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At least 1,639 records · Page 91
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Identification of blood protein biomarkers associated with prostate cancer risk using genetic prediction models: analysis of over 140,000 subjects

Prostate cancer (PCa) brings huge public health burden in men. A growing number of conventional observational studies report associations of multiple circulating proteins with PCa risk. However, the existing findings may be subject to incoherent biases of conventional epidemiologic studies. To better characterize their associations, herein, we evaluated associations of genetically predicted concentrations of plasma proteins with PCa risk. In this study, we developed comprehensive genetic prediction models for protein levels in plasma. After testing 1308 proteins in 79 194 cases and 61 112 controls of European ancestry included in the consortia of BPC3, CAPS, CRUK, PEGASUS, and PRACTICAL, 24 proteins showed significant associations with PCa risk, including 16 previously reported proteins and eight novel proteins. Of them, 14 proteins showed negative associations and 10 showed positive associations with PCa risk. For 18 of the identified proteins, potential functional somatic changes of encoding genes were detected in PCa patients in The Cancer Genome Atlas (TCGA). Genes encoding these proteins were significantly involved in cancer-related pathways. We further identified drugs targeting the identified proteins, which may serve as candidates for drug repurposing for treating PCa. In conclusion, this study identifies novel protein biomarker candidates for PCa risk, which may provide new perspectives on the etiology of PCa and improve its therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Environments of dwarf galaxies with optical AGN characteristics

ABSTRACT This study aims to explore the relation between dwarf galaxies (M* ≤ 5 × 109 M⊙) with active galactic nuclei (AGNs) and their environment by comparing neighbourhood parameters of AGN and non-AGN samples. Using the NASA-Sloan Atlas, both the local environment and the immediate environment of dwarf galaxies with z ≤ 0.055 are analysed. Of the 145 155 galaxies in the catalogue, 62 258 of them are classified as dwarf galaxies, and by employing two AGN selection methods based on emission-line fluxes (BPT and WHAN), 4476 are found to have AGN characteristics in their optical spectra. Regardless of selection method, this study finds no discernible differences in environment between AGN and non-AGN host dwarf galaxies and these results indicate that environment is not an important factor in triggering AGN activity in dwarf galaxies. This is in line with existing literature on environments of regular galaxies with AGNs and suggests universality in terms of reaction to environment across the mass regime. The biases of AGN selection in low-mass galaxies, and the biases of different measures of environment are also considered. It is found that there are several mass trends in emission-line ratios and that the SDSS fibre covers galaxies non-uniformly with redshift. These biases should be accounted for in future work by possibly including other wavelength regimes or mass weighting of emission-line ratios. Lastly, a discussion of the environment estimation methods is included since they may not gauge the desired properties due to factors such as time delay or using loosely constrained proxy parameters.

Kristensen, Mikkel T.↗
DOE OSTI2020

A search for the lenses in the Herschel Bright Sources (HerBS) sample

ABSTRACT Verifying that sub-mm galaxies are gravitationally lensed requires time-expensive observations with oversubscribed high-resolution observatories. Here, we aim to strengthen the evidence of gravitational lensing within the Herschel Bright Sources (HerBS) by cross-comparing their positions to optical (SDSS) and near-infrared (VIKING) surveys, in order to search for the foreground lensing galaxy candidates. Resolved observations of the brightest HerBS sources have already shown that most are lensed, and a galaxy evolution model predicts that ∼76 per cent of the total HerBS sources are lensed, although with the SDSS survey we are only able to identify the likely foreground lenses for 25 per cent of the sources. With the near-infrared VIKING survey, however, we are able to identify the likely foreground lenses for 57 per cent of the sources, and we estimate that 82 per cent of the HerBS sources have lenses on the VIKING images even if we cannot identify the lens in every case. We find that the angular offsets between lens and Herschel source are larger than that expected if the lensing is done by individual galaxies. We also find that the fraction of HerBS sources that are lensed falls with decreasing 500-micron flux density, which is expected from the galaxy evolution model. Finally, we apply our statistical VIKING cross-identification to the entire Herschel-ATLAS catalogue, where we also find that the number of lensed sources falls with decreasing 500-micron flux density.

Bakx, Tom J. L. C.↗
DOE OSTI2022

The ‘Giraffe’: discovery of a stripped red giant in an interacting binary with an ∼2 M ⊙ lower giant

We report the discovery of a stripped giant + lower giant Algol-type binary, 2M04123153+6738486 (2M0412), identified during a search for non-interacting compact object – star binaries. 2M0412 is an evolved ( T eff, giant ≃ 4000 K), luminous ( L giant ≃ 150 L ⊙ ) red giant in a circular P = 81.2 d binary. 2M0412 is a known variable star previously classified as a semiregular variable. The cross-correlation functions of follow-up Keck/HIRES and LBT/Potsdam Echelle Polarimetric and Spectroscopic Instrument (PEPSI) spectra show an radial velocity variable second component with implied mass ratio q = M giant / M comp ≃ 0.20 ± 0.01. The All-Sky Automated Survey for SuperNovae (ASAS-SN), Asteroid Terrestrial-impact Last Alert System (ATLAS), Transiting Exoplanet Survey Telescope ( TESS ), and Zwicky Transient Facility (ZTF) light curves show that the giant is a Roche lobe filling ellipsoidal variable with an inclination of 49.4 ± 0.3°, and a giant mass of M giant = 0.38 ± 0.01 M ⊙ for a distance of ≃ 3.7 kpc. The mass of the giant indicates that its envelope has been partially stripped. The giant companion on the lower red giant branch has a mass of M comp = 1.91 ± 0.03 M ⊙ with T eff, comp ≃ 5000 K, L comp ≃ 60 L ⊙ , and R comp ≃ 11 R ⊙ . The lower giant contributes ${\sim }35{{\ \rm per\ cent}}$ of the flux in the V band. We also identify an orbital phase dependent, broad $\rm H\,\alpha$ emission line which could indicate ongoing accretion from the stripped red giant on to the companion.

(stars:) binaries: spectroscopic↗
DOE OSTI2023

Probing quasar viewing angle with the variability structure function

Given the anisotropic emission from quasar accretion discs, their viewing angle affects estimates of the quasar luminosity, black hole mass, and Eddington ratio. Discs appear overluminous when viewed pole-on and underluminous when viewed at high inclination. In radio-quiet quasars, the viewing angle is usually unknown, although spectroscopic indicators have been proposed. Here, we use a recently discovered universality in the variability structure function (SF) of quasar light curves (LCs), where all quasars show the same SF when clocks run in units of orbital time-scale. As an offset from the mean relation can be caused by incorrect orbital time-scales and thus incorrect luminosities, we correlate these offsets with suggested inclination indicators. We derive SFs from NASA/Asteroid Terrestrial-impact Last Alert System (ATLAS) LCs spanning ~6 yr of observation, using a sample of 183 luminous quasars with measured H β lines as well as 753 quasars with C $\tiny{IV}$ and Mg $\tiny{II}$ lines. Starting from the proposed orientation indicators, we expect quasars with narrower H β lines and with more blueshifted C $\tiny{IV}$ lines to be viewed more pole-on and thus appear overluminous. In contrast, our SF analysis finds that presumed pole-on discs appear underluminous, consistently for both line indicators. We discuss possible explanations for the behaviour of quasars with highly blueshifted C $\tiny{IV}$ lines irrespective of inclination angle, including dusty outflows that might render the accretion disc underluminous and flatter disc temperature profiles with longer orbital time-scales than in thin-disc models but reach no satisfying conclusion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Photometry and astrometry with JWST – III. A NIRCam-Gaia DR3 analysis of the open cluster NGC 2506

ABSTRACT In the third paper of this series aimed at developing the tools for analysing resolved stellar populations using the cameras on board of the James Webb Space Telescope (JWST), we present a detailed multiband study of the 2 Gyr Galactic open cluster NGC 2506. We employ public calibration data sets collected in multiple filters to: (i) derive improved effective Point Spread Functions (ePSFs) for 10 NIRCam filters; (ii) extract high-precision photometry and astrometry for stars in the cluster, approaching the main sequence (MS) lower mass of ∼0.1 M⊙; and (iii) take advantage of the synergy between JWST and Gaia DR3 to perform a comprehensive analysis of the cluster’s global and local properties. We derived a MS binary fraction of ∼57.5 per cent, extending the Gaia limit (∼0.8 M⊙) to lower masses (∼0.4 M⊙) with JWST. We conducted a study on the mass functions (MFs) of NGC 2506, mapping the mass segregation with Gaia data, and extending MFs to lower masses with the JWST field. We also combined information on the derived MFs to infer an estimate of the cluster present-day total mass. Lastly, we investigated the presence of white dwarfs (WDs) and identified a strong candidate. However, to firmly establish its cluster membership, as well as that of four other WD candidates and of the majority of faint low-mass MS stars, further JWST equally deep observations will be required. We make publicly available catalogues, atlases, and the improved ePSFs.

Nardiello, D. (ORCID:0000000311493659)↗
DOE OSTI2023

Novobiocin blocks nucleic acid binding to Polθ and inhibits stimulation of its ATPase activity

Polymerase theta (Polθ) acts in DNA replication and repair, and its inhibition is synthetic lethal in BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB) is a first-in-class inhibitor of the Polθ ATPase activity, and it is currently being tested in clinical trials as an anti-cancer drug. Here, we investigated the molecular mechanism of NVB-mediated Polθ inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational and cellular assays, we found NVB is a non-competitive inhibitor of ATP hydrolysis. NVB sugar group deletion resulted in decreased potency and reduced HX-MS interactions, supporting a specific NVB binding orientation. Collective results revealed that NVB binds to an allosteric site to block DNA binding, both in vitro and in cells. Comparisons of The Cancer Genome Atlas (TCGA) tumors and matched controls implied that POLQ upregulation in tumors stems from its role in replication stress responses to increased cell proliferation: this can now be tested in fifteen tumor types by NVB blocking ssDNA-stimulation of ATPase activity, required for Polθ function at replication forks and DNA damage sites. Structural and functional insights provided in this study suggest a path for developing NVB derivatives with improved potency for Polθ inhibition by targeting ssDNA binding with entropically constrained small molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Gene and genome duplications have contrasting impacts on biosynthetic and flower developmental pathways in California poppy

Benzylisoquinoline alkaloids (BIAs) represent a vast group of specialized plant metabolites with diverse pharmaceutical applications, synthesized by a variety of gene families. Among the multiple plant lineages that produce BIAs, the most notable is the poppy family (Papaveraceae), with California poppy (Eschscholzia californica) emerging as a model organism. Here, we report a haplotype-resolved genome assembly, in combination with a high-density expression atlas, for California poppy. Genome analyses reveal recent diversification of BIA biosynthesis genes in poppy through localized duplications. Furthermore, we demonstrate that the degree of phylogenetic relatedness among paralogs within BIA biosynthesis-associated gene families correlates with similarities in gene expression. In contrast, gene families involved in carotenoid biosynthesis, which contributes to the intense orange petal pigmentation, are not phylogenetically clustered, and floral developmental regulators exhibit a high degree of retention of gene duplicates associated with ancient polyploidy events. These findings illustrate alternative roles for gene and genome duplications as drivers of trait evolution. Given the position of California poppy in the angiosperm phylogeny, the high-quality genomic resources generated for this work constitute a valuable resource for comparative genomic and transcriptomic analyses for poppies and flowering plants more generally.

Rössner, Le-Han [Justus-Liebig University, Giessen↗
DOE OSTI2024

On the nature of apparent transient sources on the National Geographic Society–Palomar Observatory Sky Survey glass copy plates

Abstract We examine critically recent claims for the presence of above-atmosphere optical transients in publicly available digitized scans of Schmidt telescope photographic plate material derived from the National Geographic Society–Palomar Observatory Sky Survey. We employ the publicly available SuperCOSMOS Sky Survey catalogues to examine statistically the morphology of the sources. We develop a simple, objective, and automated image classification scheme based on a random forest decision tree classifier. We find that the putative transients are likely to be spurious artefacts of the photographic emulsion. We suggest a possible cause of the appearance of these images as resulting from the copying procedure employed to disseminate glass copy survey atlas sets in the era before large-scale digitization programmes.

Hambly, N. C. (ORCID:0000000299019064)↗
DOE OSTI2025

Triaxiality and shape dynamics in 70 Ge

The electromagnetic properties of low-lying states in 70 Ge were investigated via multi-step Coulomb excitation of a 70 Ge beam impinging on a 208 Pb target at the ATLAS facility of the Argonne National Laboratory. A total of 27 transitional elements and six diagonal matrix elements coupling 11 low-lying states, were extracted from the measured cross sections. These were used to calculate reduced transition probabilities, spectroscopic quadrupole moments, and rotational invariant shape parameters, providing enhanced precision and expanding on previous studies. The experimental data were compared within several theoretical frameworks, including the generalized triaxial rotor model, configuration interaction shell-model calculations, and computations within the combined frameworks of relativistic density functional theory and the five-dimensional collective Hamiltonian. The results demonstrate a good agreement with the experimental data and, in conjunction with calculations using a two-state mixing model, support significant triaxiality and strong mixing between the 0$^{+}_{1}$ and 0$^{+}_{2}$ states. This results in the magnitudes of their respective quadrupole deformations [β rms (0$^{+}_{1}$) = 0.228 (3), β rms (0$^{+}_{2}$) = 0.273 (1)] being more similar than previously observed. Furthermore, the implications of these results for understanding the complex shape coexistence phenomena, the role of triaxiality, and shape evolution along the Ge isotopic chain are discussed.

59 ≤ A ≤ 89↗
DOE OSTI2025

New H erwig7 underlying event tune: From RHIC to LHC energies

We present parameter sets corresponding to new underlying event tunes for the H erwig7.3 Monte Carlo event generator. The existing H erwig tunes are in good agreement with LHC data, however, they are not typically designed for center-of-mass energies below $\sqrt{𝑠}$ = 300 GeV. The tunes presented in this study can describe midrapidity data collected at the nominal RHIC energy of $\sqrt{𝑠}$ = 200 GeV as well as higher center-of-mass energies utilized by experiments at the LHC and Tevatron. The base “New Haven” tune is developed by fitting minimum-bias simulations of proton-proton ($𝑝⁢𝑝$) collisions to midrapidity identified hadron and jet data from the STAR experiment. The “Nashville” tune includes a separate set of parameters developed by tuning to Tevatron proton-antiproton ($𝑝\bar{⁢𝑝}$) data at $\sqrt{𝑠}$ = 300, 900 and 1960 GeV from CDF, and LHC $𝑝⁢𝑝$ measurements from CMS at $\sqrt{𝑠}$ =7 TeV, in addition to the STAR measurements. Both new tunes demonstrate significant improvements over the recommended default tune currently included in the latest version of H erwig for minimum bias production. As such, we advocate using these tunes for future simulation studies at midrapidity by experimental collaborations at RHIC (STAR and sPHENIX) and the LHC (ALICE, ATLAS, and CMS).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Foundation model framework for all tasks involving jet physics

Foundation models use large datasets to build an effective representation of data that can be deployed on diverse downstream tasks. Previous research developed the omnilearn foundation model for jet physics, using unique properties of particle physics, and showed that it could significantly advance discovery potential across collider experiments. This paper introduces a major upgrade, resulting in the omnilearned framework. This framework has three new elements: (1) updates to the model architecture and training, (2) using over 1 × 10 9 jets used for training, and (3) providing well-documented software for accessing all datasets and models. We demonstrate omnilearned with three representative tasks: top-quark jet tagging with the community delphes-based benchmark dataset, b tagging with ATLAS full simulation, and anomaly detection with CMS experimental data. In each case, omnilearned is the state of the art, further expanding the discovery potential of past, current, and future collider experiments.

Bhimji, Wahid [Lawrence Berkeley National Laborato↗
DOE OSTI2024

Transverse emittance growth due to rf noise in crab cavities: Theory, measurements, cure, and high luminosity LHC estimates

The High-Luminosity LHC (HL-LHC) upgrade with planned operation from 2029 onward has a goal of achieving a tenfold increase in the integrated number of recorded collisions thanks to a doubling of the intensity per bunch ( 2.2 × 10 11 protons) and a reduction of β * (the β value in the two high luminosity detectors, namely ATLAS and CMS) to 15 cm. Such an increase in recorded collisions would significantly expedite new discoveries and exploration. Crab cavities are an important component of the HL-LHC upgrade and will contribute strongly to achieving an increase in the number of recorded collisions. However, noise injected through the crab cavity radio frequency (rf) system could cause significant transverse emittance growth and limit luminosity lifetime. We presented a theoretical formalism relating transverse emittance growth to rf noise in an earlier work. In this follow-up paper, we summarize measurements in the super-proton synchrotron (SPS) at CERN that validate the theory, we present estimates of the emittance growth rates using state-of-the-art rf and low-level rf (LLRF) technologies, and we set the rf noise specifications to achieve acceptable performance. A novel dedicated feedback system acting through the crab cavities to mitigate emittance growth will be required. In this work, we develop a theoretical formalism to evaluate the performance of such a feedback system in any collider, identify limiting components, present simulation results to validate these studies, and derive key design parameters for an HL-LHC implementation of such a feedback system. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Impact of beam coupling impedance on crab cavity noise induced emittance growth

Crab cavities will be deployed as a part of the High Luminosity Large Hadron Collider (HL-LHC) upgrade to mitigate the luminosity reduction induced by the crossing angle at the main experiments (ATLAS and CMS). Two prototype crab cavities have been installed in the CERN Super Proton Synchrotron (SPS) in 2018 for studies with proton beams. An issue of concern is the transverse emittance growth induced by noise in the crab cavity radio frequency (rf) system, which is anticipated to limit the performance of the HL-LHC. In measurements conducted in the SPS in 2018, the crab cavity noise-induced emittance growth was measured to be a factor of 4 lower than predicted from the existing analytical models. In this paper, it is shown that the observed discrepancy is explained by damping effects from the beam coupling impedance, which were not included in the models up to now. Using the van Kampen mode approach, a new theory is developed, suggesting that the impedance can separate the coherent tune from the incoherent spectrum leading to an effective reduction of the crab cavity rf noise-induced emittance growth. This mechanism is validated in tracking simulations using the SPS impedance model as well as in dedicated experimental measurements conducted in the SPS in 2022. The implications for the HL-LHC project are discussed. Published by the American Physical Society 2024

Physics↗
DOE OSTI2020

Possible octupole deformation of 208 Pb and the ultracentral v 2 to v 3 puzzle

Recent measurements have established the sensitivity of ultracentral heavy-ion collisions to the deformation parameters of nonspherical nuclei. In the case of 129 Xe collisions, a quadrupole deformation of the nuclear profile led to an enhancement of elliptic flow in the most central collisions. In 208 Pb collisions a discrepancy exists in similar centralities, where either elliptic flow is overpredicted or triangular flow is underpredicted by hydrodynamic models; this is known as the v 2 -to-v 3 puzzle in ultracentral collisions. Motivated by low-energy nuclear structure calculations, we consider the possibility that 208Pb nuclei could have a pear-shape deformation (octupole), which has the effect of increasing triangular flow in central PbPb collisions. Using the recent data from ALICE and ATLAS, we reexamine the v 2 -to-v 3 puzzle in ultracentral collisions, including new constraints from recent measurements of the triangular cumulant ratio v 3 {4}/v 3 {2} and comparing two different hydrodynamic models. We find that while an octupole deformation would slightly improve the ratio between v 2 and v 3 , it is at the expense of a significantly worse triangular flow cumulant ratio. In fact, the latter observable prefers no octupole deformation, with β 3 ≲ 0.0375 for 208 Pb, and is therefore consistent with the expectation for a doubly-magic nucleus even at top collider energies. Furthermore, the v 2 -to-v 3 puzzle remains a challenge for hydrodynamic models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Search for the 1/2 + intruder state in 35 P

The excitation energy of deformed intruder states (specifically the 2p2h bandhead) as a function of proton number Z along N = 20 is of interest both in terms of better understanding the evolution of nuclear structure between spherical Ca 40 and the Island of Inversion nuclei, and for benchmarking theoretical descriptions in this region. At the center of the N = 20 Island of Inversion, the n p n h (where n = 2 , 4 , 6 ) neutron excitations across a diminished N = 20 gap result in deformed and collective ground states, as observed in Mg 32 . In heavier isotones, n p n h excitations do not dominate in the ground states but are present in the relatively low-lying level schemes. With the aim of identifying the expected 2 p 2 h x s 1 / 2 + state in P 35 , the only N = 20 isotone for which the neutron 2p2h excitation bandhead has not yet been identified, the S 36 ( d , He 3 ) P 35 reaction has been revisited in inverse kinematics with the HELical Orbit Spectrometer (HELIOS) at the Argonne Tandem Linac Accelerator System (ATLAS). While a candidate state has not been located, an upper limit for the transfer reaction cross section to populate such a configuration within a 2.5 to 3.6 MeV energy range provides a stringent constraint on the wave function compositions in both S 36 and P 35 .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Gluonic hot spot initial conditions in heavy-ion collisions

The initial conditions in heavy-ion collisions are calculated in many different frameworks. The importance of nucleon position fluctuations within the nucleus and subnucleon structure has been established when modeling initial conditions for input to hydrodynamic calculations. However, there remain outstanding puzzles regarding these initial conditions, including the measurement of the near equivalence of the elliptical v 2 and triangular v 3 flow coefficients in ultracentral 0–1% Pb + Pb collisions at the CERN Large Hadron Collider. Recently a calculation termed magma incorporating gluonic hot spots via two-point correlators in the color glass condensate framework, and no nucleons, provided a simultaneous match to these flow coefficients measured by the ATLAS experiment, including in ultracentral 0–1% collisions. Our calculations reveal that the magma initial conditions do not describe the experimental data when run through full hydrodynamic sonic simulations or when the hot spots from one nucleus resolve hot spots from the other nucleus, as predicted in the color glass condensate framework. Finally, we also explore alternative initial condition calculations and discuss their implications.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Experimental study of the isomeric state in 16 N using the 16 N$^{g,m}$($\textit{d}$, 3 He) reaction

Here, the isomeric state of 16 N was studied using the 16 N$^{g,m}$($\textit{d}$, 3 He) proton-removal reactions at 11.8 MeV/u in inverse kinematics. The 16 N beam, of which 24% was in the isomeric state, was produced using the Argonne Tandem-Linac Accelerator System (ATLAS) in-flight system and delivered to the Helical Orbit Spectrometer (HELIOS), which was used to analyze the 3 He ions from the ($\textit{d}$, 3 He) reactions. The simultaneous measurement of reactions on both the ground state and the isomeric states, reduced the systematic uncertainties from the experiment and in the analysis. A direct and reliable extraction of the relative spectroscopic factors was made based on a distorted-wave Born approximation approach. The experimental results suggest that the isomeric state of 16N is an excited neutron-halo state. The results can be understood through calculations using a Woods-Saxon potential model, which captures the effects of weak binding.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗