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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Evolution of the X-ray profile of the Crab pulsar

Using the archival data from the Rossi X-ray Timing Explorer, we study the evolution of the Crab pulsar's X-ray profile in a time span of 11 years. The evolutionary trends of the X-ray profile are similar to that observed in radio, but with quantitative differences. Finally, we briefly discuss the constraints of these X-ray properties on the geometry of the emission region of this pulsar.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

( Hubble Space Telescope Hubble Space Telescope) proper motion (HSTPROMO) catalogs of galactic globular clusters. IV. Kinematic profiles and average masses of blue straggler stars

We make use of the Hubble Space Telescope proper-motion catalogs derived by Bellini et al. to produce the first radial velocity dispersion profiles σ(R) for blue straggler stars (BSSs) in Galactic globular clusters (GCs), as well as the first dynamical estimates for the average mass of the entire BSS population. We show that BSSs typically have lower velocity dispersions than stars with mass equal to the main-sequence turnoff mass, as one would expect for a more massive population of stars. Since GCs are expected to experience some degree of energy equipartition, we use the relation σ∝M{sup −η}, where η is related to the degree of energy equipartition, along with our velocity dispersion profiles to estimate BSS masses. We estimate η as a function of cluster relaxation from recent Monte Carlo cluster simulations by Bianchini et al. and then derive an average mass ratio M{sub BSS}/M{sub MSTO}=1.50±0.14 and an average mass M{sub BSS}=1.22±0.12 M {sub ⊙} from 598 BSSs across 19 GCs. The final error bars include any systematic errors that are random between different clusters, but not any potential biases inherent to our methodology. Our results are in good agreement with the average mass of M{sub BSS}=1.22±0.06 M {sub ⊙} for the 35 BSSs in Galactic GCs in the literature with properties that have allowed individual mass determination.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

MEASURING NEUTRON STAR RADII VIA PULSE PROFILE MODELING WITH NICER

The Neutron-star Interior Composition Explorer is an X-ray astrophysics payload that will be placed on the International Space Station . Its primary science goal is to measure with high accuracy the pulse profiles that arise from the non-uniform thermal surface emission of rotation-powered pulsars. Modeling general relativistic effects on the profiles will lead to measuring the radii of these neutron stars and to constraining their equation of state. Achieving this goal will depend, among other things, on accurate knowledge of the source, sky, and instrument backgrounds. We use here simple analytic estimates to quantify the level at which these backgrounds need to be known in order for the upcoming measurements to provide significant constraints on the properties of neutron stars. We show that, even in the minimal-information scenario, knowledge of the background at a few percent level for a background-to-source countrate ratio of 0.2 allows for a measurement of the neutron star compactness to better than 10% uncertainty for most of the parameter space. These constraints improve further when more realistic assumptions are made about the neutron star emission and spin, and when additional information about the source itself, such as its mass or distance, are incorporated.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Void Profile from Planck Lensing Potential Map

We use the lensing potential map from Planck CMB lensing reconstruction analysis and the “Public Cosmic Void Catalog” to measure the stacked void lensing potential. We have made an attempt to fit the HSW void profile parameters from the stacked lensing potential. In this profile, four parameters are needed to describe the shape of voids with different characteristic radii R {sub V}. However, we have found that after reducing the background noise by subtracting the average background, there is a residue lensing power left in the data. The inclusion of the environment shifting parameter, γ{sub V}, is necessary to get a better fit to the data with the residue lensing power. We divide the voids into two redshift bins: cmass1 (0.45<z<0.5) and cmass2 (0.5<z<0.6). Our best-fit parameters are α=1.989±0.149, β=12.61±0.56, δ{sub c}=−0.697±0.025, R{sub S}/R{sub V}=1.039±0.030, γ{sub v}=(−7.034±0.150)×10{sup −2} for the cmass1 sample with 123 voids and α=1.956±0.165, β =12.91±0.60, δ{sub c}=−0.673±0.027, R{sub S}/R{sub V}=1.115±0.032, γ{sub v}=(−4.512±0.114)×10{sup −2} for the cmass2 sample with 393 voids at 68% C.L. The addition of the environment shifting parameter is consistent with the conjecture that the Sloan Digital Sky Survey voids reside in an underdense region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

A Universal Velocity Dispersion Profile for Pressure Supported Systems: Evidence for MONDian Gravity across Seven Orders of Magnitude in Mass

For any MONDian extended theory of gravity where the rotation curves of spiral galaxies are explained through a change in physics rather than the hypothesis of dark matter, a generic dynamical behavior is expected for pressure supported systems: an outer flattening of the velocity dispersion profile occurring at a characteristic radius, where both the amplitude of this flat velocity dispersion and the radius at which it appears are predicted to show distinct scalings with the total mass of the system. By carefully analyzing the dynamics of globular clusters and elliptical galaxies, we are able to significantly extend the astronomical diversity of objects in which MONDian gravity has been tested, from spiral galaxies to the much larger mass range covered by pressure supported systems. We show that a universal projected velocity dispersion profile accurately describes various classes of pressure supported systems, and further, that the expectations of extended gravity are met across seven orders of magnitude in mass. These observed scalings are not expected under dark matter cosmology, and would require particular explanations tuned at the scales of each distinct astrophysical system.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Non-Maxwellian Analysis of the Transition-region Line Profiles Observed by the Interface Region Imaging Spectrograph

We investigate the nature of the spectral line profiles for transition-region (TR) ions observed with the Interface Region Imaging Spectrograph (IRIS) . In this context, we analyzed an active-region observation performed by IRIS in its 1400 Å spectral window. The TR lines are found to exhibit significant wings in their spectral profiles, which can be well fitted with a non-Maxwellian κ distribution. The fit with a κ distribution can perform better than a double-Gaussian fit, especially for the strongest line, Si iv 1402.8 Å. Typical values of κ found are about 2, occurring in a majority of spatial pixels where the TR lines are symmetric, i.e., the fit can be performed. Furthermore, all five spectral lines studied (from Si iv, O iv, and S iv) appear to have the same full-width at half-maximum irrespective of whether the line is an allowed or an intercombination transition. A similar value of κ is obtained for the electron distribution by the fitting of the line intensities relative to Si iv 1402.8 Å, if photospheric abundances are assumed. The κ distributions, however, do not remove the presence of non-thermal broadening. Instead, they actually increase the non-thermal width. This is because, for κ distributions, TR ions are formed at lower temperatures. The large observed non-thermal width lowers the opacity of the Si iv line sufficiently enough for this line to become optically thin.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Specific Frequencies and Luminosity Profiles of Cluster Galaxies and Intracluster Light in Abell 1689

We present magnitudes and profile fits for 180 galaxies in the central field of the massive lensing cluster Abell 1689 using very deep imaging with the Hubble Space Telescope Advanced Camera for Surveys in the F814W bandpass. Previous work revealed an exceptionally large number of globular clusters (GCs) in A1689 and mapped their number density distribution. We decompose this number density map into GCs associated with individual cluster galaxies and ICGCs (intracluster GCs) associated with the intracluster light (ICL). In all, we measure GC specific frequencies S {sub N} for 33 cluster members and the ICL. The relation between S {sub N} and galaxy magnitude is consistent with the trend observed in Virgo, although some intermediate-luminosity galaxies scatter to S{sub N}>10. We estimate that the ICL makes up 11% of the starlight in this field, whereas the ICGCs account for ∼35% of the GCs, both consistent with predictions from simulations. Galaxies with higher S {sub N} values tend to be rounder, and there is a marginally significant trend of decreasing S {sub N} with increasing specific angular momenta λ{sub R}. We also reevaluate the GC population in the A2744 Frontier Field, for which fewer than 1/10 as many GCs have been detected because of its larger distance. Finally, our core-Sérsic fit to the light profile of the A1689 brightest cluster galaxy implies a break radius of 3.8 kpc, among the largest known; we discuss implications of the sizable core and extensive GC population for the supermassive black hole in light of scaling relations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Atmospheric Temperature Inversions and He ι 5876 Core Profile Structure in White Dwarfs

Here we report distinctive core profiles in the strongest optical helium line, He ι λ5876, from high-resolution high-sensitivity observations of spectral type DB white dwarfs. By analyzing a sample of 40 stars from Keck/HIRES and VLT/UVES, we find the core appearance to be related to the degree of hydrogen and heavy element content in the atmosphere. New Ca K-line measurements or upper limits are reported for about half the sample stars. He ι λ5876 emission cores with a self-reversed central component are present for those stars with relatively low hydrogen abundance, as well as relatively low atmospheric heavy element pollution. This self-reversed structure disappears for stars with higher degrees of pollution and/or hydrogen abundance, giving way to a single absorption core. From our model atmospheres, we show that the self-reversed emission cores can be explained by temperature inversions in the upper atmosphere. We propose that the transition to a single absorption core is due to the additional opacity from hydrogen and heavy elements that inhibits the temperature inversions. Our current models do not exactly match the effective temperature range of the phenomenon or the amplitude of the self-reversed structure, which is possibly a result of missing physics such as 3D treatment, convective overshoot, and/or non-LTE effects. The He ι λ5876 line structure may prove to be a useful new diagnostic for calibrating temperature profiles in DB atmosphere models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Estimate of the Mass and Radial Profile of the Orphan–Chenab Stream's Dwarf-galaxy Progenitor Using MilkyWay@home

We fit the mass and radial profile of the Orphan–Chenab Stream's (OCS) dwarf-galaxy progenitor by using turnoff stars in the Sloan Digital Sky Survey and the Dark Energy Camera to constrain N-body simulations of the OCS progenitor falling into the Milky Way on the 1.5 PetaFLOPS MilkyWay@home distributed supercomputer. We infer the internal structure of the OCS's progenitor under the assumption that it was a spherically symmetric dwarf galaxy composed of a stellar system embedded in an extended dark matter halo. We optimize the evolution time, the baryonic and dark matter scale radii, and the baryonic and dark matter masses of the progenitor using a differential evolution algorithm. The likelihood score for each set of parameters is determined by comparing the simulated tidal stream to the angular distribution of OCS stars observed in the sky. We fit the total mass of the OCS's progenitor to (2.0 ± 0.3) × 10 7 M ⊙ with a mass-to-light ratio of γ = 73.5 ± 10.6 and (1.1 ± 0.2) × 10 6 M ⊙ within 300 pc of its center. Within the progenitor's half-light radius, we estimate a total mass of (4.0 ± 1.0) × 10 5 M ⊙ . We also fit the current sky position of the progenitor's remnant to be (α, δ) = ((166.0 ± 0.9)°, (–11.1 ± 2.5)°) and show that it is gravitationally unbound at the present time. The measured progenitor mass is on the low end of previous measurements and, if confirmed, lowers the mass range of ultrafaint dwarf galaxies. Our optimization assumes a fixed Milky Way potential, OCS orbit, and radial profile for the progenitor, ignoring the impact of the Large Magellanic Cloud.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

THE EFFECT OF UNRESOLVED BINARIES ON GLOBULAR CLUSTER PROPER-MOTION DISPERSION PROFILES

High-precision kinematic studies of globular clusters (GCs) require an accurate knowledge of all possible sources of contamination. Among other sources, binary stars can introduce systematic biases in the kinematics. Using a set of Monte Carlo cluster simulations with different concentrations and binary fractions, we investigate the effect of unresolved binaries on proper-motion dispersion profiles, treating the simulations like Hubble Space Telescope proper-motion samples. Since GCs evolve toward a state of partial energy equipartition, more-massive stars lose energy and decrease their velocity dispersion. As a consequence, on average, binaries have a lower velocity dispersion, since they are more-massive kinematic tracers. We show that, in the case of clusters with high binary fractions (initial binary fractions of 50%) and high concentrations (i.e., closer to energy equipartition), unresolved binaries introduce a color-dependent bias in the velocity dispersion of main-sequence stars of the order of 0.1–0.3 km s{sup −1} (corresponding to 1%−6% of the velocity dispersion), with the reddest stars having a lower velocity dispersion, due to the higher fraction of contaminating binaries. This bias depends on the ability to distinguish binaries from single stars, on the details of the color–magnitude diagram and the photometric errors. We apply our analysis to the HSTPROMO data set of NGC 7078 (M15) and show that no effect ascribable to binaries is observed, consistent with the low binary fraction of the cluster. Our work indicates that binaries do not significantly bias proper-motion velocity-dispersion profiles, but should be taken into account in the error budget of kinematic analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Halo Pressure Profile through the Skew Cross-power Spectrum of the Sunyaev–Zel’dovich Effect and CMB Lensing in Planck

We measure the cosmic microwave background (CMB) skewness power spectrum in Planck , using frequency maps of the HFI instrument and the Sunyaev–Zel’dovich (SZ) component map. The two-to-one skewness power spectrum measures the cross-correlation between CMB lensing and the thermal SZ effect. We also directly measure the same cross-correlation using the Planck CMB lensing map and the SZ map and compare it to the cross-correlation derived from the skewness power spectrum. We model fit the SZ power spectrum and CMB lensing–SZ cross-power spectrum via the skewness power spectrum to constrain the gas pressure profile of dark matter halos. The gas pressure profile is compared to existing measurements in the literature including a direct estimate based on the stacking of SZ clusters in Planck .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Serum bile acid and unsaturated fatty acid profiles of non-alcoholic fatty liver disease in type 2 diabetic patients

The understanding of bile acid (BA) and unsaturated fatty acid (UFA) profiles, as well as their dysregulation, remains elusive in individuals with type 2 diabetes mellitus (T2DM) coexisting with non-alcoholic fatty liver disease (NAFLD). Investigating these metabolites could offer valuable insights into the pathophy-siology of NAFLD in T2DM. Our aim is to identify potential metabolite biomarkers capable of distinguishing between NAFLD and T2DM. A training model was developed involving 399 participants, comprising 113 healthy controls (HCs), 134 individuals with T2DM without NAFLD, and 152 individuals with T2DM and NAFLD. External validation encompassed 172 participants. NAFLD patients were divided based on liver fibrosis scores. The analytical approach employed univariate testing, orthogonal partial least squares-discriminant analysis, logistic regression, receiver operating characteristic curve analysis, and decision curve analysis to pinpoint and assess the diagnostic value of serum biomarkers. Compared to HCs, both T2DM and NAFLD groups exhibited diminished levels of specific BAs. In UFAs, particular acids exhibited a positive correlation with NAFLD risk in T2DM, while the ω-6:ω-3 UFA ratio demonstrated a negative correlation. Levels of α-linolenic acid and γ-linolenic acid were linked to significant liver fibrosis in NAFLD. The validation cohort substantiated the predictive efficacy of these biomarkers for assessing NAFLD risk in T2DM patients. This study underscores the connection between altered BA and UFA profiles and the presence of NAFLD in individuals with T2DM, proposing their potential as biomarkers in the pathogenesis of NAFLD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Effect of radial pressure corrugations and profile shearing on turbulence in Fusion plasmas

Microturbulence can produce stationary fine-scale radial corrugations on the plasma density and temperature gradients in magnetic confinement fusion devices. We show that these structures play a significant role in regulating turbulent transport. We focus on the pedestal, studying electron-temperature-gradient (ETG) mode destabilisation and saturation in the presence of radial corrugations on the electron temperature gradient that could result from microtearing turbulence. A linear dispersion relation is derived for a shearless slab case, which indicates that in the presence of a sinusoidal background corrugation, each ETG mode splits into three distinct eigenvalues, with one being the original, one being more unstable and one being less unstable. However, despite the presence of more unstable linear modes, nonlinear gyrokinetic simulations of ETG with corrugated background electron temperature show a reduction of fluxes. Our investigation reveals a radial variation of the phase velocity of the modes that is proportional to the diamagnetic drift velocity and the local pressure gradient. The associated profile shearing breaks the turbulent eddies apart, reducing the transport level. This profile shearing resulting from fine-scale pressure corrugations could be a ubiquitous turbulence saturation mechanism not just in Fusion plasmas, but in Astrophysics and other areas.

FOS: Physical sciences↗
DOE OSTI2026

Modeling Temperature Profiles in the Pedestal of NSTX with Reduced Models

This paper describes new modeling capabilities for predicting H-mode pedestal profiles in spherical tokamaks. Temperature profiles for NSTX discharges 132543 and 132588 are modeled by coupling the \textsc{astra} transport solver with neoclassical transport and gyrokinetic-based reduced models for electron temperature gradient (ETG) and kinetic ballooning mode (KBM) instabilities. A quasi-linear surrogate model for ion-scale transport is developed using linear \textsc{gene} simulations, requiring only a single free parameter calibrated to one discharge. Time-evolving the temperatures with fixed density yields good agreement with experiments for both discharges. Systematic analysis of the transport mechanisms reveals that neoclassical transport is huge across the entire pedestal region for the ion channel. ETG turbulence is large in the plasma edge and low density gradient region, contributing substantially to the electron channel. However, KBM/MHD-like modes also drive significant transport in both the ion and electron thermal channels, making them essential for accurate pedestal modeling. Further refinements, including explicit E×B shear suppression and scaled ETG transport, produce quantitative but not qualitative improvements. This work lays the foundation for predictive modeling of future devices. This paper is on arxiv and has been submitted to Nuclear Fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Black Carbon Vertical Profiles Strongly Affect its Radiative Forcing Uncertainty

The impact of black carbon (BC) aerosols on the global radiation balance is not well constrained. Here twelve global aerosol models are used to show that at least 20% of the present uncertainty in modeled BC direct radiative forcing (RF) is due to diversity in the simulated vertical profile of BC mass. Results are from phases 1 and 2 of the global aerosol model intercomparison project (AeroCom). Additionally, a significant fraction of the variability is shown to come from high altitudes, as, globally, more than 40% of the total BC RF is exerted above 5 km. BC emission regions and areas with transported BC are found to have differing characteristics. These insights into the importance of the vertical profile of BC lead us to suggest that observational studies are needed to better characterize the global distribution of BC, including in the upper troposphere.

black↗
DOE OSTI2017

Derivation of aerosol profiles for MC3E convection studies and use in simulations of the 20 May squall line case

Advancing understanding of deep convection microphysics via mesoscale modeling studies of well-observed case studies requires observation-based aerosol inputs. Here, we derive hygroscopic aerosol size distribution input profiles from ground-based and airborne measurements for six convection case studies observed during the Midlatitude Continental Convective Cloud Experiment (MC3E) over Oklahoma. We demonstrate use of an input profile in simulations of the only well-observed case study that produced extensive stratiform outflow on 20 May 2011. At well-sampled elevations between -11 and -23 °C over widespread stratiform rain, ice crystal number concentrations are consistently dominated by a single mode near ~400 µm in randomly oriented maximum dimension ( D max ). The ice mass at -23 °C is primarily in a closely collocated mode, whereas a mass mode near D max ~1000 µm becomes dominant with decreasing elevation to the -11 °C level, consistent with possible aggregation during sedimentation. However, simulations with and without observation-based aerosol inputs systematically overpredict mass peak D max by a factor of 3–5 and underpredict ice number concentration by a factor of 4–10. Previously reported simulations with both two-moment and size-resolved microphysics have shown biases of a similar nature. The observed ice properties are notably similar to those reported from recent tropical measurements. Based on several lines of evidence, we speculate that updraft microphysical pathways determining outflow properties in the 20 May case are similar to a tropical regime, likely associated with warm-temperature ice multiplication that is not well understood or well represented in models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Radiative heating rate profiles over the southeast Atlantic Ocean during the 2016 and 2017 biomass burning seasons

Marine boundary layer clouds, including the transition from stratocumulus to cumulus, are poorly represented in numerical weather prediction and general circulation models. Further uncertainties in the cloud structure arise in the presence of biomass burning carbonaceous aerosol, as is the case over the southeast Atlantic Ocean, where biomass burning aerosol is transported from the African continent. As the aerosol plume progresses across the southeast Atlantic Ocean, radiative heating within the aerosol layer has the potential to alter the thermodynamic environment and therefore the cloud structure; however, limited work has been done to quantify this along the trajectory of the aerosol plume in the region. The deployment of the first Atmospheric Radiation Measurement (ARM) Mobile Facility (AMF1) in support of the Layered Atlantic Smoke Interactions with Clouds field campaign provided a unique opportunity to collect observations of cloud and aerosol properties during two consecutive biomass burning seasons during July through October of 2016 and 2017 over Ascension Island (7.96° S, 14.35° W). Using observed profiles of temperature, humidity, and clouds from the field campaign alongside aerosol optical properties from Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2), as input for the Rapid Radiation Transfer Model (RRTM), profiles of the radiative heating rate due to aerosols and clouds were computed. Radiative heating is also assessed across the southeast Atlantic Ocean using an ensemble of back trajectories from the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model. Idealized experiments using the RRTM with and without aerosols and a range of values for the single-scattering albedo (SSA) demonstrate that shortwave (SW) heating within the aerosol layer above Ascension Island can locally range between 2 and 8 K d -1 depending on the aerosol optical properties, though impacts of the aerosol can be felt elsewhere in the atmospheric column. When considered under clear conditions, the aerosol has a cooling effect at the TOA, and based on the observed cloud properties at Ascension Island, the cloud albedo is not large enough to overcome this. Shortwave radiative heating due to biomass burning aerosol is not balanced by additional longwave (LW) cooling, and the net radiative impact results in a stabilization of the lower troposphere. However, these results are extremely sensitive to the single-scattering albedo assumptions in models.

54 ENVIRONMENTAL SCIENCES↗