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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↗

NASA NTRS1983

A photoelectric lightcurve survey of small main belt asteroids

A survey to obtain photoelectric lightcurves of small main-belt asteroids was conducted from November 1981 to April 1982 using the 0.91- and 2.1-m telescopes at the University of Texas McDonald Observatory. A total of 18 main-belt asteroids having estimated dimaters under 30 km were observed with over half of these being smaller than 15 km. Rotational periods were determined or estimated from multiple nights of observation for nearly all of these yielding a sample of 17 small main-belt asteroids which is believed to be free of observational selection effects. All but two of these objects were investigated for very short periods in the range of 1 min to 2 hr using power spectrum analysis of a continuous set of integrations. No evidence for such short periods was seen in this sample. Rotationally averaged B(1,0) magnitudes were determined for most of the surveyed asteroids, allowing diameter estimates to be made. Imposing the suspected selection effects of photogaphic photometry on the results of this survey gives excellent agreement with the results from that technique. This shows that the inability of photographic photometry to obtain results for many asteroids is indeed due to the rotational parameter of those asteroids.

Binzel, R. P.↗

NASA NTRS1983

Adaptive reference voltage generator for firing angle control of line-commutated inverters

A control system for a permanent-magnet motor driven by a multiphase line-commulated inverter is described. It is provided with integrators for integrating the back EMF of each phase of the motor for use in generating system control signals for an inverter gate logic using a sync and firing angle control generator connected to the outputs of the integrators. The firing angle control signals are produced by the control generator by means for combining 120 deg segments of the integrated back EMF signals symmetrical about their maxima into composite positive and negative waveforms, and means for sampling the maxima of each waveform every 120 deg. These samples are then used as positive and negative firing angle control signals. Whereby any change in amplitude of the integrated back EMF signals will not affect a change in the operating power factor of the motor and inverter.

Dolland, C. R.↗

DOE OSTI2022

Measurement of prompt charged-particle production in pp collisions at $\sqrt{s}$ = 13 TeV

The differential cross-section of prompt inclusive production of long-lived charged particles in proton-proton collisions is measured using a data sample recorded by the LHCb experiment at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV. The data sample, collected with an unbiased trigger, corresponds to an integrated luminosity of 5.4 nb -1 . The differential cross-section is measured as a function of transverse momentum and pseudorapidity in the ranges $p_T$ ∋ [80, 10 000) MeV/c and η ∋ [2.0, 4.8) and is determined separately for positively and negatively charged particles. The results are compared with predictions from various hadronic-interaction models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Inclusive search for supersymmetry in pp collisions at $ \sqrt{s}=13 $ TeV using razor variables and boosted object identification in zero and one lepton final states

An inclusive search for supersymmetry (SUSY) using the razor variables is performed using a data sample of proton-proton collisions corresponding to an integrated luminosity of 35.9 fb$^{-1}$, collected with the CMS experiment in 2016 at a center-of-mass energy of $\sqrt{s} =$ 13 TeV. The search looks for an excess of events with large transverse energy, large jet multiplicity, and large missing transverse momentum. The razor kinematic variables are sensitive to large mass differences between the parent particle and the invisible particles of a decay chain and help to identify the presence of SUSY particles. The search covers final states with zero or one charged lepton and features event categories divided according to the presence of a high transverse momentum hadronically decaying W boson or top quark, the number of jets, the number of b-tagged jets, and the values of the razor kinematic variables, in order to separate signal from background for a broad range of SUSY signatures. The addition of the boosted W boson and top quark categories within the analysis further increases the sensitivity of the search, particularly to signal models with large mass splitting between the produced gluino or squark and the lightest SUSY particle. Furthermore, the analysis is interpreted using simplified models of $R$-parity conserving SUSY, focusing on gluino pair production and top squark pair production. Limits on the gluino mass extend to 2.0 TeV, while limits on top squark mass reach 1.14 TeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Constraints on the CKM angle γ from B ± → Dh ± decays using D → h ± h' ∓ π 0 final states

A data sample collected with the LHCb detector corresponding to an integrated luminosity of 9 fb –1 is used to measure eleven CP violation observables in B ± → Dh ± decays, where h is either a kaon or a pion. The neutral D meson decay is reconstructed in the three-body final states: K ± π ∓ π o ; π + π – π o ; K + K – π o and the suppressed π ± K ∓ π o combination. The mode where a large CP asymmetry is expected, B ± → [π ± K ∓ π o ] D K ± , is observed with a significance greater than seven standard deviations. The ratio of the partial width of this mode relative to that of the favoured mode, B ± → [K ± π ∓ π o ] D K ± , is R ADS(K) = (1.27 ± 0.16 ± 0.02) × 10 –2 . Evidence for a large CP asymmetry is also seen: A ADS(K) = –0.38 ± 0.12 ± 0.02. Constraints on the CKM angle γ are calculated from the eleven reported observables.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Study of coherent J/ ψ production in lead-lead collisions at $\sqrt{{\mathrm{s}}_{\mathrm{NN}}} $ = 5 TeV

Coherent production of J/ψ mesons is studied in ultraperipheral lead-lead collisions at a nucleon-nucleon centre-of-mass energy of 5 TeV, using a data sample collected by the LHCb experiment corresponding to an integrated luminosity of about 10 μb –1 . The J/ψ mesons are reconstructed in the dimuon final state and are required to have transverse momentum below 1 GeV. The cross-section within the rapidity range of 2.0 < y < 4.5 is measured to be 4.45 ± 0.24 ± 0.18 ± 0.58 mb, where the first uncertainty is statistical, the second systematic and the third originates from the luminosity determination. The cross-section is also measured in J/ψ rapidity intervals. The results are compared to predictions from phenomenological models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Measurement of prompt open-charm production cross sections in proton-proton collisions at $$ \sqrt{s} $$ = 13 TeV

The production cross sections for prompt open-charm mesons in proton-proton collisions at a center-of-mass energy of 13 TeV are reported. The measurement is performed using a data sample collected by the CMS experiment corresponding to an integrated luminosity of 29 nb-1. The differential production cross sections of the D *± , D ± , and D 0 $(\bar{D}^0)$ mesons are presented in ranges of transverse momentum and pseudorapidity 4 < pT < 100 GeV and |η| < 2.1, respectively. The results are compared to several theoretical calculations and to previous measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Experiments with a prototype titanium hot cavity surface ionization source intended for electromagnetic separation of radioactive samarium and other lanthanide elements

This paper reports experimental results of a prototype titanium surface ionization source. For the first time, a lanthanide ion beam has been produced with a surface ionizer composed completely of titanium metal. Titanium does not readily activate with neutron irradiation. This offers the potential for inserting an ion source made of titanium directly into a reactor with a pre-loaded non-radioactive lanthanide target. This seamlessly integrates target irradiation with isotope separation, eliminating post irradiation sample manipulation. Samarium ion beam currents up to 960 nA have been produced in an off-line test bench equipped with rudimentary beam optics. This is a crucial step toward the development of an ionization source adopted for the electromagnetic isotope separator (EMIS) facility, which has been designed for high throughput separations of radioactive 153 Sm and other lanthanides of interest in the field of nuclear medicine. The ion current and important factors affecting the performance of the ion source, such as the ionizer temperature and thermal gradient, are discussed. Lastly, the experimental results are presented together with a discussion of future modifications to optimize the overall surface ionization source performance.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2017

Assessment of Corrosion Resistance of Candidate Alloys for Accident Tolerant Fuel Cladding under Reactor Conditions

The environment of a light water reactor (LWR) core is a combination of high temperatures, high pressures, high neutron and gamma fluxes, mechanical stresses and chemical aggressive coolants. All of these factors combined can induce changes in the microstructure of the fuel and cladding that are very difficult to predict in a systematic fashion [1] and are major challenge for the safety and life extension of current reactors. Throughout reactor transients and accidents, the cladding may experience deterioration caused by a temperature increase, oxidation embrittlement [1], [2], or mechanical interaction with the fuel caused by stress [3]. These events may lead to cracking or rupture of the cladding, causing the release of fission products into the coolant. Such events have been observed at the Three Mile Island and Fukushima accidents. To avoid such occurrences in LWRs, the accident tolerant fuels (ATF) program was initiated to focus on the replacement of zirconium-based alloys with materials that exhibit slower steam oxidation kinetics. This project focuses on several iron-based alloys such as T91, APMT, MA956, experimental Fe-Cr alloys and one experimental nanofeatured alloy (NFA). Experiments have been conducted in both PWR primary water at 320°C and BWR normal water chemistry at 288°C, spanning a large range in electrochemical corrosion potential (ECP). Samples were exposed to either proton irradiation (University of Michigan) or electron irradiation (Notre Dame Radiation Laboratory) to independently assess the roles of displacement damage or radiolysis on the corrosion rate, oxide thickness, morphology, structure and resistivity. Post-irradiation characterization of various regions of the electronirradiated samples was completed by means of microscopy (Notre Dame Integrated Imaging Facility) and spectroscopy (Notre Dame Materials Characterization Facility) techniques to provide high resolution information regarding the oxide layer present on the surface of the material.

Grdanovska, Slavica↗

DOE OSTI2026

Prediction and Experimental Verification of Electrolyte Solvation Structure from an OMol25-Trained Interatomic Potential

A molecular-level understanding of electrolyte solvation structure and ion–ion correlations is critical to developing next-generation battery chemistries. Atomistic simulation capabilities with sufficient accuracy, speed, and transferability to deliver reliable structural insights while avoiding arduous system-specific reparameterization are thus highly desirable. Machine learning interatomic potentials (MLIPs) trained on large, chemically diverse data sets are revolutionizing computational chemistry, enabling molecular dynamics simulations of battery electrolytes with near-DFT accuracy over 10,000× faster than DFT. While previous MLIP training data sets with suitable elemental coverage for electrolytes have been based on inorganic materials, the Open Molecules 2025 (OMol25) data set provides large-scale molecular DFT MLIP training data with broad elemental coverage and specifically samples tens of millions of electrolyte configurations. Here, we integrate computational modeling with experimental validation to systematically assess the ability of large-scale MLIPs pretrained on materials data or on OMol25 to accurately resolve nanoscale structural organization and ion-solvation characteristics in Na-ion battery electrolytes across diverse physicochemical conditions and compositional regimes. We find that the OMol25-trained Universal Model of Atoms (UMA-OMol) predicts experimentally measured densities and X-ray structure factors in substantially better agreement compared to state-of-the-art models trained only on inorganic materials data. Using UMA-OMol, we further analyze systematic trends in solvation structure as a function of cation identity, anion chemistry, salt concentration, and solvent topology. We observe that increasing system temperature amplifies the heterogeneity within the solvation environment, perturbing cation–solvent interactions and promoting the formation of contact ion pairs (CIPs). Moreover, subtle variations in the solvent topology of glyme-based electrolytes cause pronounced changes in ion correlations and solvation structure. The experimental agreement and microscopic insights shown here position OMol25-trained MLIPs as a practical route to predictive, high-throughput electrolyte simulations beyond the limits of classical force fields and direct DFT molecular dynamics, serving as a powerful tool for accelerating the design of next-generation Na-ion battery electrolytes and beyond.

MLIPs↗

DOE OSTI2024

Linkages Between Mineral Element Composition of Soils and Sediments With Hyporheic Zone Dissolved Organic Matter Chemistry Across the Contiguous United States

The hyporheic zone is a hotspot for biogeochemical cycling where interactions with mineral metals preserve the release and biodegradation of organic matter (OM). A small fraction of OM can still be exchanged between localized sediments and the overlying water column, and recent evidence suggests there exists a longitudinal structuring in sediment dissolved OM (DOM) chemistry across the continental United States (CONUS). In this study, we tested a hypothesis that water extractable sediment DOM chemistry could be explained by sediment metal contents and integrative watershed scale features at the CONUS scale. Crowdsourced samples were characterized for high resolution mass spectrometry and coupled with sediment metals determined via x-ray fluorescence as well as with land cover and soil elemental information obtained from national databases. Our results highlight weak relationships between DOM chemistry and elemental composition at the CONUS scale indicating limited transferability of organo-metal linkages into multi-scale hydrobiogeochemical models.

58 GEOSCIENCES↗

DOE OSTI2024

Prediction of the Cu oxidation state from EELS and XAS spectra using supervised machine learning

Abstract Electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS) provide detailed information about bonding, distributions and locations of atoms, and their coordination numbers and oxidation states. However, analysis of XAS/EELS data often relies on matching an unknown experimental sample to a series of simulated or experimental standard samples. This limits analysis throughput and the ability to extract quantitative information from a sample. In this work, we have trained a random forest model capable of predicting the oxidation state of copper based on its L-edge spectrum. Our model attains an R 2 score of 0.85 and a root mean square error of 0.24 on simulated data. It has also successfully predicted experimental L-edge EELS spectra taken in this work and XAS spectra extracted from the literature. We further demonstrate the utility of this model by predicting simulated and experimental spectra of mixed valence samples generated by this work. This model can be integrated into a real-time EELS/XAS analysis pipeline on mixtures of copper-containing materials of unknown composition and oxidation state. By expanding the training data, this methodology can be extended to data-driven spectral analysis of a broad range of materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Search for the production of deuterons and antideuterons in e + e − annihilation at center-of-mass energies between 4.13 and 4.70 GeV

Using a data sample of e + e − collision data corresponding to an integrated luminosity of 19 fb − 1 collected with the BESIII detector at the BEPCII collider, we search for the production of deuterons and antideuterons via e + e − → p p π − d ¯ + c . c . for the first time at center-of-mass energies between 4.13 and 4.70 GeV. No significant signal is observed and the upper limit of the e + e − → p p π − d ¯ + c . c . cross section is determined to be from 9.0 to 145 fb depending on the center-of-mass energy at the 90% confidence level. Published by the American Physical Society 2024

Ablikim, M.↗

DOE OSTI2024

Precision measurement of the Ξ b − baryon lifetime

A sample of p p collision data, corresponding to an integrated luminosity of 5.5 fb − 1 and collected by the LHCb experiment during LHC Run 2, is used to measure the ratio of the lifetime of the Ξ b − baryon to that of the Λ b 0 baryon, r τ ≡ τ Ξ b − / τ Λ b 0 . The value r τ = 1.076 ± 0.013 ± 0.006 is obtained, where the first uncertainty is statistical and the second systematic. This value is averaged with the corresponding value from Run 1 to obtain r τ Run 1 , 2 = 1.078 ± 0.012 ± 0.007 . Multiplying by the world-average value of the Λ b 0 lifetime yields τ Ξ b − Run 1 , 2 = 1.578 ± 0.018 ± 0.010 ± 0.011 ps , where the uncertainties are statistical, systematic, and due to the limited knowledge of the Λ b 0 lifetime. This measurement improves the precision of the current world average of the Ξ b − lifetime by about a factor of 2, and is in good agreement with the most recent theoretical predictions. © 2024 CERN, for the LHCb Collaboration 2024 CERN

Aaij, R. (ORCID:0000000305331952)↗

DOE OSTI2025

Measurement of the branching fractions of the decays Λ c + → Λ K S 0 K + , Λ c + → Λ K S 0 π + , and Λ c + → Λ K * +

Studies are performed of the Cabibbo-favored decay Λ c + → Λ K S 0 K + and the singly Cabibbo-suppressed decay Λ c + → Λ K S 0 π + , based on a sample of e + e − collision data, corresponding to an integrated luminosity of 4.5 fb − 1 , accumulated at center-of-mass energies between 4599.53 MeV and 4698.82 MeV with the BESIII detector. The decay Λ c + → Λ K S 0 π + is observed for the first time. The branching fractions of Λ c + → Λ K S 0 K + and Λ c + → Λ K S 0 π + are measured to be ( 3.04 ± 0.30 ± 0.16 ) × 10 − 3 and ( 1.73 ± 0.27 ± 0.10 ) × 10 − 3 , respectively, where the first uncertainties are statistical and the second are systematic. These results correspond to the most precise measurement of these quantities for both decays. Evidence of a K * + contribution in the Λ c + → Λ K S 0 π + decay is found with a statistical significance of 4.71 σ . The branching fraction of Λ c + → Λ K * + is calculated under three possible interference scenarios, with the significance increasing to 5.03 σ when interference is taken into account. Published by the American Physical Society 2025

Ablikim, M.↗

DOE OSTI2018

Updated determination of D 0 – D ¯ 0 mixing and C P violation parameters with D 0 → K + π – decays

We report measurements of charm-mixing parameters based on the decay-time-dependent ratio of D 0 →K + π – to D 0 →K – π + rates. The analysis uses a data sample of proton-proton collisions corresponding to an integrated luminosity of 5.0 fb –1 recorded by the LHCb experiment from 2011 through 2016. Assuming charge-parity ( CP ) symmetry, the mixing parameters are determined to be x' 2 =(3.9±2.7)×10 –5 , y'=(5.28±0.52)×10 –3 , and R D =(3.454±0.031)×10 –3 . Without this assumption, the measurement is performed separately for D 0 and D¯ 0 mesons, yielding a direct CP-violating asymmetry A D =(–0.1±9.1)×10 –3 , and magnitude of the ratio of mixing parameters 1.00 < |q/p| < 1.35 at the 68.3% confidence level. All results include statistical and systematic uncertainties and improve significantly upon previous single-measurement determinations. No evidence for CP violation in charm mixing is observed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Study of the decays D + → η ( ' ) e + ν e

The charm semileptonic decays D + → ηe + v e and D + → η'e+v e are studied with a sample of e + e - collision data corresponding to an integrated luminosity of 2.93 fb -1 collected at $ \sqrt{s}=3.773 $ GeV with the BESIII detector. We measure the branching fractions for D+ → ηe+v e to be (10.74 ± 0.81 ± 0.51) x 10 -4 , and for D+ → → η'e+v e to be (1.91 ± 0.51 ± 0.13) x 10 -4 , where the uncertainties are statistical and systematic, respectively. In addition, we perform a measurement of the form factor in the decay D+ → ηe+v e . All the results are consistent with those obtained by the CLEO-c experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗