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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, in this paper, we describe and illustrate PeakQC’s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

47 OTHER INSTRUMENTATION↗
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↗
NASA NTRS2004

International GPS Service 2001 - 2002 Technical Reports

Applications of the Global Positioning System (GPS) to Earth Science are numerous. The International GPS Service (IGS), a federation of government agencies and universities, plays an increasingly critical role in support of GPS-related research and engineering activities. Contributions from the IGS Governing Board and Central Bureau, analysis and data centers, station operators, and others constitute the 2001 / 2002 Technical Reports. Hard copies of each volume can be obtained by contacting the IGS Central Bureau at the Jet Propulsion Laboratory. This report is published in black and white. To view graphs or plots that use color to represent data trends or information, please refer to the online PDF version at http://igscb.jpl.nasa.gov/overview/pubs.html.

Gowey, Ken↗
NASA NTRS1979

Chemical reaction between water vapor and stressed glass

The crack velocity in soda-lime silicate glass was determined at room temperature at water-vapor pressures of 10 to 0.04 torr using the double torsion technique. A precracked glass specimen (70 x 16 x 1.6 mm) was placed in a vacuum chamber containing a four-point bending test apparatus. The plotted experimental results show that the crack propagation curve in water agrees fairly well with that of Wiederhorn (1967). Attention is given to the effect of water vapor pressure on crack velocity at K(I) = 550,000 N/m to the 3/2 power, with (Wiederhorn's data) or without N2 present. The plotted results reveal that the present crack velocity is about two orders of magnitude higher than that of Wiederhorn at high water-vapor conditions, but the difference decreases as the water-vapor concentration diminishes or the crack velocity slows down.

Soga, N.↗
NASA NTRS2003

Comparisons of the Impact Responses of a 1/5-Scale Model and a Full-Scale Crashworthy Composite Fuselage Section

A 25-fps vertical drop test of a 1/5-scale model composite fuselage section was conducted to replicate a previous test of a full-scale fuselage section. The purpose of the test was to obtain experimental data characterizing the impact response of the 1/5-scale model fuselage section for comparison with the corresponding full-scale data. This comparison is performed to assess the scaling procedures and to determine if scaling effects are present. For the drop test, the 1/5-scale model fuselage section was configured in a similar manner as the full-scale section, with lead masses attached to the floor through simulated seat rails. Scaled acceleration and velocity responses are compared and a general assessment of structural damage is made. To further quantify the data correlation, comparisons of the average acceleration data are made as a function of floor location and longitudinal position. Also, the percentage differences in the velocity change (area under the acceleration curve) and the velocity change squared (proportional to kinetic energy) are compared as a function of floor location. Finally, correlation coefficients are calculated for corresponding 1/5- and full-scale data channels and these values are plotted versus floor location. From a scaling perspective, the differences between the 1/5- and full-scale tests are relatively small, indicating that appropriate scaling procedures were used in fabricating the test specimens and in conducting the experiments. The small differences in the scaled test data are attributed to minor scaling anomalies in mass, potential energy, and impact attitude.

Jackson, Karen E.↗
NASA NTRS1975

The Celescope survey and the galactic distribution of interstellar absorption

The instrumentation and data-reduction techniques used in the Celescope experiment conducted on board OAO-2 are reviewed. A brief summary is presented of the principles of UV astronomy, the Celescope optical package and bay E4 electronic module assembly are described, and the distribution of the Celescope pictures is plotted in galactic coordinates. Described data-reduction techniques include the determination of the U-B and B-V colors, removal of interstellar extinction effects, and construction of model atmospheres for the observed stars. Some difficulties and apparent contradictions encountered in the data interpretation are noted.

Davis, R. J.↗
NASA NTRS1975

Geological applications of LANDSAT-1 imagery to the Great Salt Lake area

The ERTS program has been designed as a research and development tool to demonstrate that remote sensing from orbital altitudes is a feasible and practical approach to efficient management of earth resources. From this synoptic view and repetitive coverage provided by ERTS imagery of the Great Salt Lake area, large geological and structural features, trends, and patterns have been identified and mapped. A comparative analysis of lineaments observed in September and December data was conducted, existing mineral locations were plotted, and areas considered prospective for mineralization based on apparent structure-mineralization relationships were defined. The additional information obtained using ERTS data provides an added source of information to aid in the development of more effective mineral exploration programs.

Anderson, A. T.↗
NASA NTRS2013

The Validation of the GEWEX SRB Surface Shortwave Flux Data Products Using BSRN Measurements: A Systematic Quality Control, Production and Application Approach

The NASA/GEWEX Surface Radiation Budget (SRB) project has produced a 24.5-year continuous record of global shortwave and longwave radiation fluxes at TOA and the Earth's surface from satellite measurements. The time span of the data is from July 1983 to December 2007, and the spatial resolution is 11 latitude11 longitude. The inputs of the latest version (Release 3.0) include the GEOS Version 4.0.3 meteorological information and cloud properties derived from ISCCP DX data. The SRB products are available on 3-hourly, 3-hourly-monthly, daily and monthly time scales. To assess the quality of the product, we extensively validated the SRB data against 5969 site-months of groundbased measurements from 52 Baseline Surface Radiation Network (BSRN) stations. This paper describes first the characteristics of the BSRN data and the GEWEX SRB data, the methodology for quality control and processing of the shortwave BSRN data, and then the systematic SRB-BSRN comparisons. It is found that, except for occasional extreme outliers as seen in scatter plots, the satellite-based surface radiation data generally agree very well with BSRN measurements. Specifically, the bias/RMS for the daily and monthly mean shortwave fluxes are, respectively, -3.6/35.5 and -5.2/23.3W1 m2 under all-sky conditions.

Zhang, Taiping↗
NASA NTRS1974

A study of the Sabatier-methanation reaction kinetics

The kinetics of the Sabatier methanation reaction, the reduction of carbon dioxide with hydrogen to methane and water, was investigated for 58 percent nickel on kieselguhr catalyst and 20 percent ruthenium on alumina catalyst. Differential rate data from an experimental program were correlated with a power function rate equation both for forward and reverse reactions. The kinetic parameters of activation energy, frequency rate constant and reaction order were determined for the rate equation. The values of these parameters were obtained from an Arrhenius plot of the experimental differential rate data. Also the carbon monoxide side reaction effect was measured and included in the correlation of parameters. The reaction was found to fit the rate equation experimentally within the temperature range 421 K, where the reaction effectively begins, the 800 K where the reaction rate drops and departs from the rate equation form.

Verostko, C. E.↗
NASA NTRS2003

Software for Preprocessing Data From Rocket-Engine Tests

Three computer programs have been written to preprocess digitized outputs of sensors during rocket-engine tests at Stennis Space Center (SSC). The programs apply exclusively to the SSC E test-stand complex and utilize the SSC file format. The programs are the following: (1) Engineering Units Generator (EUGEN) converts sensor-output-measurement data to engineering units. The inputs to EUGEN are raw binary test-data files, which include the voltage data, a list identifying the data channels, and time codes. EUGEN effects conversion by use of a file that contains calibration coefficients for each channel. (2) QUICKLOOK enables immediate viewing of a few selected channels of data, in contradistinction to viewing only after post-test processing (which can take 30 minutes to several hours depending on the number of channels and other test parameters) of data from all channels. QUICKLOOK converts the selected data into a form in which they can be plotted in engineering units by use of Winplot. (3) EUPLOT provides a quick means for looking at data files generated by EUGEN without the necessity of relying on the PVWAVE based plotting software.

Cheng, Chiu-Fu↗
NASA NTRS1984

A crack opening stress equation for fatigue crack growth

A general crack opening stress equation is presented which may be used to correlate crack growth rate data for various materials and thicknesses, under constant amplitude loading, once the proper constraint factor has been determined. The constraint factor, alpha, is a constraint on tensile yielding; the material yields when the stress is equal to the product of alpha and sigma. Delta-K (LEFM) is plotted against rate for 2024-T3 aluminum alloy specimens 2.3 mm thick at various stress ratios. Delta-K sub eff was plotted against rate for the same data with alpha = 1.8; the rates correlate well within a factor of two.

Newman, J. C., Jr.↗
NASA NTRS1991

The analysis of high pressure experimental data

This letter is concerned with the analysis of high pressure experimental data. It is demonstrated that ln H plots based on the Vinet et al. (1988) universal equation of state are a simple sensitive means for identifying anomalous P-V data in high pressure experiments and for detecting structural and phase transitions in solids subjected to high pressure.

Schlosser, Herbert↗
NASA NTRS2001

Physical Processes Governing Atmospheric Trace Constituents Measured from an Aircraft on PEM-Tropics

Before the mission, the PI (principal investigator) was instrumental in securing real-time use of the new 51-level ECMWF (European Centre for Medium Range Weather Forecasts) meteorological data. During the mission, he provided flight planning and execution guidance as meteorologist for the P-3B. Mr. Yong Zhu computed and plotted meteorological forecast maps using the ECMWF data and transmitted them to the field from MIT (Massachusetts Institute of Technology). Dr. John Cho was in the field for the Christmas Island portion to extract data from the on-site NOAA (National Oceanic and Atmospheric Administration) radars for local wind profiles that were used at the flight planning meetings. When the power supply for the VHF radar failed, he assisted the NOAA engineer in its repair. After the mission, Mr. Zhu produced meteorological data memos, which were made available to the PEM (Pacific Exploratory Mission)-Tropics B science team on request. An undergraduate student, Ms. Danielle Morse, wrote memos annotating the cloud conditions seen on the aircraft external monitor video tapes. Dr. Cho and the PI circulated a memo regarding the status (and associated problems) of the meteorological measurement systems on the DC-8 and P-3B to the relevant people on the science team. Several papers by members of our project were completed and accepted by JGR (Journal of Geophysical Research) for the first special section on PEM-Tropics B. These papers included coverage of the following topics: 1) examination of boundary layer data; 2) water vapor transport; 3) tropospheric trace constituent layers; 4) summarizations of the meteorological background and events during PEM-Tropics B; 5) concomitant lidar measurements of ozone, water vapor, and aerosol.

Newell, Reginald E.↗
NASA NTRS1980

Confidence regions of planar cardiac vectors

A method for plotting the confidence regions of vectorial data obtained in electrocardiology is presented. The 90%, 95% and 99% confidence regions of cardiac vectors represented in a plane are obtained in the form of an ellipse centered at coordinates corresponding to the means of a sample selected at random from a bivariate normal distribution. An example of such a plot for the frontal plane QRS mean electrical axis for 80 horses is also presented.

Dubin, S.↗
DOE OSTI2020

Neural MUSE Analysis

Researchers at Oak Ridge National Laboratory (ORNL) created data as part of the MUSE (Multi-Agency Urban Search Experiment Detector and Algorithm Test Bed) project simulating illicit nuclear materials located in various buildings along a road. In the simulation, a truck containing a radiation detector drives down the road gathering listmode data (counting the and energy of incident gamma radiation). Building materials, source shielding, driving speed, truck direction, truck location on the road, source type, and source placement are all varied between runs of the data set. This data was created using deterministic neutron transport and Monte Carlo methods through a combination of SCALE, MAVRIC, MCNP, and GADRAS. As part of a follow-on NA-22 project, two Kaggle competitions were created to determine the best algorithms for finding and identifying gamma sources in this simulated urban environment. The winning algorithm was neural network-based and had a test accuracy of 76.4% accuracy for source identification. This work seeks to build upon this work and improve the results through the application of novel machine learning techniques. As a first step, the data was classified by a simple Convolutional Neural Network (CNN) To accomplish this, the data was first preprocessed into “waterfall plots.” These plots are composed of energy vs count plots that are stacked vertically to show progression in time. The horizontal axis indicating the particle energy incorporated user defined bin spacing with options for in linear-, logarithmic-, square root-, and user-spaced bins. The z or color dimension showed the number of counts corresponding the energy-time combination. This data was then used to generate more data, by generating a local estimate of the mean of the distribution for a bin and then randomly re-sampling that bin from a Poisson distribution. Once all of this data was generated, it was fed into a well-known CNN architecture, ResNet50. The output layer of this model was removed and replaced with layers corresponding to the shape desired isotope outputs. The provided training data was used to train the classifier and the remaining testing data was used to evaluate the model. Results are soon to be forthcoming.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

Thresholding Analysis and Feature Extraction from 3D Ground Penetrating Radar Data for Noninvasive Assessment of Peanut Yield

This study explores the efficacy of utilizing a novel ground penetrating radar (GPR) acquisition platform and data analysis methods to quantify peanut yield for breeding selection, agronomic research, and producer management and harvest applications. Sixty plots comprising different peanut market types were scanned with a multichannel, air-launched GPR antenna. Image thresholding analysis was performed on 3D GPR data from four of the channels to extract features that were correlated to peanut yield with the objective of developing a noninvasive high-throughput peanut phenotyping and yield-monitoring methodology. Plot-level GPR data were summarized using mean, standard deviation, sum, and the number of nonzero values (counts) below or above different percentile threshold values. Best results were obtained for data below the percentile threshold for mean, standard deviation and sum. Data both below and above the percentile threshold generated good correlations for count. Correlating individual GPR features to yield generated correlations of up to 39% explained variability, while combining GPR features in multiple linear regression models generated up to 51% explained variability. The correlations increased when regression models were developed separately for each peanut type. This research demonstrates that a systematic search of thresholding range, analysis window size, and data summary statistics is necessary for successful application of this type of analysis. The results also establish that thresholding analysis of GPR data is an appropriate methodology for noninvasive assessment of peanut yield, which could be further developed for high-throughput phenotyping and yield-monitoring, adding a new sensor and new capabilities to the growing set of digital agriculture technologies.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2011

Draper Station Analysis Tool

Draper Station Analysis Tool (DSAT) is a computer program, built on commercially available software, for simulating and analyzing complex dynamic systems. Heretofore used in designing and verifying guidance, navigation, and control systems of the International Space Station, DSAT has a modular architecture that lends itself to modification for application to spacecraft or terrestrial systems. DSAT consists of user-interface, data-structures, simulation-generation, analysis, plotting, documentation, and help components. DSAT automates the construction of simulations and the process of analysis. DSAT provides a graphical user interface (GUI), plus a Web-enabled interface, similar to the GUI, that enables a remotely located user to gain access to the full capabilities of DSAT via the Internet and Webbrowser software. Data structures are used to define the GUI, the Web-enabled interface, simulations, and analyses. Three data structures define the type of analysis to be performed: closed-loop simulation, frequency response, and/or stability margins. DSAT can be executed on almost any workstation, desktop, or laptop computer. DSAT provides better than an order of magnitude improvement in cost, schedule, and risk assessment for simulation based design and verification of complex dynamic systems.

Bedrossian, Nazareth↗
NASA NTRS2006

On the Mixing of Single and Opposed Rows of Jets With a Confined Crossflow

The primary objectives of this study were 1) to demonstrate that contour plots could be made using the data interface in the NASA GRC jet-in-crossflow (JIC) spreadsheet, and 2) to investigate the suitability of using superposition for the case of opposed rows of jets with their centerlines in-line. The current report is similar to NASA/TM-2005-213137 but the "basic" effects of a confined JIC that are shown in profile plots there are shown as contour plots in this report, and profile plots for opposed rows of aligned jets are presented here using both symmetry and superposition models. Although superposition was found to be suitable for most cases of opposed rows of jets with jet centerlines in-line, the calculation procedure in the JIC spreadsheet was not changed and it still uses the symmetry method for this case, as did all previous publications of the NASA empirical model.

Holdeman, James D.↗