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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 OSTI2023

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

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↗
NASA NTRS2022

Vision-based Velocimetry over Unknown Terrain with a Low-Noise IMU

This paper presents a novel approach to terrain-relative navigation with a visual camera and Inertial Measurement Unit (IMU). The proposed algorithm uses an Extended Kalman Filter (EKF) to combine an IMU propagated state estimate with batch correction estimates computed over a sliding window of measurements. The batch correction algorithm follows the Maximum Likelihood Estimation (MLE) approach used in other Bundle Adjustment systems. Unlike other systems, the proposed system parameterizes the state over the entire window in terms of the state at a single epoch. By ignoring IMU error over the window duration, we obtain a state epoch MLE that jointly estimates the epoch state and terrain parameters with drastically reduced computationally cost. This paper presents the general architecture which can be adapted for various state parameterizations and measurement inputs. For space applications with high-accuracy IMUs, the reduction in computational cost comes with only a modest increase in estimation errors. The increase in error is quantified via a linear covariance analysis presented in this paper. Furthermore, we present simulation results which show the applicability of this algorithm to planetary landing problems.

San Martin, A. Miguel↗
DOE OSTI2025

Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes

The deployment of liquid chromatography-mass spectrometry-based plasma proteomics experiments in a large cohort is sparse, leading to a lack of data available for benchmarking, method development or validation. Comprised of 6,426 plasma analyses, The Environmental Determinants of Diabetes in the Young (TEDDY) proteomics validation study constitutes one of the largest targeted proteomics experiments in the literature to date. The proteomics data from this study were generated over the course of 2.5 years from over 900 study subjects, each providing up to 29 longitudinal samples. The data also includes 916 quality control samples. The targeted mass spectrometry assay was comprised of 694 peptides mapping to 167 proteins and the panel was measured in each subject and QC sample. The targeted proteomic dataset presented here can be used as a resource for new computational method development, such as for batch correction, as well as for benchmarking and comparing the performance of different methods/tools.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

PNNL-Predictive-Phenomics/ProteoMeter

ProteoMeter is a Python package that assists in the statistical analysis of global proteomics, protein post-translation modification (PTM), and limited proteolysis (LiP) data. It contains batch correction, normalization, and statistical testing methods, as well as functions that "roll up" peptide-level data to the single-site level. It has a robust user configuration system, allowing it to flexibly integrate different types of experiment designs. For basic usage, a simple configuration file provides the essential functionality. Advanced users have access to the entire statistical pipeline for fine-tuning analyses. Processed data is easily exported to many common spreadsheet and data-frame formats.

Rozum, Jordan [Pacific Northwest National Lab]↗
NASA NTRSDate not supplied

Evaluation of Correction Methods for NASA GeneLab Transcriptomic Datasets

Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets. In the present study, NASA GeneLab-hosted RNAseq datasets from mouse liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC to determine statistical differences between datasets before and after correction, Principal Component Analysis to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. The results showed that the reference-based approach introduced several additional (and likely artificial) DEGs when compared with the respective standard approach. Of the methods tested, standard ComBat and DESeq2 were identified as the most robust correction methods for combining spaceflight mouse liver RNAseq datasets hosted on GeneLab.

GeneLab↗
NASA NTRSDate not supplied

Evaluation of Correction Methods for NASA GeneLab Transcriptomic Datasets

Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets such as sex or age of the model organism used. In the present study, NASA GeneLab-hosted RNAseq datasets from rodent liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC, to determine statistical differences between datasets before and after correction, Principal Component Analysis, to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. The results showed that the reference-based approach introduced several additional (and likely artificial) DEGs when compared with the standard approach. Thus, the most robust standard correction will be implemented in the GeneLab Visualization 2.0 platform when datasets are combined.

GeneLab, RNA-seq, Batch Correction↗
NASA NTRS1990

Comparison and testing of extended Kalman filters for attitude estimation of the Earth Radiation Budget Satellite

This paper presents the testing and comparison of two extended Kalman filters (EKFs) developed for the Earth Radiation Budget Satellite (ERBS). One EKF updates the attitude quaternion using a four-component additive error quaternion. This technique is compared to that of a second EKF, which uses a multiplicative error quaternion. Brief developments of the algorithms are included. The convergence properties, singularity problems, and normalization techniques of the two filters are addressed. Both filters are tested with simulated ERBS sensor data in addition to real ERBS sensor data. The results of the two filters are also compared to those from the ERBS operational ground support software, which uses a batch differential correction algorithm to estimate attitude and gyro biases.

Bar-Itzhack, Itzhack Y.↗
NASA NTRS1990

Comparison and testing of extended Kalman filters for attitude estimation of the Earth radiation budget satellite

The testing and comparison of two Extended Kalman Filters (EKFs) developed for the Earth Radiation Budget Satellite (ERBS) is described. One EKF updates the attitude quaternion using a four component additive error quaternion. This technique is compared to that of a second EKF, which uses a multiplicative error quaternion. A brief development of the multiplicative algorithm is included. The mathematical development of the additive EKF was presented in the 1989 Flight Mechanics/Estimation Theory Symposium along with some preliminary testing results using real spacecraft data. A summary of the additive EKF algorithm is included. The convergence properties, singularity problems, and normalization techniques of the two filters are addressed. Both filters are also compared to those from the ERBS operational ground support software, which uses a batch differential correction algorithm to estimate attitude and gyro biases. Sensitivity studies are performed on the estimation of sensor calibration states. The potential application of the EKF for real time and non-real time ground attitude determination and sensor calibration for future missions such as the Gamma Ray Observatory (GRO) and the Small Explorer Mission (SMEX) is also presented.

Deutschmann, Julie↗
NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗
DOE OSTI2025

In‐situ Analysis of Paste Properties in Resonant Acoustic Mixers for Quality Monitoring

Formulation control is key to achieving consistent target properties of energetic materials, as feedstock variations and slight deviations in the ratios of different ingredients can have major effects on final product properties, particularly in dense pastes with high particle loading >65 vol.%. In large‐scale operations, it is imperative to either correct or remove batches of material that perform outside baseline property specifications as early as possible to avoid unnecessary processing of suboptimal material. Quality monitoring is the practice of measuring material properties during processing using process analytical technologies as opposed to only testing the properties of the final product; it is a key principle in the quality‐by‐design frameworks used for designing formulations and manufacturing processes. Herein, a process analytical technology method for correlating material properties of dense pastes directly after mixing in a Resonant Acoustic Mixer to motor data is developed and used to detect differences in the particle content of dense paste formulations. This method was also capable of detecting variations in powder feedstock properties, such as particle packing efficiency, and is sensitive enough to detect changes of 2 wt.% in the total solids content of the formulation. The techniques presented herein show excellent promise for use as a process analytical technology capable of quantifying formulation effects on material movement modes during resonant acoustic mixing.

Materials science↗
NASA NTRS2007

Tracking and Data Relay Satellite (TDRS) Orbit Estimation Using an Extended Kalman Filter

Alternatives to the Tracking and Data Relay Satellite (TDRS) orbit estimation procedure were studied to develop a technique that both produces more reliable results and is more amenable to automation than the prior procedure. The Earth Observing System (EOS) Terra mission has TDRS ephemeris prediction 3(sigma) requirements of 75 meters in position and 5.5 millimeters per second in velocity over a 1.5-day prediction span. Meeting these requirements sometimes required reruns of the prior orbit determination (OD) process, with manual editing of tracking data to get an acceptable solution. After a study of the available alternatives, the Flight Dynamics Facility (FDF) began using the Real-Time Orbit Determination (RTOD(Registered TradeMark)) Kalman filter program for operational support of TDRSs in February 2007. This extended Kalman filter (EKF) is used for daily support, including within hours after most thrusting, to estimate the spacecraft position, velocity, and solar radiation coefficient of reflectivity (C(sub R)). The tracking data used are from the Bilateration Ranging Transponder System (BRTS), selected TDRS System (TDRSS) User satellite tracking data, and Telemetry, Tracking, and Command (TT&C) data. Degraded filter results right after maneuvers and some momentum unloads provided incentive for a hybrid OD technique. The results of combining EKF strengths with the Goddard Trajectory Determination System (GTDS) Differential Correction (DC) program batch-least-squares solutions, as recommended in a 2005 paper on the chain-bias technique, are also presented.

Ward, Douglas T.↗
NASA NTRS2008

Photochemically Synthesized Polyimides

An alternative to the conventional approach to synthesis of polyimides involves the use of single monomers that are amenable to photopolymerization. Heretofore, the synthesis of polyimides has involved multiple-monomer formulations and heating to temperatures that often exceed 250 C. The present alternative approach enables synthesis under relatively mild conditions that can include room temperature. The main disadvantages of the conventional approach are the following: Elevated production temperatures can lead to high production costs and can impart thermal stresses to the final products. If the proportions of the multiple monomeric ingredients in a given batch are not exactly correct, the molecular weight and other physical properties of the final material could be reduced from their optimum or desired values. To be useful in the alternative approach, a monomer must have a molecular structure tailored to exploit Diels-Alder trapping of a photochemically generated ortho-quinodimethane. (In a Diels-Alder reaction, a diene combines with a dienophile to form molecules that contain six-membered rings.) In particular, a suitable monomer (see figure) contains ortho-methylbenzophenone connected to a dienophile (in this case, a maleimide) through a generic spacer group. Irradiation with ultraviolet light gives rise to a photochemical intermediate the aforementioned ortho-quinodimethane from the ortho-methylbenzophenone. This group may react with the dienophile on another such monomer molecule to produce an oligomer that, in turn may react in a stepgrowth manner to produce a polyimide. This approach offers several advantages in addition to those mentioned above: The monomer can be stored for a long time because it remains unreactive until exposed to light. Because the monomer is the only active starting ingredient, there is no need for mixing, no concern for ensuring correct proportions of monomers, and the purity of the final product material is inherently high. The use of solvents is optional: The synthesis can be performed using the neat monomer or the monomer mixed with one or more solvent(s) in dilute or concentrated solution. The solubility of the monomer and the physical and chemical properties of the final polymer can be tailored through selection of the spacer group.

Meador, Michael A.↗
NASA NTRS1980

Analysis of estimation algorithms for autonomous navigation with TDRSS data

Estimation techniques for onboard orbit determination using Tracking and Data Relay Satellite System (TDRSS) data are investigated. The two user satellite orbits studied are similar to Landsat-D (near-circular, 700 kilometers altitude, near-polar inclination). The following estimation algorithms are identified as candidates for use in autonomous navigation: (1) the extended Kalman filter with process noise, (2) the EKF with consider parameters, (3) the sequential Kalman filter with consider parameters, and (4) the batch least-squares differential correction technique. The candidate estimators are evaluated with respect to their performance with both baseline and worst TDRSS measurement errors and tracking configurations.

Dunham, J.↗
NASA NTRS1989

Simultaneous quaternion estimation (QUEST) and bias determination

Tests of a new method for the simultaneous estimation of spacecraft attitude and sensor biases, based on a quaternion estimation algorithm minimizing Wahba's loss function are presented. The new method is compared with a conventional batch least-squares differential correction algorithm. The estimates are based on data from strapdown gyros and star trackers, simulated with varying levels of Gaussian noise for both inertially-fixed and Earth-pointing reference attitudes. Both algorithms solve for the spacecraft attitude and the gyro drift rate biases. They converge to the same estimates at the same rate for inertially-fixed attitude, but the new algorithm converges more slowly than the differential correction for Earth-pointing attitude. The slower convergence of the new method for non-zero attitude rates is believed to be due to the use of an inadequate approximation for a partial derivative matrix. The new method requires about twice the computational effort of the differential correction. Improving the approximation for the partial derivative matrix in the new method is expected to improve its convergence at the cost of increased computational effort.

Markley, F. Landis↗
NASA NTRS1989

Automation of orbit determination functions for National Aeronautics and Space Administration (NASA)-supported satellite missions

The Flight Dynamics Facility (FDF) at Goddard Space Flight Center (GSFC) provides spacecraft trajectory determination for a wide variety of National Aeronautics and Space Administration (NASA)-supported satellite missions, using the Tracking Data Relay Satellite System (TDRSS) and Ground Spaceflight and Tracking Data Network (GSTDN). To take advantage of computerized decision making processes that can be used in spacecraft navigation, the Orbit Determination Automation System (ODAS) was designed, developed, and implemented as a prototype system to automate orbit determination (OD) and orbit quality assurance (QA) functions performed by orbit operations. Based on a machine-resident generic schedule and predetermined mission-dependent QA criteria, ODAS autonomously activates an interface with the existing trajectory determination system using a batch least-squares differential correction algorithm to perform the basic OD functions. The computational parameters determined during the OD are processed to make computerized decisions regarding QA, and a controlled recovery process isactivated when the criteria are not satisfied. The complete cycle is autonomous and continuous. ODAS was extensively tested for performance under conditions resembling actual operational conditions and found to be effective and reliable for extended autonomous OD. Details of the system structure and function are discussed, and test results are presented.

Mardirossian, H.↗
NASA NTRS1990

Attitude determination and parameter estimation using vector observations - Application

This paper presents tests of a new method for the simultaneous estimation of spacecraft attitude and sensor biases, based on a quaternion estimation algorithm minimizing Wahba's loss function. The new method is compared with a conventional batch least-squares differential correction algorithm. The estimates are based on data from strapdown gyros and star trackers, simulated with varying levels of Gaussian noise for both inertially-fixed and earth-pointing attitudes. Both algorithms solve for the spacecraft attitude and the gyro drift rate biases. In the majority of tests performed, the two methods converge to the same estimates in the same number of iterations, but the new algorithm requires about 60 percent more computational effort. Some cases were found in which the new method converges in fewer iterations than the differential correction, and some for which the differential correction requires fewer iterations.

Markley, F. Landis↗