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DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗

DOE OSTI2022

Chandra measurements of gas homogeneity and turbulence at intermediate radii in the Perseus Cluster

ABSTRACT We present a Chandra study of surface brightness fluctuations in the diffuse intracluster medium of the Perseus Cluster. Our study utilizes deep, archival imaging of the cluster core as well as a new mosaic of 29 short $\, 5\,$-ks observations extending in eight different directions out to radii of $r_{500} \sim 2.2\, r_{2500}$. Under the assumption that the distribution of densities at a given radius is log-normally distributed, two important quantities can be derived from the width of the log-normal density distribution on a given spatial scale: the density bias, that is equal to the square root of the clumping factor C; and the one-component turbulent velocity, vk,1D. We forward-model all contributions to the measured surface brightness, including astrophysical and particle background components, and account for the Poisson nature of the measured signal. Measuring the distribution of surface brightness fluctuations in 1 arcmin2 regions, spanning the radial range $0.3\rm {-}2.2\, r_{2500}$ ($7.8\rm {-}57.3\,$ arcmin), we find a small to moderate average density bias of around $3{{\ \rm per\ cent}}$ at radii below $1.6\, r_{2500}$. We also infer an average turbulent velocity at these radii of V1D < 400 km s−1. Direct confirmation of our results on turbulent velocities inferred from surface brightness fluctuations should be possible using the X-ray calorimeter spectrometers to be flown aboard the XRISM and Athena observatories.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

The XRISM first-light observation: Velocity structure and thermal properties of the supernova remnant N 132D

Abstract We present an initial analysis of the X-Ray Imaging and Spectroscopy Mission (XRISM) first-light observation of the supernova remnant (SNR) N 132D in the Large Magellanic Cloud. The Resolve microcalorimeter has obtained the first high-resolution spectrum in the 1.6–10 keV band, which contains K-shell emission lines of Si, S, Ar, Ca, and Fe. We find that the Si and S lines are relatively narrow, with a broadening represented by a Gaussian-like velocity dispersion of $\sigma _v \sim 450$ km s$^{-1}$. However, the Fe He$\alpha$ lines are substantially broadened with $\sigma _v \sim 1670$ km s$^{-1}$. This broadening can be explained by a combination of the thermal Doppler effect due to the high ion temperature and the kinematic Doppler effect due to the SNR expansion. Assuming that the Fe He$\alpha$ emission originates predominantly from the supernova ejecta, we estimate the reverse shock velocity at the time when the bulk of the Fe ejecta were shock heated to be $-1000 \lesssim V_{\rm rs}$ (km s$^{-1}$) $\lesssim 3300$ (in the observer frame). We also find that Fe Ly$\alpha$ emission is redshifted with a bulk velocity of $\sim 890$ km s$^{-1}$, substantially larger than the radial velocity of the local interstellar medium surrounding N 132D. These results demonstrate that high-resolution X-ray spectroscopy is capable of providing constraints on the evolutionary stage, geometry, and velocity distribution of SNRs.

individual objects↗

DOE OSTI2024

Overionized plasma in the supernova remnant Sagittarius A East anchored by XRISM observations

Sagittarius A East is a supernova remnant with a unique surrounding environment, as it is located in the immediate vicinity of the supermassive black hole at the Galactic center, Sagittarius A$^{*}$. The X-ray emission of the remnant is suspected to show features of overionized plasma, which would require peculiar evolutionary paths. We report on the first observation of Sagittarius A East with the X-Ray Imaging and Spectroscopy Mission (XRISM). Equipped with a combination of a high-resolution microcalorimeter spectrometer and a large field-of-view CCD imager, we for the first time resolved the Fe xxv K-shell lines into fine structure lines and measured the forbidden-to-resonance intensity ratio to be $1.39 \pm 0.12$, which strongly suggests the presence of overionized plasma. We obtained a reliable constraint on the ionization temperature just before the transition into the overionization state, of $\gt\! 4\:$keV. The recombination timescale was constrained to be $\lt\! 8 \times 10^{11} \:$cm$^{-3}\:$s. The small velocity dispersion of $109 \pm 6\:$km$\:$s$^{-1}$ indicates a low Fe ion temperature $\lt\! 8\:$keV and a small expansion velocity $\lt\! 200\:$km$\:$s$^{-1}$. The high initial ionization temperature and small recombination timescale suggest that either rapid cooling of the plasma via adiabatic expansion from dense circumstellar material or intense photoionization by Sagittarius A$^{*}$ in the past may have triggered the overionization.

galaxy center↗

DOE OSTI2025

Constraining gas motion and non-thermal pressure beyond the core of the Abell 2029 galaxy cluster with XRISM

We report on a detailed spectroscopic study of the gas dynamics and hydrostatic mass bias of the galaxy cluster Abell 2029, utilizing high-resolution observations from XRISM Resolve. Abell 2029, known for its cool core and relaxed X-ray morphology, provides an excellent opportunity to investigate the influence of gas motions beyond the central region. Expanding upon prior studies that revealed low turbulence and bulk motions within the core, our analysis covers regions out to the scale radius $R_{2500}$ (670 kpc) based on three radial pointings extending from the cluster center toward the northern side. We obtain accurate measurements of bulk and turbulent velocities along the line of sight. The results indicate that non-thermal pressure accounts for no more than 2% of the total pressure at all radii, with a gradual decrease outward. The observed radial trend differs from many numerical simulations, which often predict an increase in non-thermal pressure fraction at larger radii. These findings suggest that deviations from hydrostatic equilibrium are small, leading to a hydrostatic mass bias of around 2% across the observed area.

X-rays: galaxies: clusters↗

DOE OSTI2025

Thermal and kinematic properties of ejecta in SN1987A revealed by XRISM

We present an analysis of high-resolution spectra from the shock-heated plasmas in SN 1987A, based on an observation using the Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM). The 1.7–10 keV Resolve spectra are accurately represented by a single-component, plane-parallel shock plasma model, with a temperature of $2.84_{-0.08}^{+0.09}$ keV and an ionization parameter of $2.64_{-0.45}^{+0.58}$ × $10^{11}\,\,{\rm s\,\, cm}^{-3}$. The Resolve spectra are also well reproduced by the 3D magneto-hydrodynamic simulation presented by Orlando et al. (2020, A&A, 636, A22) suggesting substantial contribution from the ejecta. The metal abundances obtained with Resolve align with the Large Magellanic Cloud value, indicating that the X-rays in 2024 originate from “non-metal-rich” shock-heated ejecta and the reverse shock has not reached the inner metal-rich region of ejecta. Doppler widths of the atomic lines from Si, S, and Fe correspond to velocities of 1500–1700 km s$^{-1}$, where the thermal broadening effects in this non-metal-rich plasma are negligible. Therefore, the line broadening seen in Resolve spectra is determined by the large bulk motion of ejecta. For reference, we determined a $90\%$ upper limit on non-thermal emission from a pulsar wind nebula at $4.3 \times 10^{-13}$ erg cm$^{-2}$ s$^{-1}$ in the 2–10 keV range, aligning with NuSTAR findings by Greco et al. (2022, ApJ, 931, 132). Additionally, we searched for the $^{44}$Sc K line feature and found a $1\sigma$ upper limit of $1.0 \times 10^{-6}$ photons cm$^{-2}$ s$^{-1}$, which translates to an initial $^{44}$Ti mass of approximately $2 \times 10^{-4}\, M_{\odot }$, consistent with previous X-ray to soft gamma-ray observations (Boggs et al. 2015, Science, 348, 670; Grebenev et al. 2012, Nature, 490, 373; Leising 2006, ApJ, 651, 1019).

ISM: supernova remnants↗

DOE OSTI2025

XRISM/Resolve view of Abell 2319: Turbulence, sloshing, and ICM dynamics

Here, we present results from XRISM/Resolve observations of the core of the galaxy cluster Abell 2319, focusing on its kinematic properties. The intracluster medium (ICM) exhibits temperatures of approximately 8 keV across the core, with a prominent cold front and a high-temperature region (⁠~11 keV) in the north-west. The average gas velocity in the 3' x 4' region around the brightest cluster galaxy (BCG) covered by two Resolve pointings is consistent with that of the BCG to within 40 km s -1 ⁠ and we found modest average velocity dispersion of 230–250 km s -1 ⁠. On the other hand, spatially resolved spectroscopy reveals interesting variations. A blueshift of up to ~230 km s -1 ⁠ is observed around the east edge of the cold front, where the gas with the lowest specific entropy is found. The region further south inside the cold front shows only a small velocity difference from the BCG; however, its velocity dispersion is enhanced to ~400 km s -1 ⁠, implying the development of turbulence. These characteristics indicate that we are observing sloshing motion with some inclination angle following BCG and that gas phases with different specific entropy participate in sloshing with their own velocities, as expected from simulations. No significant evidence for a high-redshift ICM component associated with the subcluster Abell 2319B was found in the region covered by the current Resolve pointings. These results highlight the importance of sloshing and turbulence in shaping the internal structure of Abell 2319. Further deep observations are necessary to better understand the mixing and turbulent processes within the cluster.

Astronomy and AstroPhysics↗

DOE OSTI2026

Constraints on Large-Scale White Noise in the Cosmic Density Field

We present observational constraints on large-scale white noise (LSWN) in the cosmic density field, a phenomenon predicted to arise from non-linear mode coupling during cosmological evolution. Building on the theoretical framework of Paper I, where we demonstrated that non-linearities inevitably redistribute power from small to large scales through mode mixing, we confront these predictions with current cosmological data. We modify the CLASS Boltzmann code to incorporate a white noise component $k_\mathrm{BH}/k$ in the primordial power spectrum and perform parameter estimation using current cosmological data. The non-detection of excess power on the largest observable scales places stringent upper bounds: $k_\mathrm{BH} \leq 1.80 \times 10^{-13}~\mathrm{Mpc}^{-1}$ at 99% confidence. These constraints imply the primordial power spectrum must deviate from perfect scale invariance on small scales, either through a cutoff at $k_{\mathrm{cut}} \lesssim 3~\mathrm{pc}^{-1}$ or through running of the spectral index with $α_s \lesssim -0.015$. Our results demonstrate that LSWN provides a powerful probe of the primordial spectrum at scales orders of magnitude smaller than directly observable, offering unique constraints on early-universe physics.

Barenboim, Gabriela [Valencia U., IFIC; Valencia U↗

DOE OSTI2026

Affleck-Dine curvaton

The Standard Model of particle physics does not explain the origin of the universe’s baryon asymmetry or its primordial fluctuations. The Affleck-Dine mechanism is a well motivated scenario for generating the baryon asymmetry through the postinflationary dynamics of a complex scalar field with baryon number. The curvaton mechanism is a popular approach for producing curvature perturbations through the dynamics of a light spectator field that decays after inflation. We demonstrate that the same complex field can viably perform both roles without any modifications to the minimal realization of Affleck-Dine baryogenesis. This scenario can also accommodate appreciable levels of primordial non-Gaussianity, beyond those achievable with only a real-valued curvaton field, and may be observable with future cosmic microwave background experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Observable CMB B -modes from cosmological phase transitions

A B -mode polarization signal in the cosmic microwave background (CMB) is widely regarded as smoking gun evidence for gravitational waves produced during inflation. Here, we demonstrate that tensor perturbations sourced during noninflationary epochs can yield non-negligible B -mode signals, which can in principle complicate the interpretation of future observational data. As a case study, we consider tensor perturbations sourced in the bubble collision stage of a first-order cosmological phase transition occurring in a secluded dark sector. Although phase transitions arise from causal subhorizon physics, they nevertheless exhibit a white noise power spectrum on superhorizon scales. Power is suppressed on the large scales relevant for CMB B -mode polarization, but it is not necessarily negligible. We show that for appropriately chosen phase transition parameters, the maximal B -mode amplitude can compete with inflationary predictions that can be tested with current and future experiments. These scenarios can be differentiated by performing measurements on multiple angular scales, since the phase transition signal predicts peak power on smaller scales.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020