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DOE OSTI2020

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Imaging the dome of Santa Maria del Fiore using cosmic rays

The dome of Santa Maria del Fiore, Florence Cathedral, was built between 1420 and 1436 by architect Filippo Brunelleschi and it is now cracking under its own weight. Engineering efforts are under way to model the dome's structure and reinforce it against further deterioration. According to some scholars, Brunelleschi might have built reinforcement structures into the dome itself; however, the only known reinforcement is a wood chain 7.75 m above the springing of the Cupola. Multiple scattering muon radiography is a non-destructive imaging method that can be used to image the interior of the dome's wall and therefore ascertain the layout and status of any iron substructure in it. A demonstration measurement was performed at the Los Alamos National Laboratory on a mock-up wall to show the feasibility of the work proposed, and a lightweight and modular imaging system is currently under construction. Here, we will discuss here the results of the demonstration measurement and the potential of the proposed technique, describe the imaging system under construction and outline the plans for the measurement.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Filter pruning of Convolutional Neural Networks for text classification: A case study of cancer pathology report comprehension

Convolutional Neural Networks (CNN) have recently demonstrated effective performance in many Natural Language Processing tasks. In this study, we explore a novel approach for pruning a CNN's convolution filters using our new data-driven utility score. We have applied this technique to an information extraction task of classifying a dataset of cancer pathology reports by cancer type, a highly imbalanced dataset. Compared to standard CNN training, our new algorithm resulted in a nearly .07 increase in the micro-averaged F1-score and a strong .22 increase in the macro-averaged F1-score using a model with nearly a third fewer network weights. We show how directly utilizing a network's interpretation of data can result in strong performance gains, particularly with severely imbalanced datasets.

Yoon, Hong-Jun↗

DOE OSTI2024

Signatures of cysteine oxidation on muscle structural and contractile proteins are associated with physical performance and muscle function in older adults: Study of Muscle, Mobility and Aging (SOMMA)

Oxidative stress is considered a contributor to declining muscle function and mobility during aging; however, the underlying molecular mechanisms remain poorly described. We hypothesized that greater levels of cysteine (Cys) oxidation on muscle proteins are associated with decreased measures of mobility. Herein, we applied a novel redox proteomics approach to measure reversible protein Cys oxidation in vastus lateralis muscle biopsies collected from 56 subjects in the Study of Muscle, Mobility and Aging (SOMMA), a community-based cohort study of individuals aged 70 years and older. We tested whether levels of Cys oxidation on key muscle proteins involved in muscle structure and contraction were associated with muscle function (leg power and strength), walking speed, and fitness (VO 2 peak on cardiopulmonary exercise testing) using linear regression models adjusted for age, sex, and body weight. Higher oxidation levels of select nebulin Cys sites were associated with lower VO 2 peak, while greater oxidation of myomesin-1, myomesin-2, and nebulin Cys sites was associated with slower walking speed. Higher oxidation of Cys sites in key proteins such as myomesin-2, alpha-actinin-2, and skeletal muscle alpha-actin were associated with lower leg power and strength. We also observed an unexpected correlation (R = 0.48) between a higher oxidation level of eight Cys sites in alpha-actinin-3 and stronger leg power. Despite this observation, the results generally support the hypothesis that Cys oxidation of muscle proteins impairs muscle power and strength, walking speed, and cardiopulmonary fitness with aging.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. II. Experiment

Purpose: A C-arm CT system has been shown to be capable of scanning a single cadaver leg under loaded conditions by virtue of its highly flexible acquisition trajectories. In Part I of this study, using the 4D XCAT-based numerical simulation, the authors predicted that the involuntary motion in the lower body of subjects in weight-bearing positions would seriously degrade image quality and the authors suggested three motion compensation methods by which the reconstructions could be corrected to provide diagnostic image quality. Here, the authors demonstrate that a flat-panel angiography system is appropriate for scanning both legs of subjectsin vivo under weight-bearing conditions and further evaluate the three motion-correction algorithms using in vivo data. Methods: The geometry of a C-arm CT system for a horizontal scan trajectory was calibrated using the PDS-2 phantom. The authors acquired images of two healthy volunteers while lying supine on a table, standing, and squatting at several knee flexion angles. In order to identify the involuntary motion of the lower body, nine 1-mm-diameter tantalum fiducial markers were attached around the knee. The static mean marker position in 3D, a reference for motion compensation, was estimated by back-projecting detected markers in multiple projections using calibrated projection matrices and identifying the intersection points in 3D of the back-projected rays. Motion was corrected using three different methods (described in detail previously): (1) 2D projection shifting, (2) 2D deformable projection warping, and (3) 3D rigid body warping. For quantitative image quality analysis, SSIM indices for the three methods were compared using the supine data as a ground truth. Results: A 2D Euclidean distance-based metric of subjects’ motion ranged from 0.85 mm (±0.49 mm) to 3.82 mm (±2.91 mm) (corresponding to 2.76 to 12.41 pixels) resulting in severe motion artifacts in 3D reconstructions. Shifting in 2D, 2D warping, and 3D warping improved the SSIM in the central slice by 20.22%, 16.83%, and 25.77% in the data with the largest motion among the five datasets (SCAN5); improvement in off-center slices was 18.94%, 29.14%, and 36.08%, respectively. Conclusions: The authors showed that C-arm CT control can be implemented for nonstandard horizontal trajectories which enabled us to scan and successfully reconstruct both legs of volunteers in weight-bearing positions. As predicted using theoretical models, the proposed motion correction methods improved image quality by reducing motion artifacts in reconstructions; 3D warping performed better than the 2D methods, especially in off-center slices.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2025

Reweighting simulated events using machine-learning techniques in the CMS experiment

Data analyses in particle physics rely on an accurate simulation of particle collisions and a detailed simulation of detector effects to extract physics knowledge from the recorded data. Event generators together with a GEANT -based simulation of the detectors are used to produce large samples of simulated events for analysis by the LHC experiments. These simulations come at a high computational cost, where the detector simulation and reconstruction algorithms have the largest CPU demands. This article describes how machine-learning (ML) techniques are used to reweight simulated samples obtained with a given set of parameters to samples with different parameters or samples obtained from entirely different simulation programs. The ML reweighting method avoids the need for simulating the detector response multiple times by incorporating the relevant information in a single sample through event weights. Results are presented for reweighting to model variations and higher-order calculations in simulated top quark pair production at the LHC. This ML-based reweighting is an important element of the future computing model of the CMS experiment and will facilitate precision measurements at the High-Luminosity LHC.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Universal suppression of superfluid weight by non-magnetic disorder in $s$-wave superconductors independent of quantum geometry and band dispersion

Motivated by the experimental progress in controlling the properties of the energy bands in superconductors, significant theoretical efforts have been devoted to study the effect of the quantum geometry and the flatness of the dispersion on the superfluid weight. In conventional superconductors, where the energy bands are wide and the Fermi energy is large, the contribution due to the quantum geometry is negligible, but in the opposite limit of flat-band superconductors the superfluid weight originates purely from the quantum geometry of Bloch wave functions. Here, we study how the energy band dispersion and the quantum geometry affect the disorder-induced suppression of the superfluid weight. In particular, we consider non-magnetic disorder and s-wave superconductivity. Surprisingly, we find that the disorder-dependence of the superfluid weight is universal across a variety of models, and independent of the quantum geometry and the flatness of the dispersion. Our results suggest that a flat-band superconductor is as resilient to disorder as a conventional superconductor.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Modeling Workloads of a Linear Electromagnetic Code for Load Balancing Matrix Assembly

This report presents our work to model the workloads of a linear electromagnetic application based on the method of moments in the frequency domain to effectively load balance the matrix assembly. This application is particularly challenging to load balance due to its lack of persistent iterative behavior, its operation under tight memory constraint (where the matrix may fill 80% of memory on each node), and the algorithmic complexity of the computational method. This report describes the first step in our work to apply an inspector-executor approach for load balancing workloads where key parameters are exposed during the inspector phase and a pre-trained model is applied to predict relative task weights for the load balancer.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1976

Toward more environmentally resistant gas turbines - Progress in NASA-Lewis programs

The paper surveys programs for improving the environmental resistance of gas turbine and power system materials to oxidation and hot corrosion. A computer program Corest has been produced which provides an initial method for predicting long-time metal loss using short-time oxidation data. The role of the coefficient of thermal expansion mismatch on oxide spallation is being studied. A paralinear oxidation attack model in conjunction with regression analysis of weight change data has been applied to the study of oxidation and hot corrosion attack of some Ni-Cr-Al system alloys. Oxide-dispersion strengthened alloys based on the Ni-Cr-Al system are being developed. Sodium sulfate formation during turbine combustion is being investigated from a thermodynamic viewpoint.

Lowell, C. E.↗

NASA NTRS1983

A least squares finite element scheme for transonic flow around harmonically oscillating airfoils

The present investigation shows that a finite element scheme with a weighted least squares variational principle is applicable to the problem of transonic flow around a harmonically oscillating airfoil. For the flat plate case, numerical results compare favorably with the exact solution. The obtained numerical results for the transonic problem, for which an exact solution is not known, have the characteristics of known experimental results. It is demonstrated that the performance of the employed numerical method is independent of equation type (elliptic or hyperbolic) and frequency. The weighted least squares principle allows the appropriate modeling of singularities, which such a modeling of singularities is not possible with normal least squares.

Cox, C. L.↗

NASA NTRS1978

Advanced composite stabilizer for Boeing 737 aircraft

Activities related to development of an advanced composites stabilizer for the Boeing 737 commercial transport are reported. Activities include discussion of the design and weight status, stiffness requirements, the finite element model, test programs, quality assurance, and manufacturing producibility studies. Design details of the graphite/epoxy components are virtually complete. Emphasis is placed on the metal and fiberglass trailing edge components. The bending and torsional stiffness properties are satisfactory for both stability/control and for flutter requirements. The finite element model input geometry is revised to reflect the latest changes to production drawings.

Source record↗

NASA NTRS1986

Bailout from the Space Shuttle

Studies to investigate the bailout characteristics from the Space Shuttle Orbiter at low-subsonic speeds have been made in the Langley 12-foot Low-Speed Tunnel and the Langley 4- by 7Meter Tunnel with 0.03-scale models. The effect of crew-model exit velocity, body posture, and body weight were studied with egress from the Orbiter main side hatch and from the upper cabin hatch. Force tests were made to determine the high angle-of-attack trim characteristics of the Orbiter in an attempt to improve bailout conditions. A computer simulation was made to evaluate the maneuver necessary to attain the high-angle trim.

Ware, G. M.↗

NASA NTRS1988

Cost estimating methods for advanced space systems

The development of parametric cost estimating methods for advanced space systems in the conceptual design phase is discussed. The process of identifying variables which drive cost and the relationship between weight and cost are discussed. A theoretical model of cost is developed and tested using a historical data base of research and development projects.

Cyr, Kelley↗

NASA NTRS1990

Supersonic combustion engine testbed, heat lightning

The design of a supersonic combustion engine testbed (SCET) aircraft is presented. The hypersonic waverider will utilize both supersonic combustion ramjet (SCRAMjet) and turbofan-ramjet engines. The waverider concept, system integration, electrical power, weight analysis, cockpit, landing skids, and configuration modeling are addressed in the configuration considerations. The subsonic, supersonic and hypersonic aerodynamics are presented along with the aerodynamic stability and landing analysis of the aircraft. The propulsion design considerations include: engine selection, turbofan ramjet inlets, SCRAMjet inlets and the SCRAMjet diffuser. The cooling requirements and system are covered along with the topics of materials and the hydrogen fuel tanks and insulation system. A cost analysis is presented and the appendices include: information about the subsonic wind tunnel test, shock expansion calculations, and an aerodynamic heat flux program.

Hoying, D.↗

NASA NTRS1991

Tailoring of composite wing structures for elastically produced camber deformations

Structural concepts have been created which produce chordwise camber deformation that results in enhanced lift. A wing box can be tailored to utilize these concepts with composites. In attempting to optimize the aerodynamic benefits, it is found that there are two optimum designs that are of interest. There is a 'weight' optimum which corresponds to the maximum lift per unit structural weight. There is also a 'lift' optimum that corresponds to maximum absolute lift. Experience indicates that a large weight penalty accompanies the transition from weight to lift optimum designs. New structural models, the basic deformation mechanisms that are utilized and typical analytical results are presented. It appears that lift enhancements of sufficient magnitude can be produced to render this type of wing tailoring of practical interest.

Rehfield, Lawrence W.↗

NASA NTRS1991

Tailored composite wings with elastically produced chordwise camber

Four structural concepts were created which produce chordwise camber deformation that results in enhanced lift. A wing box can be tailored to utilize each of these with composites. In attempting to optimize the aerodynamic benefits, researchers found that there are two optimum designs that are of interest. There is a weight optimum which corresponds to the maximum lift per unit structural weight. There is also a lift optimum that corresponds to maximum absolute lift. Experience indicates that a large weight penalty accompanies the transition from weight to lift optimum designs. New structural models, the basic deformation mechanisms that are utilized, and typical analytical results are presented. It appears that lift enhancements of sufficient magnitude can be produced to render this type of wing tailoring of practical interest.

Rehfield, Lawrence W.↗

NASA NTRS1993

A time domain, weighted residual formulation of Maxwell's equations

A finite element model is developed and used to simulate two-dimensional electromagnetic wave propagation and scattering. The spatial discretization of the time-domain electrodynamic equations is accomplished by a Galerkin approach. The semi-discrete equations are solved explicitly using a second-order Runge-Kutta scheme. Both the electric and magnetic fields are discretized using a single grid, with the divergence-free conditions satisfied through a correction approach. Examples depicting the scattering of plane waves in 2D geometries are given to demonstrate the validity of the methodology.

Young, Jeffrey L.↗

NASA NTRS1993

Analysis of plume backflow around a nozzle lip in a nuclear rocket

The structure of the flow around a nuclear thermal rocket nozzle lip has been investigated using the direct simulation Monte Carlo method. Special attention has been paid to the behavior of a small amount of harmful particles that may be present in the rocket exhaust gas. The harmful fission product particles are modeled by four inert gases whose molecular weights are in a range of 4 131. Atomic hydrogen, which exists in the flow due to the extremely high nuclear fuel temperature in the reactor, is also included. It is shown that the plume backflow is primarily determined by the thin subsonic fluid layer adjacent to the surface of the nozzle lip, and that the inflow boundary in the plume region has negligible effect on the backflow. It is also shown that a relatively large amount of the lighter species is scattered into the backflow region while the amount of the heavier species becomes negligible in this region due to extreme separation between the species. Results indicate that the backscattered molecules are very energetic and are fast-moving along the surface in the backflow region near the nozzle lip.

Chung, Chan H.↗