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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Inference of gene regulatory networks from genome-wide knockout fitness data

Motivation: Genome-wide fitness is an emerging type of highthroughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compared with results of more conventional gene expression analysis. Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference. Results: In this article, we describe a model and propose an inference algorithm for using fitness data from knockout libraries to identify underlying gene regulatory networks. Unlike most prior methods, the presented approach captures not only structural, but also dynamical and non-linear nature of biomolecular systems involved. A state– space model with non-linear basis is used for dynamically describing gene regulatory networks. Network structure is then elucidated by estimating unknown model parameters. Unscented Kalman filter is used to cope with the non-linearities introduced in the model, which also enables the algorithm to run in on-line mode for practical use. Here, we demonstrate that the algorithm provides satisfying results for both synthetic data as well as empirical measurements of GAL network in yeast Saccharomyces cerevisiae and TyrR–LiuR network in bacteria Shewanella oneidensis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Hybrid PSO-ASVR-based method for data fitting in the calibration of infrared radiometer

The present paper describes a hybrid particle swarm optimization-adaptive support vector regression (PSO-ASVR)-based method for data fitting in the calibration of infrared radiometer. The proposed hybrid PSO-ASVR-based method is based on PSO in combination with Adaptive Processing and Support Vector Regression (SVR). The optimization technique involves setting parameters in the ASVR fitting procedure, which significantly improves the fitting accuracy. However, its use in the calibration of infrared radiometer has not yet been widely explored. Bearing this in mind, the PSO-ASVR-based method, which is based on the statistical learning theory, is successfully used here to get the relationship between the radiation of a standard source and the response of an infrared radiometer. Main advantages of this method are the flexible adjustment mechanism in data processing and the optimization mechanism in a kernel parameter setting of SVR. Numerical examples and applications to the calibration of infrared radiometer are performed to verify the performance of PSO-ASVR-based method compared to conventional data fitting methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Abstract The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene‐protein‐reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high‐throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗
DOE OSTI2021

Simulating and benchmarking neutron total scattering instrumentation from inception of events to reduced and fitted data

In the design and realization of modern neutron scattering instrumentation, particularly when designing beamline concepts from the ground up, it is desirable to fully benchmark against realistically simulated data. This is especially true for total scattering beamlines, where the future deliverable data is to be analysed in both reciprocal- and real-space representations, and needs must be carefully balanced to ensure sufficient range, resolution and flux of the instrument. An approach to optimize the design of neutron scattering instrumentation via a workflow including ray-tracing simulations, event-based data reduction, heuristic analysis and fitting against realistically simulated spectra is demonstrated here. The case of the DISCOVER beamline concept at the Spallation Neutron Source is used as an example. The results of the calculations are benchmarked through simulation of existing instrumentation and subsequent direct comparison with measured data. Finally, on the basis of the validated models, the ability to explore design characteristics for future beamline concepts or future instrument improvements is demonstrated through the examples of detector tube size and detector layout.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Investigation of goodness of model data fit using PLSR and PCR regression models to determine informative wavelength band in NIR region for non-invasive blood glucose prediction

Diabetes mellitus is a metabolic disorder characterized by the deficiency in insulin secretion or insulin action on target tissues. Diabetes being diagnosed, requires frequent monitoring. Current measurement techniques are invasive in nature, which is painful. Non-invasive measurement methods for the prediction of blood glucose is a big challenge. Hence this paper focuses on a comparative study to analyze the performance of the two regression models: partial least square regression (PLSR) and principal component regression (PCR) models to arrive at the best regression model for the prediction of blood glucose non-invasively based on NIR diffuse reflectance spectroscopy. The regression model developed involves spectral data collected from 32 subjects from a diabetic center using diffuse reflectance spectrometer (DRS). The spectroscopic data were acquired from the subjects both invasively using clinical method and non-invasively using DRS setup in the NIR spectral range whose wavelength ranges from 750 to 1040 nm. Multivariate analysis using PLSR is found to be a better regression model in terms of the fitted response and estimated mean square prediction error. It is observed that the mean square error value is 0.04 mg/dl for the tenth component in the PLSR model. The developed regression model also proves to be a useful tool in identifying the informative wavelength bands for blood glucose measurement.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Automated Resonance Fitting for Nuclear Data Evaluation

Global and national efforts to deliver high-quality nuclear data to users have a wide-ranging impact, affecting applications in national security, reactor operations, basic science, medicine, and more. Cross section evaluation is a major part of this effort, combining theory and experimentation to produce recommended values and uncertainties for reaction probabilities. Resonance region evaluation is a specialized type of nuclear data evaluation that can require significant manual effort and months of time from expert scientists. In this article, non-convex non-linear optimization methods are combined with concepts of inferential statistics to infer a resonance model from experimental data in an automated manner that is not dependent on prior evaluation(s). This methodology aims to enhance the workflow of a resonance evaluator by minimizing time, effort, and the potential for bias from prior assumptions, while enhancing reproducibility and documentation, thereby addressing well-known challenges in the field.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Gaining insight into the $T\,_2^*$– T 2 relationship in surface NMR free-induction decay measurements

One of the primary shortcomings of the surface nuclear magnetic resonance (NMR) freeinduction decay (FID) measurement is the uncertainty surrounding which mechanism controls the signal’s time dependence. Ideally, the FID-estimated relaxation time T$*\atop{2}$ that describes the signal’s decay carries an intimate link to the geometry of the pore space. In this limit the parameter T$*\atop{2}$ is closely linked to a related parameter T 2 , which is more closely linked to pore-geometry. If T$*\atop{2}$ T 2 the FID can provide valuable insight into relative pore-size and can be used to make quantitative permeability estimates. However, given only FID measurements it is difficult to determine whether T$*\atop{2}$ is linked to pore geometry or whether it has been strongly influenced by background magnetic field inhomogeneity. If the link between an observed T$*\atop{2}$ and the underlying T 2 could be further constrained the utility of the standard surface NMR FID measurement would be greatly improved. We hypothesize that an approach employing an updated surface NMR forward model that solves the full Bloch equations with appropriately weighted relaxation terms can be used to help constrain the T$*\atop{2}$ –T 2 relationship. Weighting the relaxation terms requires estimating the poorly constrained parameters T 2 and T 1 ; to deal with this uncertainty we propose to conduct a parameter search involving multiple inversions that employ a suite of forward models each describing a distinct but plausible T$*\atop{2}$ –T 2 relationship. We hypothesize that forward models given poor T 2 estimates will produce poor data fits when using the complex-inversion, while forward models given reliable T 2 estimates will produce satisfactory data fits. By examining the data fits produced by the suite of plausible forward models, the likely T$*\atop{2}$ –T 2 can be constrained by identifying the range of T 2 estimates that produce reliable data fits. Synthetic and field results are presented to investigate the feasibility of the proposed technique.

58 GEOSCIENCES↗
DOE OSTI2022

A modified Susceptible-Infected-Recovered model for observed under-reported incidence data

Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data when a fixed fraction of newly infected individuals are not observed. The parameters of the resulting system of differential equations are identifiable. Using these differential equations, we develop a stochastic model for the conditional distribution of current disease incidence given the entire past history of reported cases. We estimate the model parameters using Bayesian Markov Chain Monte-Carlo sampling of the posterior distribution. We use our model to estimate the transmission rate and fraction of asymptomatic individuals for the current Coronavirus 2019 outbreak in eight American Countries: the United States of America, Brazil, Mexico, Argentina, Chile, Colombia, Peru, and Panama, from January 2020 to May 2021. Our analysis reveals that the fraction of reported cases varies across all countries. For example, the reported incidence fraction for the United States of America varies from 0.3 to 0.6, while for Brazil it varies from 0.2 to 0.4.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Combined selection of the dynamic model and modeling error in nonlinear aeroelastic systems using Bayesian Inference

Here, we report a Bayesian framework for concurrent selection of physics-based models and (modeling) error models. We investigate the use of colored noise to capture the mismatch between the predictions of calibrated models and observational data that cannot be explained by measurement error alone within the context of Bayesian estimation for stochastic ordinary differential equations. Proposed models are characterized by the average data-fit, a measure of how well a model fits the measurements, and the model complexity measured using the Kullback–Leibler divergence. The use of a more complex error models increases the average data-fit but also increases the complexity of the combined model, possibly over-fitting the data. Bayesian model selection is used to find the optimal physical model as well as the optimal error model. The optimal model is defined using the evidence, where the average data-fit is balanced by the complexity of the model. The effect of colored noise process is illustrated using a nonlinear aeroelastic oscillator representing a rigid NACA0012 airfoil undergoing limit cycle oscillations due to complex fluid–structure interactions. Several quasi-steady and unsteady aerodynamic models are proposed with colored noise or white noise for the model error. The use of colored noise improves the predictive capabilities of simpler models.

42 ENGINEERING↗
DOE OSTI2024

How robust are estimates of key parameters in standard viral dynamic models?

Mathematical models of viral infection have been developed, fitted to data, and provide insight into disease pathogenesis for multiple agents that cause chronic infection, including HIV, hepatitis C, and B virus. However, for agents that cause acute infections or during the acute stage of agents that cause chronic infections, viral load data are often collected after symptoms develop, usually around or after the peak viral load. Consequently, we frequently lack data in the initial phase of viral growth, i.e., when pre-symptomatic transmission events occur. Missing data may make estimating the time of infection, the infectious period, and parameters in viral dynamic models, such as the cell infection rate, difficult. However, having extra information, such as the average time to peak viral load, may improve the robustness of the estimation. Here, we evaluated the robustness of estimates of key model parameters when viral load data prior to the viral load peak is missing, when we know the values of some parameters and/or the time from infection to peak viral load. Although estimates of the time of infection are sensitive to the quality and amount of available data, particularly pre-peak, other parameters important in understanding disease pathogenesis, such as the loss rate of infected cells, are less sensitive. Viral infectivity and the viral production rate are key parameters affecting the robustness of data fits. Fixing their values to literature values can help estimate the remaining model parameters when pre-peak data is missing or limited. We find a lack of data in the pre-peak growth phase underestimates the time to peak viral load by several days, leading to a shorter predicted growth phase. On the other hand, knowing the time of infection (e.g., from epidemiological data) and fixing it results in good estimates of dynamical parameters even in the absence of early data. While we provide ways to approximate model parameters in the absence of early viral load data, our results also suggest that these data, when available, are needed to estimate model parameters more precisely.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Simple analytical model for fitting QENS data from liquids

The advent of new generation of neutron spectrometers for quasielastic scattering measurements has demonstrated the need for multi-component (at least two-component) fitting of data collected from liquids. The narrowest component is associated with long-range translational diffusion, whereas the broader component originates from localized center-of-mass motions in the transient cage of the nearest neighbors. Intra-particle dynamics (e.g., of molecular side groups) may give rise to additional components besides the center-of-mass motions. We present a simple analytical model for two-component fits of quasielastic neutron scattering data collected from liquids. Here, the use of such models is optional (albeit helpful) in the traditional approach, where fits are performed sequentially and independently for the data collected at separate Q values, but imperative in the global fitting, where the data are fitted simultaneously at all Q values, which may be necessary to rationalize the data from increasingly complex systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Generation and Validation of the iKp1289 Metabolic Model for Klebsiella pneumoniae KPPR1

Klebsiella pneumoniae has a reputation for causing a wide range of infectious conditions, with numerous highly virulent and antibiotic-resistant strains. Metabolic models have the potential to provide insights into the growth behavior, nutrient requirements, essential genes, and candidate drug targets in these strains. Here we develop a metabolic model for KPPR1, a highly virulent strain of K. pneumoniae. We apply a combination of Biolog phenotype data and fitness data to validate and refine our KPPR1 model. The final model displays a predictive accuracy of 75% in identifying potential carbon and nitrogen sources for K. pneumoniae and of 99% in predicting nonessential genes in rich media. We demonstrate how this model is useful in studying the differences in the metabolic capabilities of the low-virulence MGH 78578 strain and the highly virulent KPPR1 strain. For example, we demonstrate that these strains differ in carbohydrate metabolism, including the ability to metabolize dulcitol as a primary carbon source. Our model makes numerous other predictions for follow-up verification and analysis.

bacteria↗