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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 NTRS1985

Atmospheric transmittance from spacecraft using multiple view angle imagery

A procedure for determining atmospheric transmittance using surface images acquired at several view angles from space is presented. Fourier filtering of the image data is used to mitigate the effects of atmospheric path radiance and instrument noise. Although it is essential for some contrast to be present in the images, knowledge of the atmospheric scattering phase function or the surface bidirectional reflectance function is not required. The method appears to provide absolute transmittances with an accuracy of better than 10 percent, which is useful in some applications.

Diner, D. J.↗

NASA NTRS2007

Filter Function for Wavefront Sensing Over a Field of View

A filter function has been derived as a means of optimally weighting the wavefront estimates obtained in image-based phase retrieval performed at multiple points distributed over the field of view of a telescope or other optical system. When the data obtained in wavefront sensing and, more specifically, image-based phase retrieval, are used for controlling the shape of a deformable mirror or other optic used to correct the wavefront, the control law obtained by use of the filter function gives a more balanced optical performance over the field of view than does a wavefront-control law obtained by use of a wavefront estimate obtained from a single point in the field of view.

Dean, Bruce H.↗

DOE OSTI2024

The Role of Data Filtering in Open Source Software Ranking and Selection

Faced with more than 100M open source projects, a more manageable small subset is needed for most empirical investigations. More than half of the research papers in leading venues investigated filtering projects by some measure of popularity with explicit or implicit arguments that unpopular projects are not of interest, may not even represent "real" software projects, or that less popular projects are not worthy of study. However, such filtering may have enormous effects on the results of the studies if and precisely because the sought-out response or prediction is in any way related to the filtering criteria.This paper exemplifies the impact of this common practice on research outcomes, specifically how filtering of software projects on GitHub based on inherent characteristics affects the assessment of their popularity. Using a dataset of over 100,000 repositories, we used multiple regression to model the number of stars -a commonly used proxy for popularity- based on factors such as the number of commits, the duration of the project, the number of authors and the number of core developers. Our control model included the entire dataset, while a second filtered model considered only projects with ten or more authors. The results indicated that while certain characteristics of the repository consistently predict popularity, the filtering process significantly alters the relationships between these characteristics and the response. We found that the number of commits exhibited a positive correlation with popularity in the control sample but showed a negative correlation in the filtered sample. These findings highlight the potential biases introduced by data filtering and emphasize the need for careful sample selection in empirical research of mining software repositories. We recommend that empirical work should either analyze complete datasets such as World of Code, or employ stratified random sampling from a complete dataset to ensure that filtering is not biasing the results.

Malviya Thakur, Addi↗

DOE OSTI2022

Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands

Climate influences soil microbial composition and function, but the relative importance of a site's historic climate versus its more immediate environmental conditions is unclear. Using quantitative stable isotope probing (qSIP), we characterized actively growing soil microbial communities and soil properties in three California annual grasslands that span a rainfall gradient and have developed on similar parent material. The soils were assayed in the wet winter season, when environmental conditions are most similar across sites. Since growing populations might be expected to be most responsive to contemporary environmental conditions, we hypothesized that the structure of growing microbial communities would be more similar across the gradient than that of total communities (i.e., including non-growing populations). In addition, we hypothesized that population growth rates would be slowest in the driest site, reflecting a legacy effect of low soil moisture on microbial growth. Soils along the rainfall gradient differed in pH, texture, and cation exchange capacity, but not in total C, C:N or dominant minerals. The radiocarbon (14C) age of soil C (reflecting turnover time) increased with mean annual precipitation but soil respiration was uniformly modern, reflecting microbial reliance on recent C inputs across the sites. The structure of both total and growing microbial communities differed across sites. Across major microbial phyla, including the Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Proteobacteria, bacterial growth rates were consistently lower in the site with the lowest mean annual precipitation. Taxa that were growing at the dry site alone grew more slowly than taxa that grew at multiple sites. These results reflect the influence of climate history and point to the role of environmental filtering at the driest site in shaping its slower growing microbial community, possibly reflecting adaptation to repeated exposure to water stress. Lastly, across taxa, the growth rate of a taxon at one site was correlated with its growth rate in the other sites. Furthermore, this growth rate coherence is likely a consequence of genetically determined physiological traits and is consistent with the idea that evolutionary history constrains growth rate.

Environmental filtering↗

DOE OSTI2021

Large-eddy simulation of a multi-injection flame in a diesel engine environment using an unsteady flamelet/progress variable approach

In this work, large-eddy simulations (LESs) are conducted for a multiple-injection flame in a diesel engine environment using an unsteady flamelet/progress variable (UFPV) approach in which differential diffusion is considered. The suitability of the UFPV tabulation approach is first evaluated through a priori analyses using the state-of-the-art direct numerical simulation (DNS) dataset. Both the instantaneous data and the conditional values for the major and minor species' mass fractions are compared between the UFPV and the DNS. The comparisons show that the proposed UFPV tabulation approach can give good predictions for the multiple-injection flame at different injection phases. While the gas temperature and major species mass fractions can be accurately predicted with or without differential diffusion being considered in the UFPV flamelet library, the prediction accuracy for the highly diffusive species (e.g., hydrogen) in the main injection phase can be noticeably improved when differential diffusion is taken into account. The fully coupled LES/UFPV simulations show that the overall structure of the multiple-injection flame can be predicted, and the conditional thermo-chemical values are close to the filtered DNS dataset. The reasons for the remaining discrepancies found in the a priori analyses and the a posteriori simulations using the UFPV approach are analyzed.

Wen, Xu (ORCID:0000000331334292)↗

DOE OSTI2021

Genomic Metrics Applied to Rhizobiales ( Hyphomicrobiales ): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Legacy Survey of Space and Time Data Preview 1: deep_coadd dataset type

The Legacy Survey of Space and Time Data Preview 1 (DP1) is the first release of data from the NSF-DOE Vera C. Rubin Observatory. It consists of raw and calibrated single-epoch images, co-adds, difference images, detection catalogs, and other derived data products. DP1 is based on 1792 science-grade optical/near-infrared exposures acquired over 48 distinct nights by the Rubin Commissioning Camera, LSSTComCam, on the Simonyi Survey Telescope at the Summit Facility on Cerro Pachón, Chile during the first on-sky commissioning campaign in late 2024. DP1 covers a total of approximately 15 sq. deg. over seven roughly equally-sized non-contiguous fields, each independently observed in six broad photometric bands, ugrizy, spanning a range of stellar densities and latitudes and overlapping with external reference datasets. This dataset is a subset of the full data release consisting of the deep_coadd dataset type. These are the combination of multiple processed, calibrated, and background- subtracted images, for a patch of sky, for each of the six filters. This release contains 2,644 datasets of this type.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1980

Digital preprocessing of SEASAT imagery

A model for radar image data is derived for use in developing enhancement techniques. This model describes the image data as the result of a multiplicative-convolved noise process. This information is then used to design a minimum mean square error (MMSE) filter. The resulting filter is implemented adaptively to change with local statistics. A radar image processing technique which provides the MMSE estimate inside homogeneous areas and tends to preserve edge structure is thus developed. This technique has been implemented and tested using digitally correlated SEASAT-A synthetic aperture radar (SAR) imagery.

Frost, V. S.↗

NASA NTRS1991

Maximum expiratory flow-volume curves during short periods of microgravity

Nine normal subjects were studied in a NASA microgravity research aircraft to elucidate the effect of normal gravitation on the shape of the maximum expiratory flow-volume (MEFV). They performed multiple MEFV maneuvers at 0, 1, and approximately 2 G. The MEFV curves for each subject were filtered, aligned at residual volume, and ensemble-averaged to produce an average MEFV curve for each state, allowing differences to be studied. Most subjects showed a decrease in the forced vital capacity at 0 G. The mean lung volume associated with a given flow was lower at 0 G over about the upper half of the vital capacity. There were consistent but highly individual changes in the position and magnitude of detailed features of the curve. This supports the concept that the location and motion of choke points that determine the detailed individual configuration of MEFG curves can be significantly influenced by gravitational forces, presumably via the effects of change in longitudinal tension on local airway pressure-diameter behavior and thus wave speed.

Guy, H. J. B.↗

NASA NTRS2003

Entry Trajectory and Atmosphere Reconstruction Methodologies for the Mars Exploration Rover Mission

The Mars Exploration Rover (MER) mission will land two landers on the surface of Mars, arriving in January 2004. Both landers will deliver the rovers to the surface by decelerating with the aid of an aeroshell, a supersonic parachute, retro-rockets, and air bags for safely landing on the surface. The reconstruction of the MER descent trajectory and atmosphere profile will be performed for all the phases from hypersonic flight through landing. A description of multiple methodologies for the flight reconstruction is presented from simple parameter identification methods through a statistical Kalman filter approach.

Desai, Prasun N.↗

NASA NTRS2015

Summer 2015 Internship Abstract

Green fluorescent protein (GFP) visually shows the expression of proteins by fluorescing when exposed to certain wavelengths of light. The GFP in this experiment was used to identify cells actively releasing viruses. The experiment focused on the effect of microgravity on the GFP expression of Akata B-cells infected with Epstein Barr Virus (EBV). Two flasks were prepared with 30 million cells each and two bioreactors were prepared with 50 million cells each. All four cultures were incubated for 16 days and fed every four days. Cellometer readings were taken on the feeding days to find cell size, viability, and GFP expression. In addition, the cells were treated with Propodium monoazide (PMA) and run through real time PCR to determine viral load on the feeding days. On the International Space Station air samples are taken to analyze the bacterial and fungal organisms in the air. The Sartorius Portable Airport is being investigated for potential use on the ISS to analyze for viral content in the air. Multiple samples were taken around Johnson Space Center building 37 and in Clear Lake Pediatric Clinic. The filter used was the gelatin membrane filter and the DNA was extracted directly from the filter. The DNA was then run through real time PCR for Varicella Zoster Virus (VZV) and EBV as well as GAPDH to test for the presence of DNA. The results so far have shown low DNA yield and no positive results for VZV or EBV. Further inquiry involves accurately replicating an atmosphere with high viral load from saliva as would be found on the ISS to run the air sampler in. Another line of research is stress hormones that may be correlated to the reactivation of latent viruses. The stress hormones from saliva samples are analyzed rather than blood samples. The quantity found in saliva shows the quantity of the hormones actually attached to cells and causing a reaction, whereas in the blood the quantity of hormones is the total amount released to cause a reaction. The particular hormones tested for were cortisol, alpha-amylase, and DHEA. The DHEA was very high in the two control samples tested. Regularly, samples came into the lab from local clinics to be tested for various viruses. Saliva, blood, body scrapes, and tears were received from the clinics and then run for VZV, EBV, and Human Simplex Virus 1 (HSV-1) with the results then reported back to the clinician. Blood, saliva, and urine from astronauts were also tested for viruses and logged. In addition, several cell cultures were brought up and grown, including adherent Human Lung Fibroblast (HFL) cells infected with VZV, and Akata B-cells infected with EBV.

Smith, Courtney↗

DOE OSTI2023

Process Cycle Modeling with AI

Here a convoluted process model-filtering technique is presented that can build and successfully train the structural property artifacts of materials after multiple heat treatment cycles.

Romanov, Vyacheslav↗

NASA NTRS2014

Advanced Sine Wave Modulation of Continuous Wave Laser System for Atmospheric CO2 Differential Absorption Measurements

NASA Langley Research Center in collaboration with ITT Exelis have been experimenting with Continuous Wave (CW) laser absorption spectrometer (LAS) as a means of performing atmospheric CO2 column measurements from space to support the Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) mission.Because range resolving Intensity Modulated (IM) CW lidar techniques presented here rely on matched filter correlations, autocorrelation properties without side lobes or other artifacts are highly desirable since the autocorrelation function is critical for the measurements of lidar return powers, laser path lengths, and CO2 column amounts. In this paper modulation techniques are investigated that improve autocorrelation properties. The modulation techniques investigated in this paper include sine waves modulated by maximum length (ML) sequences in various hardware configurations. A CW lidar system using sine waves modulated by ML pseudo random noise codes is described, which uses a time shifting approach to separate channels and make multiple, simultaneous online/offline differential absorption measurements. Unlike the pure ML sequence, this technique is useful in hardware that is band pass filtered as the IM sine wave carrier shifts the main power band. Both amplitude and Phase Shift Keying (PSK) modulated IM carriers are investigated that exibit perfect autocorrelation properties down to one cycle per code bit. In addition, a method is presented to bandwidth limit the ML sequence based on a Gaussian filter implemented in terms of Jacobi theta functions that does not seriously degrade the resolution or introduce side lobes as a means of reducing aliasing and IM carrier bandwidth.

Campbell, Joel F.↗

NASA NTRS2021

Unsteady Pressure-Sensitive-Paint Shot Noise Reduction

In the study of unsteady Pressure-Sensitive Paint (uPSP) image data sets, pixel intensity values collected by Phantom cameras from multiple perspectives are used to calculate the surface pressure of an experimental model. This paper focuses on mitigation of shot noise which is introduced into the image data set by the cameras. Shot noise impacts the quality of data collected, increasing the system error in its pressure value calculations. This paper characterises statistical methods to reduce shot noise within experimental data by taking an average or weighted average across an area of pixels of their respective counts. Each combined-pixel has a higher total effective intensity value and therefore exhibits reduced noise throughout its time history. This is demonstrated by calculating the standard deviations of the combined pixel values through time, which decrease as the combined pixel area increases. Finally, these methods are compared across experimental wind tunnel conditions to examine their effectiveness at different Mach numbers. Ultimately, the results are used to recommend a blur filter type and size which will be applied to the raw image data prior to processing, as well as a minimum camera resolution for future experiments. Downstream of the filter application, the software to convert the 2D image data sets into surface pressure readings on a 3D grid use a ratio of decimation that assigns multiple pixels to each 3D grid node. This decimation ratio will also be aligned with the size of the blur filter, resulting in a more manageable data set size and compromised spatial resolution. Combined with the effect of the blur filter, the resulting pixel intensity readings will exhibit significantly reduced shot noise, reducing the magnitude of uncertainty and error in the final calculated pressure. For future tests, the camera spatial resolution must be sufficient to capture small flow and model features even after the recommended blur filter is applied. The image data set is taken from a uPSP experiment of the Space Launch System Block 1 cargo vehicle model in September 2019.

Lucy Tang↗

NASA NTRS2021

Unsteady Pressure-Sensitive Paint (UPSP) Shot Noise Reduction

Lucy Tang↗

NASA NTRS1994

Call sign intelligibility improvement using a spatial auditory display

A spatial auditory display was designed for separating the multiple communication channels usually heard over one ear to different virtual auditory positions. The single 19 foot rack mount device utilizes digital filtering algorithms to separate up to four communication channels. The filters use four different binaural transfer functions, synthesized from actual outer ear measurements, to impose localization cues on the incoming sound. Hardware design features include 'fail-safe' operation in the case of power loss, and microphone/headset interfaces to the mobile launch communication system in use at KSC. An experiment designed to verify the intelligibility advantage of the display used 130 different call signs taken from the communications protocol used at NASA KSC. A 6 to 7 dB intelligibility advantage was found when multiple channels were spatially displayed, compared to monaural listening. The findings suggest that the use of a spatial auditory display could enhance both occupational and operational safety and efficiency of NASA operations.

Begault, Durand R.↗

NASA NTRS2011

NASA Tech Briefs, January 2011

The topics include: 1) Distributed Aerodynamic Sensing and Processing Toolbox; 2) Collaborative Supervised Learning for Sensor Networks; 3) Hazard Detection Software for Lunar Landing; 4) Onboard Nonlinear Engine Sensor and Component Fault Diagnosis and Isolation Scheme; 5) Network-Capable Application Process and Wireless Intelligent Sensors for ISHM; 6) Interface Supports Multiple Broadcast Transceivers for Flight Applications; 7) FPGA Sequencer for Radar Altimeter Applications; 8) Miniature Sapphire Acoustic Resonator - MSAR; 9) Process-Hardened, Multi-Analyte Sensor for Characterizing Rocket Plume Constituents; 10) SAD5 Stereo Correlation Line-Striping in an FPGA; 11) Hybrid Composite Cryogenic Tank Structure; 12) Nanoscale Deformable Optics; 13) Reliability-Based Design Optimization of a Composite Airframe Component; 14) Zinc Oxide Nanowire Interphase for Enhanced Lightweight Polymer Fiber Composites; 15) Plasma Igniter for Reliable Ignition of Combustion in Rocket Engines; 16) Wire Test Grip Fixture; 17) A Sub-Hertz, Low-Frequency Vibration Isolation Platform; 18) Carbon Nanofibers Synthesized on Selective Substrates for Nonvolatile Memory and 3D Electronics; 19) Nanoparticle/Polymer Nanocomposite Bond Coat or Coating; 20) High-Resolution Wind Measurements for Offshore Wind Energy Development; 21) Spring Tire; 22) Marsviewer 2008; 23) Mission Services Evolution Center Message Bus; 24) Major Constituents Analysis for the Vehicle Cabin Atmosphere Monitor; 25) Astronaut Health Participant Summary Application; 26) Adaption of the AMDIS Method to Flight Status on the VCAM Instrument; 27) Natural Language Interface for Safety Certification of Safety-Critical Software; 28) Cryogenic Caging for Science Instrumentation; 29) Wide-Range Neutron Detector for Space Nuclear Applications; 30) In Situ Guided Wave Structural Health Monitoring System; 31) Multiplexed Energy Coupler for Rotating Equipment; 32) Attitude Estimation in Fractionated Spacecraft Cluster Systems; 33) Full Piezoelectric Multilayer-Stacked Hybrid Actuation/Transduction Systems; 34) Active Flow Effectors for Noise and Separation Control; 35) Method and System for Temporal Filtering in Video Compression Systems; 36) Apparatus for Measuring Total Emissivity of Small, Low-Emissivity Samples; 37) Multiple-Zone Diffractive Optic Element for Laser Ranging Applications; 38) Simplified Architecture for Precise Aiming of a Deep-Space Communication Laser Transceiver; 39) Two-Photon-Absorption Scheme for Optical Beam Tracking; 40) High-Sensitivity, Broad-Range Vacuum Gauge Using Nanotubes for Micromachined Cavities; 41) Wide-Field Optic for Autonomous Acquisition of Laser Link; 42) Extracting Zero-Gravity Surface Figure of a Mirror; 43) Modeling Electromagnetic Scattering From Complex Inhomogeneous Objects; 44) Visual Object Recognition and Tracking of Tools; 45) Method for Implementing Optical Phase Adjustment; 46) Visual SLAM Using Variance Grid Maps; 47) Rapid Calculation of Spacecraft Trajectories Using Efficient Taylor Series Integration; 48) Efficient Kriging Algorithms; 49) Predicting Spacecraft Trajectories by the WeavEncke Method; 50) An Augmentation of G-Guidance Algorithms; 51) Comparison of Aircraft Icing Growth Assessment Software; 52) Silicon-Germanium Voltage-Controlled Oscillator at 105 GHz; 53) Estimation of Coriolis Force and Torque Acting on Ares-1; 54) Null Lens Assembly for X-Ray Mirror Segments; and 55) High-Precision Pulse Generator.

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