretation have therefore focused on model development in the framework of modified kappa-Koehler theory. Kappa is a single parameter describing effective hygroscopicity, grouping together several separate physicochemical parameters (e.g., molar volume, surface tension, and van't Hoff factor) that otherwise must be tracked and evaluated in an iterative full-Koehler equation in a large-scale model. A major finding of the project was that secondary organic materials produced by the oxidation of a range of biogenic volatile organic compounds for diverse conditions have kappa values bracketed in the range of 0.10 +/- 0.05. In these same experiments, somewhat incongruently there was significant chemical variation in the secondary organic material, especially oxidation state, as was indicated by changes in the particle mass spectra. Taken together, these findings then support the use of kappa as a simplified yet accurate general parameter to represent the CCN activation of secondary organic material in large-scale atmospheric and climate models, thereby greatly reducing the computational burden while simultaneously including the most recent mechanistic findings of laboratory studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Organic Aerosol Component (OACOMP) Value-Added Product (Report)

Significantly improved returns in their aerosol chemistry data can be achieved via the development of a value-added product (VAP) of deriving OA components, called Organic Aerosol Components (OACOMP). OACOMP is primarily based on multivariate analysis of the measured organic mass spectral matrix. The key outputs of OACOMP are the concentration time series and the mass spectra of OA factors that are associated with distinct sources, formation and evolution processes, and physicochemical properties.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Study of Orbitally Excited $B_{(s)}$ Mesons and Evidence for a New $B\pi$ Resonance with the CDF II Detector

This thesis presents an analysis of excited states of B0, B+ and B0 s mesons, decaying to B mesons while emitting a pion or kaon. They are reconstructed from their decay products and a selection is performed to discard wrongly reconstructed B(s) mesons with the multivariate analysis software NeuroBayes, as described in chapter 5. In the training process, the sPlot method and measured and simulated data are used. Chapter 6 describes how the properties of excited B(s) are determined by an unbinned maximum likelihood t to their mass spectra. The systematic uncertainties determined in this analysis are described in chapter 7. The results of this thesis are presented in chapter 8 and a conclusion is given in chapter 9. The results shown in this thesis have been published before in [1].

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗