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At least 73 records · Page 4

Residual tissue repositories as a resource for population-based cancer proteomic studies

Background: Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected fresh frozen or optimal cutting temperature (OCT) embedded specimens. However, such specimens are often difficult to obtain, in limited in supply, and clinical information and outcomes on patients are inherently delayed as compared to banked samples. Annotated formalin fixed, paraffin embedded (FFPE) tumor tissue specimens are available for research use from a variety of tissue banks, such as from the surveillance, epidemiology and end results (SEER) registries’ residual tissue repositories. Given the wealth of outcomes information associated with such samples, the reuse of archived FFPE blocks for deep proteomic characterization with mass spectrometry technologies would provide a valuable resource for population-based cancer studies. Further, due to the widespread availability of FFPE specimens, validation of specimen integrity opens the possibility for thousands of studies that can be conducted worldwide. Methods: To examine the suitability of the SEER repository tissues for proteomic and phosphoproteomic analysis, we analyzed 60 SEER patient samples, with time in storage ranging from 7 to 32 years; 60 samples with expression proteomics and 18 with phosphoproteomics, using isobaric labeling. Linear modeling and gene set enrichment analysis was used to evaluate the impacts of collection site and storage time. Results: All samples, regardless of age, yielded suitable protein mass after extraction for expression analysis and 18 samples yielded sufficient mass for phosphopeptide analysis. Although peptide, protein, and phosphopeptide identifications were reduced by 50, 20 and 76% respectively, from comparable OCT specimens, we found no statistically significant differences in protein quantitation correlating with collection site or specimen age. GSEA analysis of GOterm level measurements of protein abundance differences between FFPE and OCT embedded specimens suggest that the formalin fixation process may alter representation of protein categories in the resulting dataset. Conclusions: These studies demonstrate that residual FFPE tissue specimens, of varying age and collection site, are a promising source of protein for proteomic investigations if paired with rigorously verified mass spectrometry workflows.

60 APPLIED LIFE SCIENCES↗

High-energy processes in solar flares

A detailed study of high-energy processes in solar flares is reported, including the production of neutrons and pions, and incorporating isobaric and scaling models and a recent compilation of pion production data (Dermer, 1986). The broad-band gamma-ray spectrum resulting from the decay of neutral pions, the bremsstrahlung of positrons and electrons from the decay of charged pions, and the annihilation in flight of positrons is evaluated. Also evaluated is the 0.511 MeV gamma-ray line resulting from the annihilation of the positrons which survive annihilation in flight. Calculations were based on an isotropic, thick-target model using the best available nuclear data and models. Results are compared with extensive observation of the June 3, 1982 flare (10-120 MeV gamma rays), 0.511 and 2.2 MeV line emission, nuclear line emission, high-energy neutrons, and interplanetary charged particles.

Murphy, R. J.↗

XMM-Newton Observations of the Cluster of Galaxies Sersic 159-03

The cluster of galaxies Sersic 159-03 was observed with the XMM-Newton X-ray observatory as part of the Guaranteed Time program. X-ray spectra taken with the EPIC and RGS instruments show no evidence for the strong cooling flow derived from previous X-ray observations. There is a significant lack of cool gas below 1.5 keV as compared to standard isobaric cooling flow models. While the oxygen is distributed more or less uniformly over the cluster, iron shows a strong concentration in the center of the cluster, slightly offset from the brightness center but within the central cD galaxy. This points to enhanced type Ia supernova activity in the center of the cluster. There is also an elongated iron-rich structure ex- tending to the east of the cluster, showing the inhomogeneity of the iron distribution. Finally, the temperature drops rapidly beyond 4' from the cluster center.

Kaastra, J. S.↗

Mass measurements of 60–63 Ga reduce x-ray burst model uncertainties and extend the evaluated T=1 isobaric multiplet mass equation

We report precision mass measurements of neutron-deficient gallium isotopes approaching the proton drip line. The measurements of 60–63 Ga performed with the TITAN multiple-reflection time-of-flight mass spectrometer provide a more than threefold improvement over the current literature mass uncertainty of 61 Ga and mark the first direct mass measurement of 60 Ga. The improved precision of the 61 Ga mass has important implications for the astrophysical rp process, as it constrains essential reaction Q values near the 60 Zn waiting point. Based on calculations with a one-zone model, we demonstrate the impact of the improved mass data on prediction uncertainties of x-ray burst models. The first-time measurement of the 60 Ga ground-state mass establishes the proton-bound nature of this nuclide, thus constraining the location of the proton drip line along this isotopic chain. Including the measured mass of 60 Ga further enables us to extend the evaluated T = 1 isobaric multiplet mass equation up to A = 60.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On Degeneracies in Retrievals of Exoplanetary Transmission Spectra

Accurate estimations of atmospheric properties of exoplanets from transmission spectra require the understanding of degeneracies between model parameters and observations that can resolve them. We conduct a systematic investigation of such degeneracies using a combination of detailed atmospheric retrievals and a range of model assumptions, focusing on H{sub 2}-rich atmospheres. As a case study, we consider the well-studied hot Jupiter HD 209458 b. We perform extensive retrievals with models ranging from simple isothermal and isobaric atmospheres to those with full pressure–temperature profiles, inhomogeneous cloud/haze coverage, multiple-molecular species, and data in the optical–infrared wavelengths. Our study reveals four key insights. First, we find that a combination of models with minimal assumptions and broadband transmission spectra with current facilities allows precise estimates of chemical abundances. In particular, high-precision optical and infrared spectra, along with models including variable cloud coverage and prominent opacity sources, with Na and K being important in the optical, provide joint constraints on cloud/haze properties and chemical abundances. Second, we show that the degeneracy between planetary radius and its reference pressure is well characterized and has little effect on abundance estimates, contrary to previous claims using semi-analytic models. Third, collision-induced absorption due to H{sub 2}–H{sub 2} and H{sub 2}–He interactions plays a critical role in correctly estimating atmospheric abundances. Finally, our results highlight the inadequacy of simplified semi-analytic models with isobaric assumptions for reliable retrievals of transmission spectra. Transmission spectra obtained with current facilities such as the Hubble Space Telescope and Very Large Telescope can provide strong constraints on atmospheric abundances of exoplanets.

79 ASTRONOMY AND ASTROPHYSICS↗

Investigation of Isobaric Mixing as a Mechanism for Boundary‐Layer Cloud Formation

This study investigates the potential role of isobaric mixing in the formation of marine boundary layer clouds. Cloud formation theory emphasizes uplift and adiabatic cooling, but recent observations support the existence of small clouds forming at various altitudes, even below the lifting condensation level. Isobaric mixing of air with different thermodynamic properties can generate localized supersaturation. A Gaussian mixing model is employed to simulate this process, considering the correlation between temperature and water vapor. Cloud droplet size distributions from aircraft measurements show a persistent and prominent mode of small droplets at 9 m, and the size of this mode compares favorably with predictions from the model. The results suggests that isobaric mixing plausibly contributes to the formation of clouds, particularly those observed at multiple altitudes with narrow droplet size distributions. This finding highlights the importance of considering isobaric mixing processes in understanding and modeling cloud formation.

54 ENVIRONMENTAL SCIENCES↗

Modeling of diffuse interstellar clouds - The case of Gamma Arae

Observations of the interstellar cloud toward Gamma Arae (Morton and Hu, 1975) are analyzed with an improved version of the isobaric, steady-state model of Glassgold and Langer (1974). Good agreement is obtained using parameters which are close to those which represent the average properties of many diffuse interstellar clouds. The successful correlation of the data for H, H2, C II, C I, OI, CO, and OH supports current concepts on interstellar thermodynamics and chemistry.

Federman, S. R.↗

Self-consistent theory of the Darrieus–Landau and Rayleigh–Taylor instabilities with self-generated magnetic fields

The Rayleigh–Taylor (RT) and Darrieus–Landau (DL) instabilities are studied in an inertial confinement fusion context within the framework of small critical-to-shell density ratio D R and weak acceleration regime, i.e., large Froude number Fr. The quasi-isobaric analysis in Sanz et al. is completed with the inclusion of non-isobaric and self-generated magnetic-field effects. The analysis is restricted to perturbation wavelengths k~1 larger than the conduction length scale at the ablation front, yet its validity ranges from wavelengths shorter and larger than the conduction layer width (distance between the ablation front and the critical surface). The use of a sharp boundary model leads to a single analytical expression of the dispersion relation encompassing both instabilities. The two new effects come into play by modifying the perturbed mass and momentum fluxes at the ablation front. The momentum flux (perturbed pressure at the spike) is the predominant stabilizing mechanism in the RT instability (overpressure) and the driving mechanism in the DL instability (underpressure). The non-isobaric effects notably modify the scaling laws in the DL limit, leading to an underpressure scaling as ~k –11/15 rather than ~k –2/5 obtained in the quasi-isobaric model. The magnetic fields are generated due to misalignment between pressure and density gradients (Biermann battery effect). They affect the hydrodynamics by bending the heat flux lines. Within the framework of this paper, they enhance ablation, resulting in a stabilizing effect that peaks for perturbation wavelengths comparable to the conduction layer width. Here, the combination of parameters D R Fr 2/3 defines the region of predominance of each instability in the dispersion relation. It is proven that the DL region falls outside of the parameter range in inertial confinement fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The reaction π{sup −}p → π{sup −}π{sup −}π{sup +}p: Development of the analysis methods and selected results

We present the description of the analysis methods and results of applying them to the exclusive diffractive reaction π{sup −}p → π{sup −}π{sup −}π{sup +}p of 50 · 10{sup 6} events measured with COMPASS detector. The large statistics of π{sup −}π{sup −}π{sup +} events enables the two-dimensional partial-wave analysis independently in 100 bins of m(3π) with 0.5 < m(3π) < 2.5 GeV/c{sup 2} and in 11 intervals of squared momentum transfer with 0.1 < t′ < 1 GeV{sup 2}/c{sup 2}. The partial-wave analysis sub-density matrix is the subject to further mass-dependent fits describing the data in terms of resonances in 3π system and coherent background contributions. The novel approach of extracting J{sup PC} = 0{sup ++}(π{sup +}π{sup −}){sub S} isobar amplitudes as model-free functions, different for several J{sup PC} 3π states, is used. It demonstrates the presence of processes π(1800) → f{sub 0}(980)π and π(1800) → f{sub 0}(1500)π as well as π{sub 2}(1880) → f{sub 0}(980)π and new narrow signal a{sub 1}(1420) → f{sub 0}(980)π, without any established shapes used for (π{sup +}π{sup −}){sub S} isobars. The presented analysis is subject to further development and refinements which currently take place.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Properties of hot-spot emission in a warm plastic-shell implosion on the OMEGA laser system

A warm plastic-shell implosion was performed on the OMEGA laser system. The measured corona plasma evolution and shell trajectory in the acceleration phase are reasonably simulated by the one-dimensional LILAC simulation including the nonlocal and cross-beam energy transfer models. The results from analytical thin-shell model reproduce the time-dependent shell radius by LILAC simulation, and also the hot-spot x-ray emissivity profile at stagnation predicted by Spect3D. In the Spect3D simulations within a clean implosion, a “U”-shaped hot-spot radius evolution can be observed with the Kirkpatrick-Baez microscope response (the photon energy is from 4 to 8 keV). However, a fading away hot-spot radius evolution was measured in OMEGA warm plastic-shell implosion because of mixings. In order to recover the measured hot-spot x-ray emissivity profile at stagnation, a non-isobaric hot-spot model is built, and the normalized hot-spot temperature, density, and pressure profiles (normalized to the corresponding target-center values) are obtained.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Emulating ab initio computations of infinite nucleonic matter

We construct efficient emulators for the computation of the infinite nuclear matter equation of state. These emulators are based on the subspace-projected coupled-cluster method for which we here develop a new algorithm called small-batch voting to eliminate spurious states that might appear when emulating quantum many-body methods based on a non-Hermitian Hamiltonian. The efficiency and accuracy of these emulators facilitate a rigorous statistical analysis within which we explore nuclear matter predictions for > 10 6 different parametrizations of a chiral interaction model with explicit Δ -isobars at next-to-next-to leading order. Constrained by nucleon-nucleon scattering phase shifts and bound-state observables of light nuclei up to He 4 , we use history matching to identify nonimplausible domains for the low-energy coupling constants of the chiral interaction. Within these domains we perform a Bayesian analysis using sampling and importance resampling with different likelihood calibrations and study correlations between interaction parameters, calibration observables in light nuclei, and nuclear matter saturation properties. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cross sections for the γp \to K^{*+} Lambda$ and $γp \to K^{*+} Sigma^{0}$ reactions measured at CLAS

The first high-statistics cross sections for the reactions $\gamma p \to K^{*+} \Lambda$ and $\gamma p \to K^{*+} \Sigma^0$ were measured using the CLAS detector at photon energies between threshold and 3.9 GeV at the Thomas Jefferson National Accelerator Facility. Differential cross sections are presented over the full range of the center-of-mass angles, $\theta^{CM}_{K^{*+}}$, and then fitted to Legendre polynomials to extract the total cross section. Results for the $K^{*+}\Lambda$ final state are compared with two different calculations in an isobar and a Regge model, respectively. Theoretical calculations significantly underestimate the $K^{*+} \Lambda$ total cross sections between 2.1 and 2.6 GeV, but are in better agreement with present data at higher photon energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Off-gas Adsorption Model and Simulation - OSPREY

The absence of industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other countries. Thus, it is essential to model complex series of unit operations to simulate, understand, and predict inherent transient behavior. A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes is expected to provide substantial cost savings and many technical benefits. To support this capability, a modeling effort focused on the off-gas treatment system of a used nuclear fuel recycling facility is in progress. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic models are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone model and in series with multiple others. Currently, an adsorption model has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and REcoverY (OSPREY) models the adsorption of offgas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the model include gas composition, sorbent and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data can be obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. In addition to concentration data, the model predicts temperature along the column length as a function of time and pressure drop along the column length. A description of the OSPREY model, results from krypton adsorption modeling and plans for modeling the behavior of iodine, xenon, and tritium will be discussed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Off-gas adsorption model and simulation - OSPREY

A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes is expected to provide substantial cost savings and many technical benefits. To support this capability, a modeling effort focused on the off-gas treatment system of a used nuclear fuel recycling facility is in progress. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic models are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone model and in series with multiple others. Currently, an adsorption model has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and Recovery (OSPREY) models the adsorption of offgas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the model include gas composition, sorbent and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data can be obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. In addition to concentration data, the model predicts temperature along the column length as a function of time and pressure drop along the column length. A description of the OSPREY model, results from krypton adsorption modeling and plans for modeling the behavior of iodine, xenon, and tritium will be discussed. (author)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

OSPREY Model

The absence of industrial scale nuclear fuel reprocessing in the U.S. has precluded the necessary driver for developing the advanced simulation capability now prevalent in so many other countries. Thus, it is essential to model complex series of unit operations to simulate, understand, and predict inherent transient behavior and feedback loops. A capability of accurately simulating the dynamic behavior of advanced fuel cycle separation processes will provide substantial cost savings and many technical benefits. The specific fuel cycle separation process discussed in this report is the off-gas treatment system. The off-gas separation consists of a series of scrubbers and adsorption beds to capture constituents of interest. Dynamic models are being developed to simulate each unit operation involved so each unit operation can be used as a stand-alone model and in series with multiple others. Currently, an adsorption model has been developed within Multi-physics Object Oriented Simulation Environment (MOOSE) developed at the Idaho National Laboratory (INL). Off-gas Separation and REcoverY (OSPREY) models the adsorption of off-gas constituents for dispersed plug flow in a packed bed under non-isothermal and non-isobaric conditions. Inputs to the model include gas, sorbent, and column properties, equilibrium and kinetic data, and inlet conditions. The simulation outputs component concentrations along the column length as a function of time from which breakthrough data is obtained. The breakthrough data can be used to determine bed capacity, which in turn can be used to size columns. It also outputs temperature along the column length as a function of time and pressure drop along the column length. Experimental data and parameters were input into the adsorption model to develop models specific for krypton adsorption. The same can be done for iodine, xenon, and tritium. The model will be validated with experimental breakthrough curves. Customers will be given access to OSPREY to used and evaluate the model.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Theoretical spectral distributions and total cross sections for neutral subthreshold pion production in carbon-carbon collisions

A coherent isobar formalism is employed to model subthreshold production of neutral pions in carbon-carbon collisions at energies below 100 MeV/nucleon. No arbitrary scale factors or adjustable free parameters are used in calculation of the Lorentz-invariant cross sections for pion production in the projectile, which produces an excited state that goes to M1 resonance in the target by conservation of spin and isospin. Pion production is also modeled for the projectile, which also reaches M1 resonance. The overall pion spectral distribution in the center of mass system is then integrated over the energy range 35-84 MeV/nucleon. The results expose an energy loss in the incident ions, as observed experimentally, and indicate that an isobar mechanism is responsible for higher energy pion production. Lower energy pions are a result of thermal processes.

Norbury, J. W.↗

Stochastic symplectic reduced-order modeling for model-form uncertainty quantification in molecular dynamics simulations in various statistical ensembles

Here, this work focuses on the representation of model-form uncertainties in molecular dynamics simulations in various statistical ensembles. In prior contributions, the modeling of such uncertainties was formalized and applied to quantify the impact of, and the error generated by, pair-potential selection in the microcanonical ensemble (NVE). In this work, we extend this formulation and present a linear-subspace reduced-order model for the canonical (NVT) and isobaric (NPT) ensembles. The symplectic reduced-order basis is randomized on the tangent space of the Stiefel manifold to provide topological relationships and capture model-form uncertainty. Using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), we assess the relevance of these stochastic reduced-order atomistic models on canonical problems involving a Lennard-Jones fluid and an argon crystal melt.

42 ENGINEERING↗

Structure of the spatial periphery of the {sup 11}Li and {sup 11}Be isobars

On the basis of the shell model with an extended basis, the structure of {sup 9}Li-{sup 9}Be to {sup 11}Li-{sup 11}Be nuclei is examined with allowance for the competition of {sup jj} coupling and Majorana exchange forces via considering the sequential addition of neutrons, and the respective wave functions are determined. A formalism for calculating the spectroscopic factor for a dineutron and for individual neutrons in nuclei whose wave functions incorporate the mixing of shell configurations is developed. The reactions {sup 9}Li(t, p){sup 11}Li and {sup 9}Be(t, p){sup 11}Be treated with allowance for the mechanisms of dineutron stripping and a sequential transfer of two neutrons are considered as an indicator of the proposed structure of lithium and berylliumisotopes. The parameters of the optical potentials, the wave functions for the bound states of transferred particles, and the interaction potentials corresponding to them are determined from a comparison of the theoretical angular distribution of protons from the reaction {sup 9}Be(t, p){sup 11}Be with its experimental counterpart. It is shown that a dineutron periphery of size about 6.4 fm is present in the {sup 11}Li nucleus and that a single-neutron periphery of size about 8 fm is present in the {sup 11}Be nucleus.

74 ATOMIC AND MOLECULAR PHYSICS↗