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DOE OSTI2024

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1993

On the estimation algorithm for adaptive performance optimization of turbofan engines

The performance seeking control (PSC) algorithm is designed to continuously optimize the performance of propulsion systems. The PSC algorithm uses a nominal propulsion system model and estimates, in flight, the engine deviation parameters (EDPs) characterizing the engine deviations with respect to nominal conditions. In practice, because of measurement biases and/or model uncertainties, the estimated EDPs may not reflect the engine's actual off-nominal condition. This factor has a direct impact on the PSC scheme exacerbated by the open-loop character of the algorithm. In this paper, the effects produced by unknown measurement biases over the estimation algorithm are evaluated. This evaluation allows for identification of the most critical measurements for application of the PSC algorithm to an F100 engine. An equivalence relation between the biases and EDPs stems from the analysis; therefore, it is undecided whether the estimated EDPs represent the actual engine deviation or whether they simply reflect the measurement biases. A new algorithm, based on the engine's (steady-state) optimization model, is proposed and tested with flight data. When compared with previous Kalman filter schemes, based on local engine dynamic models, the new algorithm is easier to design and tune and it reduces the computational burden of the onboard computer.

Espana, Martin D.↗

NASA NTRS1997

Micro-Optic Color Separation Technology for Efficient Projection Displays

Phase 1 of this project focused on development of an overall optical concept which incorporated a single liquid crystal spatial light modulator. The system achieved full color by utilizing an echelon grating, which diffracted the incident light into three orders with different color spectra, in combination with a microlens array, which spatially separated RGB bands and directed the light of the appropriate wavelength to the appropriate color dot. Preliminary echelon grating designs were provided by MIT/LL and reviewed by Rockwell. Additional Rockwell activities included the Identification of microlens designs, light sources (ILC), and projection optics to fulfill the overall design requirements. An Internal subcontract was established with Rockwell's Collins Avionics and Communications Division (CACD) which specified the liquid crystal SLM (Sharp Model No. LQ 46EO2) and built the projection display baseline projector. Full Color projected video images were produced and shown at the 1995 HDS meeting in Washington. Analysis of the luminance performance of the projector and detailed parameter trade studies helped define the dependence of overall display efficiency on lamp collimation, and indicated that a lamp with very small arc dimension is required for the optical concept to be viable.

Gunning, W. J.↗

NASA NTRS2006

Estimation of Longitudinal Unsteady Aerodynamics of a Wing-Tail Combination From Wind Tunnel Data

This paper presents an initial step toward model identification from wind tunnel data for an airliner configuration. Two approaches to modeling a transport configuration are considered and applied to both steady and large-amplitude forced-oscillation wind tunnel data taken over a wide range of angles of attack. Only limited conclusions could be drawn from this initial data set. Although model estimated time histories of normal force and pitching moment agree reasonably well with the corresponding measured values, model damping parameters did not, for some cases, have values consistent with small amplitude oscillatory data. In addition, large parameter standard errors implied poor information content for model structure determination and parameter estimation. Further investigation of the modeling problem for more general aerodynamic models is recommended with close attention to experiment design for obtaining parameters with high accuracy.

Murphy, Patrick C.↗

NASA NTRS2015

Development and Execution of the RUNSAFE Runway Safety Bayesian Belief Network Model

One focus area of the National Aeronautics and Space Administration (NASA) is to improve aviation safety. Runway safety is one such thrust of investigation and research. The two primary components of this runway safety research are in runway incursion (RI) and runway excursion (RE) events. These are adverse ground-based aviation incidents that endanger crew, passengers, aircraft and perhaps other nearby people or property. A runway incursion is the incorrect presence of an aircraft, vehicle or person on the protected area of a surface designated for the landing and take-off of aircraft; one class of RI events simultaneously involves two aircraft, such as one aircraft incorrectly landing on a runway while another aircraft is taking off from the same runway. A runway excursion is an incident involving only a single aircraft defined as a veer-off or overrun off the runway surface. Within the scope of this effort at NASA Langley Research Center (LaRC), generic RI, RE and combined (RI plus RE, or RUNSAFE) event models have each been developed and implemented as a Bayesian Belief Network (BBN). Descriptions of runway safety issues from the literature searches have been used to develop the BBN models. Numerous considerations surrounding the process of developing the event models have been documented in this report. The event models were then thoroughly reviewed by a Subject Matter Expert (SME) panel through multiple knowledge elicitation sessions. Numerous improvements to the model structure (definitions, node names, node states and the connecting link topology) were made by the SME panel. Sample executions of the final RUNSAFE model have been presented herein for baseline and worst-case scenarios. Finally, a parameter sensitivity analysis for a given scenario was performed to show the risk drivers. The NASA and LaRC research in runway safety event modeling through the use of BBN technology is important for several reasons. These include: 1) providing a means to clearly understand the cause and effect patterns leading to safety issues, incidents and accidents, 2) enabling the prioritization of specialty areas needing more attention to improve aviation safety, and 3) enabling the identification of gaps within NASA's Aviation Safety funding portfolio

Green, Lawrence L.↗

NASA NTRS2009

Identification of Trends into Dose Calculations for Astronauts through Performing Sensitivity Analysis on Calculational Models Used by the Radiation Health Office

The Radiation Health Office (RHO) determines each astronaut s cancer risk by using models to associate the amount of radiation dose that astronauts receive from spaceflight missions. The baryon transport codes (BRYNTRN), high charge (Z) and energy transport codes (HZETRN), and computer risk models are used to determine the effective dose received by astronauts in Low Earth orbit (LEO). This code uses an approximation of the Boltzman transport formula. The purpose of the project is to run this code for various International Space Station (ISS) flight parameters in order to gain a better understanding of how this code responds to different scenarios. The project will determine how variations in one set of parameters such as, the point of the solar cycle and altitude can affect the radiation exposure of astronauts during ISS missions. This project will benefit NASA by improving mission dosimetry.

Adams, Thomas↗

DOE OSTI2022

Speaker-targeted Synthetic Speech Detection

Text-to-speech technologies are evolving quickly towards realistic-sounding human-like voices. As this technology improves, so does the opportunity for malpractice in speaker identification (SID) via spoofing, the process of impersonating a voice biometric via synthesis. More data typically equates to a more realistic voice model, which poses an issue for well-known subjects, such as politicians and celebrities, who have vast amounts of multimedia available online. Detection of synthetic speech has relied on signal processing techniques that focus on the generation of new acoustic features and train deep learning models to detect when an audio file has been manipulated through the characterization of unnatural changes or artifacts. However, these techniques do not use any information from the speaker they are evaluating. This paper proposes to incorporate information from the speaker-of-interest (SoI) into the models to avoid specific spoofing attacks for certain vulnerable people. The wealth of data for well-known people can also be used to train a speaker-specific spoofing detector with a higher level of accuracy than a speaker-independent model. The paper proposes a new xResNet-PLDA system and compares it to three different baseline systems: a state-of-the-art speaker identification system, an xResNet system trained to discriminate between bona fide and fake speech, and a speaker identification system in which the PLDA and calibration models were trained with bona fide and fake speech. We evaluated the systems in two different scenarios — a cross-validation scenario and a hold-out scenario — with three different databases. We show how the proposed system outperforms dramatically the baseline systems in each scenario and for each database. Finally, we show how using a small amount of the SoI’s speech to adapt global calibration parameters improves the performance of the system, especially in unseen conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Recognizability of Demographically Altered Computerized Facial Approximations in an Automated Facial Recognition Context for Potential Application in Unidentified Persons Data Repositories

This study examined the recognizability of demographically altered facial approximations for potential utility in unidentified persons tracking systems. Five computer-generated approximations were generated for each of 26 African male participants using the following demographic parameters: (i) African male (true demographics), (ii) African female, (iii) Caucasian male, (iv) Asian male, and (v) Hispanic male. Overall, 62% of the true demographic facial approximations for the 26 African male participants examined were matched to a corresponding life photo within the top 50 images of a candidate list generated from an automated blind search of an optimally standardized gallery of 6159 photographs. When the African male participants were processed as African females, the identification rate was 50%. In contrast, less congruent identification rates were observed when the African male participants were processed as Caucasian (42%), Asian (35%), and Hispanic (27%) males. The observed results suggest that approximations generated using the opposite sex may be operationally informative if sex is unknown. The performance of approximations generated using alternative ancestry assignments, however, was less congruent with the performance of the true demographic approximation (African male) and may not yield as operationally constructive data as sex-altered approximations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1978

Determination of navigation FDI thresholds using a Markov model

A method for determining time-varying Failure Detection and Identification (FDI) thresholds for single sample decision functions is described in the context of a triplex system of inertial platforms. A cost function consisting of the probability of vehicle loss due to FDI decision errors is minimized. A discrete Markov model is constructed from which this cost can be determined as a function of the decision thresholds employed to detect and identify the first and second failures. Optimal thresholds are determined through the use of parameter optimization techniques. The application of this approach to threshold determination is illustrated for the Space Shuttle's inertial measurement instruments.

Walker, B. K.↗

NASA NTRS1986

Thermoluminescence of Antarctic meteorites: A rapid screening technique for terrestrial age estimation, pairing studies and identification of specimens with unusual prefall histories

Thermoluminescence (TL) is a promising technique for rapid screening of the large numbers of Antarctic meteorites, permitting identification of interesting specimens that can then be studied in detail by other, more definite techniques. Specifically, TL permits determination of rough terrestrial age, identification of potential paired groups and location of specimens with unusual pre-fall histories. Meteorites with long terrestrial ages are particularly valuable for studying transport and weathering mechanisms. Pairing studies are possible because TL variations among meteorites are large compared to variations within individual objects, especially for natural TL. Available TL data for several L3 fragments, three of which were paired by other techniques, are presented as an example of the use of TL parameters in pairing studies. Additional TL measurements, specifically a blind test, are recommended to satisfactorily establish the reliability of this pairing property. The TL measurements also identify fragments with unusual pre-fall histories, such an near-Sun orbits.

Sutton, S. R.↗

NASA NTRSDate not supplied

Li-ion Battery Aging with Hybrid Physics-Informed Neural Networks and Fleet-wide Data

In this work, we propose a hybrid model for Li-ion battery discharge and aging prediction that leverages fleet-wide data to predict future capacity drops.The model is built upon an hybrid approach merging physics-based and empirical equations, as well as neural network models in a recurrent neural network cell. The hybrid physics-informed neural network can predict voltage discharge cycles given the loading profile, and estimate the used capacity of the battery under random-loading conditions by tracking aging parameters connected to the residual capacity of the battery. By merging information on the battery aging parameters with existing fleet-wide aging data, the model can predict the future residual capacity of the battery that is being monitored, and therefore enable predictions of voltage discharge curves far ahead in the battery life cycle. We validated the approach using the NASA Prognostics Data Repository Battery data-set, which contains experimental data on Li-ion batteries discharged at random loading conditions in a controlled environment. The approach also allows the identification of discrepancies between the battery aging trend and the trend observed at the fleet level, so that batteries behaving differently from the rest of the fleet can be subject to closer monitoring and further testing to refine predictions.

PINN↗

NASA NTRS1970

Detection and identification of benthic communities and shoreline features in Biscayne Bay

Progress made in the development of a technique for identifying and delinating benthic and shoreline communities using multispectral imagery is described. Images were collected with a multispectral scanner system mounted in a C-47 aircraft. Concurrent with the overflight, ecological ground- and sea-truth information was collected at 19 sites in the bay and on the shore. Preliminary processing of the scanner imagery with a CDC 1604 digital computer provided the optimum channels for discernment among different underwater and coastal objects. Automatic mapping of the benthic plants by multiband imagery and the mapping of isotherms and hydrodynamic parameters by digital model can become an effective predictive ecological tool when coupled together. Using the two systems, it appears possible to predict conditions that could adversely affect the benthic communities. With the advent of the ERTS satellites and space platforms, imagery data could be obtained which, when used in conjunction with water-level and meteorological data, would provide for continuous ecological monitoring.

Kolipinski, M. C.↗

NASA NTRS1986

Identification of nonlinear structural elements by force-state mapping

A major contributor to the passive damping and potentially nonlinear behavior of large space structures is the behavior of the joints. Proposed is an experimental technique called 'force-state mapping' that will allow ground testing of these key structural elements. The technique includes the use of very accurate instrumentation to measure the force transmission properties of a structural element as a function of its mechanical state. When these data are presented in the form of a force-state map, the nonlinearities exhibit distinctively recognizable patterns. This presentation of the data allows the extraction of the describing parameters of the linear and nonlinear behavior and the energy dissipation characteristics of the joint. A series of tests were carried out on an idealized laboratory test article to demonstrate the technique. Strong structural nonlinearities, including a cubic hardening spring, friction, and impact phenomena, were introduced and measured. Parameters identified by the force-state mapping technique are compared with those made by traditional techniques and the errors involved in the measurement are estimated.

Crawley, E. F.↗

DOE OSTI2025

Pyrrole‐Imine Macrocycle: Self‐Organizing Cross‐Reactive Anion Receptor and Sensor

Self-organizing macrocyclic receptor-sensors for phosphorus oxyanions, phosphates, and phosphonates comprising imine moieties were prepared by condensation of dipyrrolylmethane dicarbaldehyde with diethylene triamine. The incorporation of flexible ethylene moieties endows the macrocycle with unprecedented flexibility and ability to accommodate numerous phosphorus oxyanions from orthophosphate to large anions such as ATP or phosphonate glyphosate. The anion binding was elucidated by NMR titrations, low-temperature NMR, and NOESY NMR. The incorporation of dansyl fluorophore enables sensing of anions using the fluorescence signal, whereas the changes in fluorescence intensity, width of the fluorescence band, and position of the maxima are analyte-specific and useful in recognition and identification of eleven different P-oxyanions in water. The affinity (K assoc ) for Na + salts was H 2 PO 4 − ≈ Methylphosphonate > H 2 P 2 O 7 2− > Phenylphosphonate- > Glyphosate 2− > AMP 2− > ADP 2− > ATP 2− . Interestingly, phosphonates, including methylphosphonate and glyphosate anions, were also found to display a strong affinity (K assoc ∼10 6 M −1 ) while halides, nitrate, carbonates, or hydrogen sulfate did not show a significant affinity. The determined fluorescence spectral parameters were used to classify the 12 analytes (11 anions and water) using Linear Discriminant Analysis (LDA). Quantification was performed using LDA and Support Vector Machine (SVM), and the phosphonate concentrations in unknown samples were determined with an error of 3.5% or lower.

anions↗

DOE OSTI2015

Automating linear accelerator quality assurance

Purpose: The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. Methods: The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. Results: For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs. Conclusions: The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Long-Term Evaluation of Remedial Technology Performance in the Laboratory: Multi-year Experimental Test Plan

An understanding of the long-term effectiveness of remediation technologies is central to sustainable environmental cleanup. Long-term experiments are valuable for reducing uncertainty and predicting remediation outcomes at scales required for regulatory compliance. However, these types of tests can be costly and challenging to interpret. Therefore, contaminated sites often rely on short-term laboratory experiments that may not account for the potentially significant effects of gradual, time- dependent processes governing contaminant retention, release, and species transformation. For example, short-term lab experiments (from months to a year) conducted with sediments from the unsaturated and saturated zones at the Hanford Site play an important role in initial evaluations of remediation technologies but cannot capture the full extent of time-dependent reactions, leaving uncertainties in field-scale deployment. Here, long-term testing will be conducted on select technologies based on their performance in short-term testing. The overall objective is to directly address the challenges described above by generating and analyzing data on long-term (2–10 years) efficacy of selected remediation technologies, integrating this understanding into models, and providing critical input for remediation planning, monitoring, and 5-year review cycles for field-implemented remedies. Specific objectives include: 1. Evaluating long-term efficiency of promising remedies under site-specific conditions. 2. Generating robust parameters for modeling, reducing uncertainty in predictive simulations. 3. Advancing integrated monitoring by combining geochemical and geophysical observations. 4. Informing field-scale implementation by incrementally advancing technologies, identifying failure mechanisms early, and prioritizing robust, cost-effective remedies. Through systematic evaluation of technologies in laboratory-scale column experiments, integrated monitoring, and modeling support, this project is designed to bolster confidence in the long-term robustness of selected technologies. The ultimate outcome is the identification and deployment of more reliable, cost-effective remedies that safeguard human health and the environment while reducing the uncertainties that have historically hindered cleanup progress at Hanford Site. An experimental approach was developed and initiated for long-term testing potentially up to 10 years. The table below summarizes the experimental approach developed for testing select technologies and presented in this multi-year experimental test plan.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1977

Observation of a kink instability in a solar flare

The morphological evolution of XUV flare emissions is studied for a solar flare observed during the Skylab mission, and observational evidence is found for a possible identification of a kink or helical instability in a magnetic flux loop associated with the flare. The evolution of the loop as seen in 256-A He II emission is described, showing that the kink instability lasted about 2 to 4 min, caused the flux tube to wriggle, and produced lateral motion of the loop in the observations with theoretical calculations of the kink instability reveals a close correspondence between observed and theoretical values of such parameters as critical current for instability and growth rate.

Cheng, C.-C.↗

NASA NTRS1991

Atmospheric turbulence review of space shuttle launches

Research and analysis on the identification of turbulent regions from the surface to 16 km during Space Shuttle launches are discussed. It was demonstrated that the results from the FPS-16 radar/jimsphere balloon system in measuring winds can indeed indicate the presence or conditions ripe for turbulence in the troposphere and lower stratosphere. It was further demonstrated that atmospheric data obtained during the shuttle launches by the rawinsonde in conjunction with the jimsphere provides the necessary meteorological data to compute aerodynamic parameters to identify turbulence, such as Reynolds number drag coefficient, turbulent stresses, total energy, stability parameter, vertical gradient of kinetic energy, Richardson number, and the turbulence probability index. Enhanced temperature lapse rates and inversion rates, strong vector wind shears, and large changes in wind direction identify the occurrence of turbulence at the troposphere. When any two of the above conditions occur simultaneously, a significant probability of turbulence can occur.

Susko, Michael↗

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