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Batch Effect Correction Methods for NASA GeneLab Transcriptomic Datasets

RNA sequencing (RNA-seq) data from space biology experiments promise to yield invaluable insights into the effects of spaceflight on terrestrial biology. However, sample numbers from each study are low due to limited crew availability, hardware, and space. To increase statistical power, spaceflight RNA-seq datasets from different missions are often aggregated together. However, this can introduce technical variation or "batch effects", often due to differences in sample handling, sample processing, and sequencing platforms. Several computational methods have been developed to correct for technical batch effects, thereby reducing their impact on true biological signals. In this study, we combined 7 mouse liver RNA-seq datasets from NASA GeneLab (part of the NASA Open Science Data Repository) to evaluate several common batch effect correction methods (ComBat and ComBat-seq from the sva R package, and Median Polish, Empirical Bayes, and ANOVA from the MBatch R package). We quantitatively evaluated the ability of these methods to correct for technical batch variables in space biology RNA-seq data using the following criteria: BatchQC, principal component analysis, dispersion separability criterion, log fold change correlation, and differential gene expression analysis. Each batch variable / correction method combination was then assessed using a custom scoring approach to identify the optimal correction method for the combined dataset, by geometrically probing the space of all allowable scoring functions to yield an aggregate volume-based scoring measure. Finally, we describe the way in which the GeneLab multi-study analysis and visualization portal will allow users to examine the presence or absence of batch effects using multiple metrics. If the user chooses to perform batch effect correction, the scoring approach described here can be implemented to identify the optimal correction method to use for their specific combined dataset prior to analysis.

Lauren M. Sanders↗

DOE OSTI2022

Finding Electronic Structure Machine Learning Surrogates without Training

A myriad of phenomena in materials science and chemistry rely on quantum-level simulations of the electronic structure in matter. While moving to larger length and time scales has been a pressing issue for decades, such large-scale electronic structure calculations are still challenging despite modern software approaches and advances in high-performance computing. The silver lining in this regard is the use of machine learning to accelerate electronic structure calculations – this line of research has recently gained growing attention. The grand challenge therein is finding a suitable machine-learning model during a process called hyperparameter optimization. This, however, causes a massive computational overhead in addition to that of data generation. We accelerate the construction of machine-learning surrogate models by roughly two orders of magnitude by circumventing excessive training during the hyperparameter optimization phase. We demonstrate our workflow for Kohn-Sham density functional theory, the most popular computational method in materials science and chemistry.

36 MATERIALS SCIENCE↗

NASA NTRS1982

Synoptic studies of chromospheric variability in F - K dwarfs with the IUE

Time-sequential series of IUE spectra for ten F, G and K dwarfs were obtained in 1980 and 1981 to study the rotational dependence of chromospheric flux in the ultraviolet. An interactive computational method using unbiased estimators was developed to measure emission line fluxes free of arbitrary judgement concerning the behavior of the underlying spectrum and shapes of the line profiles. Due to the limited number of observational samples per star, we have used special techniques to analyze the sparsely and anharmonically sampled emission line flux data. Two different autocorrelation measures were computed for each emission line as a function of temporal frequency. Examples and results of this analysis now in progress are given for several stars.

Hallam, K. L.↗

NASA NTRS1984

Three-dimensional Navier-Stokes calculations of multiple interacting vortex rings

Results from a finite-difference Navier-Stokes code for three-dimensional, unsteady, vortical flows in unbounded domains are presented and analyzed in this paper. The vortical flows presented are representative of vortex rings and other closed vortical tubes or structures in fluid mechanics. Such structures are important elements in fluid flows such as jets, atmospheric turbulence, and the far-field wakes of aircraft, and studies of their interaction may aid in an understanding of complex fluid flows. The paper demonstrates that computational methods can be used as a viable alternative or supplement to experimental techniques for studying the physics of vortex flows. The separate visualization of vortex stretching, convection, and diffusion is presented in this paper for a single elliptical vortex ring.The calculations employ a truncated series expansion technique to simulate the unbounded nature of the fluid flow with a finite computational domain, which is a more accurate technique than the conventional freestream boundary specification. The numerical divergence of the three-dimensional vorticity field is considered as a useful estimate of truncation error, and the use of a kinetic energy decay law as a calculation check is demonstrated. Results from the Navier-Stokes code are presented for the unsteady motion of two and four vortex rings along parallel axes, and the results agree qualitatively with experimental flow visualization.

Chamberlain, J. P.↗

NASA NTRS1989

A finite difference treatment of Stokes-type flows: Preliminary report

The equations Laplacian operator omega = 0, (1.1a) and omega = Laplacian operator Chi, (1.1b) describe, in suitable units, 2-D Stokes flow of an incompressible fluid occupying a domain D in which omega is the vorticity and Chi is the stream function. The flow is uniquely determined by specifying the velocity on the boundary B of D, a condition which leads to specifying the stream function Chi and its normal derivative Chi sub n on B. A mathematically similar problem arises in describing the equilibrium of a flat plate in structural mechanics where a related 1-D problem by finite difference or finite element methods is to introduce effective methods for imposing the boundary conditions through which (1.1a) is coupled to (1.1b). These models thus provide a simple starting point for examining the general treatment of boundary conditions for more general time dependent Navier-Stokes incompressible flows. For the purpose of discussion it is assumed that D is a square domain. A standard finite difference method to solve (1.1) is to introduce a uniform grid and then use standard five point finite difference operators to express each equation in (1.1). At any point on the boundary B a value of Chi is specified by the boundary conditions but a value of omega at the same boundary mesh point will also be required to complete the computation. Methods are discussed which overcome the difficulty in solving these problems.

Rose, M. E.↗

DOE OSTI2022

Geometrically necessary dislocation fingerprints of dislocation loop absorption at grain boundaries

Here we present a numerical methodology to compute the Nye-tensor fingerprints of dislocation loop absorption at grain boundaries (GBs) for comparison with TEM observations of irradiated polycrystals. Our approach links atomistic simulations of self-interstitial atom (SIA) prismatic loops gliding toward and interacting with GBs in body-centered cubic iron with experimentally extracted geometrically necessary dislocation (GND) maps to facilitate the interpretation of damage processes. The Nye-tensor analysis is strongly mesh-size dependent—corresponding to resolution-dependent TEM observations. The method computes GND fingerprints from discretized dislocation line segments extracted from molecular dynamics simulations of dislocation loops being absorbed at a GB. Specifically, we perform MD simulation of prismatic loops of two diameters and monitor the three stages of the absorption process: loop glide, the partial, and full absorption of the loops at a [1 0 0] symmetric tilt GB. These methods provide a framework for future investigations of the nature of defect absorption by grain boundaries under irradiation conditions.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Kernel-based global sensitivity analysis obtained from a single data set

Results from global sensitivity analysis (GSA) often guide the understanding of complicated input–output systems. Kernel-based GSA methods have recently been proposed for their capability of treating a broad scope of complex systems. In this paper, we develop a new set of kernel GSA tools when only a single set of input–output data is available. Three key advances are made: (1) A new numerical estimator is proposed that demonstrates an empirical improvement over previous procedures. (2) A computational method for generating inner statistical functions from a single data set is presented. (3) A theoretical extension is made to define conditional sensitivity indices, which reveal the degree that the inputs carry shared information about the output when inherent input–input correlations are present. Utilizing these conditional sensitivity indices, a decomposition is derived for the output uncertainty based on what is called the optimal learning sequence of the input variables, which remains consistent when correlations exist between the input variables. Further, while these advances cover a range of GSA subjects, a common single data set numerical solution is provided by a technique known as the conditional mean embedding of distributions. The new methodology is implemented on benchmark systems to demonstrate the provided insights.

42 ENGINEERING↗

NASA NTRS1986

Computational wing design studies relating to natural laminar flow

Two research studies are described which directly relate to the application of natural laminar flow (NLF) technology to transonic transport-type wing planforms. Each involved using state-of-the-art computational methods to design three-dimensional wing contours which generate significant runs of favorable pressure gradients. The first study supported the Variable Sweep Transition Flight Experiment and involves design of a full-span glove which extends from the leading edge to the spoiler hinge line on the upper surface of an F-14 outer wing panel. A wing was designed computationally for a corporate transport aircraft in the second study. The resulting wing design generated favorable pressure gradients from the leading edge aft to the mid-chord on both upper and lower surfaces at the cruise design point. Detailed descriptions of the computational design approach are presented along with the various constraints imposed on each of the designs.

Waggoner, Edgar G.↗

DOE OSTI2022

Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase

Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis beyond the relative scales typically employed. In principle, theoretical methods can provide such quantification but are often hindered by the innate complexity of strong electron correlation and dynamic relaxation of solvent environments. Here, we present and validate a protocol for calculating the redox potentials of ferrocene/ferrocenium redox pair in the acetonitrile. Equation-of-motion ionization potential coupled-cluster single-double (EOM-IP-CCSD) and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials (IP) as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrated the ability of modern computational methods to predict absolute redox potentials quantitatively and, more critically, quantify the correlation of dynamic effects, which underlie their origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Transplatformer: translating toxicogenomic profiles between generations of platforms

Background Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. Results We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation ( ≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra Conclusions TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Analysis and Preliminary Design of an Advanced Technology Transport Flight Control System

The analysis and preliminary design of an advanced technology transport aircraft flight control system using avionics and flight control concepts appropriate to the 1980-1985 time period are discussed. Specifically, the techniques and requirements of the flight control system were established, a number of candidate configurations were defined, and an evaluation of these configurations was performed to establish a recommended approach. Candidate configurations based on redundant integration of various sensor types, computational methods, servo actuator arrangements and data-transfer techniques were defined to the functional module and piece-part level. Life-cycle costs, for the flight control configurations, as determined in an operational environment model for 200 aircraft over a 15-year service life, were the basis of the optimum configuration selection tradeoff. The recommended system concept is a quad digital computer configuration utilizing a small microprocessor for input/output control, a hexad skewed set of conventional sensors for body rate and body acceleration, and triple integrated actuators.

Frazzini, R.↗

NASA NTRS1981

Two-component Navier-Stokes computational model of viscous sublayer turbulence

A new computational method is presented for developing a quantitative model of viscous sublayer turbulence in incompressible flow. Appropriate space- and time-dependent boundary conditions are constructed for the three fluctuating velocity components at the outer edge of the viscous sublayer. This construction is formulated so as to model essential coherent structures observed in experiments. Time dependent Navier-Stokes equations are used to compute the characteristics of turbulence in the viscous sublayer.

Chapman, D. R.↗

NASA NTRS1990

Numerical study of vortical flow over a sideslipping delta wing

The three-dimensional vortical viscous flow past a sideslipping delta wing at a high angle of attack is numerically investigated. A computational method for calculating low-speed viscous flowfields is developed. The time-iterative method uses an implicit upwind-relaxation finite-difference algorithm with a nonsingular eigensystem to solve the preconditioned, three-dimensional, incompressible Navier-Stokes equations in curvilinear coordinates. An algebraic turbulence model is implemented to account for the eddy viscosity. The technique of local time stepping is incorporated to accelerate the rate of convergence to a steady-state solution. Computed results are compared with experimental data.

Hsu, C.-H.↗

DOE OSTI2024

Analysis of buffer-IPyC separation in TRISO fuel particles

During High Temperature Gas-cooled Reactor (HTGR) operation, and due to the neutron irradiation in the reactor core, damage of the nuclear fuel coating layers occurs. The mechanism of damage formation in the TRISO fuel is explored by the Advanced Gas Reactor (AGR) Fuel Development and Qualification Program, in which the debonding process between coating layers was also investigated. The purpose of this paper is to report simulation results for two models. Firstly, the debonding restricted model, where no gap formation between buffer and IPyC layers is permitted. Secondly, a debonding enabled model, where the gap between those layers is created. The simulations were performed with the Bison code. The inputs of the simulated models are based on data from the AGR-1 experiment. Further, the research included simulations on spherical and aspherical fuel types. The simulations match results obtained by the AGR-1 experiment, which as such shows that the Bison code is a good computational method for simulating the behavior of the gap between buffer and IPyC layers in TRISO fuel. Based on the irradiation experiments, and the Bison simulations, it was concluded that the most common scenario is a gap formation along the buffer-IPyC interface, while the least possible scenario is the situation where there is no gap formation at the buffer-IPyC junction. The computational results confirmed that the sphericity of the fuel influences the thickness of the gap that occurs at the buffer-IPyC junction, in a way that with increasing aspect ratio the gap thickness increases. In addition, the fuel sphericity does not influence the Weibull failure probability. The results obtained for spherical and aspherical fuel are nearly identical.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide. Automated reversed-phase column separation was used to achieve fractions with distinct colors, including blue, cyan, green, yellow, orange and red. This work explores the physicochemical properties and fluorescence origins of the red, green, and blue fractions in depth with combined experimental and computational methods. Three dominant fluorescence mechanism hypotheses were evaluated by comparing time-dependent density functional theory and molecular dynamics calculation results to measured characteristics. We find that blue fluorescence likely comes from embedded small molecules trapped in carbonaceous cages, while pyrene analogs are the most likely origin for emission at other wavelengths, especially in the red. Also important, upon interaction with live cells, different CD color fractions are trafficked to different sub-cellular locations. Super-resolution imaging shows that the blue CDs were found in a variety of organelles, such as mitochondria and lysosomes, while the red CDs were primarily localized in lysosomes. These findings significantly advance our understanding of the photoluminescence mechanism of multicolor CDs and help to guide future design and applications of these promising nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1977

Initial values for the integration scheme to compute the eigenvalues for propagation in ducts

A scheme for the calculation of eigenvalues in the problem of acoustic propagation in a two-dimensional duct is described. The computation method involves changing the coupled transcendental nonlinear algebraic equations into an initial value problem involving a nonlinear ordinary differential equation. The simplest approach is to use as initial values the hardwall eigenvalues and to integrate away from these values as the admittance varies from zero to its actual value with a linear variation. The approach leads to a powerful root finding routine capable of computing the transverse and axial wave numbers for two-dimensional ducts for any frequency, lining, admittance and Mach number without requiring initial guesses or starting points.

Eversman, W.↗

NASA NTRS1975

Subgrid or Reynolds stress-modeling for three-dimensional turbulence computations

A review is given of recent advances in two distinct computational methods for evaluating turbulence fields, namely, statistical Reynolds stress modeling and turbulence simulation, where large eddies are followed in time. It is shown that evaluation of the mean Reynolds stresses, rather than use of a scalar eddy viscosity, permits an explanation of streamline curvature effects found in several experiments. Turbulence simulation, with a new volume averaging technique and third-order accurate finite-difference computing is shown to predict the decay of isotropic turbulence in incompressible flow with rather modest computer storage requirements, even at Reynolds numbers of aerodynamic interest.

Rubesin, M. W.↗