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DOE OSTI2024

Using intrahost single nucleotide variant data to predict SARS-CoV-2 detection cycle threshold values

Over the last four years, each successive wave of the COVID-19 pandemic has been caused by variants with mutations that improve the transmissibility of the virus. Despite this, we still lack tools for predicting clinically important features of the virus. In this study, we show that it is possible to predict the PCR cycle threshold (Ct) values from clinical detection assays using sequence data. Ct values often correspond with patient viral load and the epidemiological trajectory of the pandemic. Using a collection of 36,335 high quality genomes, we built models from SARS-CoV-2 intrahost single nucleotide variant (iSNV) data, computing XGBoost models from the frequencies of A, T, G, C, insertions, and deletions at each position relative to the Wuhan-Hu-1 reference genome. Our best model had an R 2 of 0.604 [0.593–0.616, 95% confidence interval] and a Root Mean Square Error (RMSE) of 5.247 [5.156–5.337], demonstrating modest predictive power. Overall, we show that the results are stable relative to an external holdout set of genomes selected from SRA and are robust to patient status and the detection instruments that were used. This study highlights the importance of developing modeling strategies that can be applied to publicly available genome sequence data for use in disease prevention and control.

COVID19↗

NASA NTRS1989

IBIS: An Interferometer-Based Imaging System for Detecting Extrasolar Planets with a Next Generation Space Telescope

The direct detection of extrasolar planetary systems is a challenging observational objective. The observing system must be able to detect faint planetary signals against the background of diffracted and scattered starlight, zodiacal light, and in the IR, mirror thermal radiation. As part of a JPL study, we concluded that the best long-term approach is a 10-20 m filled-aperture telescope operating in the thermal IR (10-15 microns). At these wavelengths, the star/planet flux ratio is on the order of 10(exp 6)-10(exp 8). Our study supports the work of Angel et al., who proposed a cooled 16-m IR telescope and a special apodization mask to suppress the stellar light within a limited angular region around the star. Our scheme differs in that it is capable of stellar suppression over a much broader field-of- view, enabling more efficient planet searches. To do this, certain key optical signal-processing components are needed, including a coronagraph to apodize the stellar diffraction pattern, an infrared interferometer to provide further starlight suppression, a complementary visible-wavelength interferometer to sense figure errors in the telescope optics, and a deformable mirror to adaptively compensate for these errors. Because of the central role of interferometry we have designated this concept the Interferometer-Based Imaging System (IBIS). IBIS incorporates techniques originally suggested by Ken Knight for extrasolar planet detection at visible wavelengths. The type of telescope discussed at this workshop is well suited to implementation of the IBIS concept.

Diner, David J.↗

NASA NTRS2023

Software Error Incident Categorizations in Aerospace

Since the first use of computers in space and aircraft, software errors have occurred. These errors can manifest as loss-of-life or less catastrophically. As the demand for automation increases, software in safety-critical systems should be designed to be tolerant to the most likely software faults. This paper categorizes historic aerospace software errors to determine trends of how and where automation is most likely to fail. A distinction between software producing wrong (erroneous) output versus no output (fail-silent) is introduced. Of the historical incidents analyzed, 87% were from software acting unexpectedly rather than simply stopping. Rebooting was found to be ineffective to clear erroneous behavior, and only partially effective for silent software. Errors were traced back to the software logic itself in 62% of cases, 13% within configurable data, and 25% introduced through input. Thirty percent (30%) of unexpected software behavior was caused by the absence of software and 20% was due to “unknown-unknowns”. These findings indicate that to achieve fault tolerance in safety-critical systems, backup strategies must be employed to detect and respond to erroneous software behavior beyond only fail-silent cases, and robust off-nominal testing should be performed to uncover unanticipated situations.

Software↗

NASA NTRS2017

Assessment of the Impact of Spatial Heterogeneity on Microwave Satellite Soil Moisture Periodic Error

An accurate temporal and spatial characterization of errors is required for the efficient processing, evaluation, and assimilation of remotely-sensed surface soil moisture retrievals. However, empirical evidence exists that passive microwave soil moisture retrievals are prone to periodic artifacts which may complicate their application in data assimilation systems (which commonly treat observational errors as being temporally white). In this paper, the link between such temporally-periodic errors and spatial land surface heterogeneity is examined. Both the synthetic experiment and site-specified cases reveal that, when combined with strong spatial heterogeneity, temporal periodicity in satellite sampling patterns (associated with exact repeat intervals of the polar-orbiting satellites) can lead to spurious high frequency spectral peaks in soil moisture retrievals. In addition, the global distribution of the most prominent and consistent 8-day spectral peak in the Advanced Microwave Scanning Radiometer - Earth Observing System soil moisture retrievals is revealed via a peak detection method. Three spatial heterogeneity indicators - based on microwave brightness temperature, land cover types, and long-term averaged vegetation index - are proposed to characterize the degree to which the variability of land surface is capable of inducing periodic error into satellite-based soil moisture retrievals. Regions demonstrating 8-day periodic errors are generally consistent with those exhibiting relatively higher heterogeneity indicators. This implies a causal relationship between spatial land surface heterogeneity and temporal periodic error in remotely-sensed surface soil moisture retrievals.

Fangni Lei↗

NASA NTRS2004

Planetary Transmission Diagnostics

This report presents a methodology for detecting and diagnosing gear faults in the planetary stage of a helicopter transmission. This diagnostic technique is based on the constrained adaptive lifting algorithm. The lifting scheme, developed by Wim Sweldens of Bell Labs, is a time domain, prediction-error realization of the wavelet transform that allows for greater flexibility in the construction of wavelet bases. Classic lifting analyzes a given signal using wavelets derived from a single fundamental basis function. A number of researchers have proposed techniques for adding adaptivity to the lifting scheme, allowing the transform to choose from a set of fundamental bases the basis that best fits the signal. This characteristic is desirable for gear diagnostics as it allows the technique to tailor itself to a specific transmission by selecting a set of wavelets that best represent vibration signals obtained while the gearbox is operating under healthy-state conditions. However, constraints on certain basis characteristics are necessary to enhance the detection of local wave-form changes caused by certain types of gear damage. The proposed methodology analyzes individual tooth-mesh waveforms from a healthy-state gearbox vibration signal that was generated using the vibration separation (synchronous signal-averaging) algorithm. Each waveform is separated into analysis domains using zeros of its slope and curvature. The bases selected in each analysis domain are chosen to minimize the prediction error, and constrained to have the same-sign local slope and curvature as the original signal. The resulting set of bases is used to analyze future-state vibration signals and the lifting prediction error is inspected. The constraints allow the transform to effectively adapt to global amplitude changes, yielding small prediction errors. However, local wave-form changes associated with certain types of gear damage are poorly adapted, causing a significant change in the prediction error. The constrained adaptive lifting diagnostic algorithm is validated using data collected from the University of Maryland Transmission Test Rig and the results are discussed.

Lewicki, David G.↗

DOE OSTI2026

Wasserstein normalized autoencoder for anomaly detection

A novel anomaly detection algorithm is presented. The Wasserstein normalized autoencoder (WNAE) is a normalized probabilistic model that minimizes the Wasserstein distance between the learned probability distribution—a Boltzmann distribution where the energy is the reconstruction error of the autoencoder (AE)—and the distribution of the training data. This algorithm has been developed and applied to the identification of semivisible jets—conical sprays of visible standard model (SM) particles and invisible dark matter states—with the CMS experiment at the CERN LHC. Trained on jets of particles from simulated SM processes, the WNAE is shown to learn the probability distribution of the input data in a fully unsupervised fashion, such that it effectively identifies new physics jets as anomalies. The model exhibits stable, convergent training and recovers strong classification performance for a wide range of signals against the selected background process, for which a standard AE fails because of outlier reconstruction. In addition, the model improves upon standard normalized autoencoders while remaining fully agnostic to the signal. The WNAE directly tackles the problem of outlier reconstruction, a common failure mode of autoencoders in anomaly detection tasks.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

DOE OSTI2021

Experimental decoy-state Bennett-Brassard 1984 quantum key distribution through a turbulent channel

In free-space quantum key distribution (QKD) in turbulent conditions, scattering and beam wandering cause intensity fluctuations which decrease the detected signal-to-noise ratio. This effect can be mitigated by rejecting received bits when the channel's transmittance is below a threshold. Thus, the overall error rate is reduced and the secure key rate increases despite the deletion of bits. In this work, we implement recently proposed selection methods focusing on the prefixed-threshold real-time selection (P-RTS) where a cutoff can be chosen prior to data collection and independently of the transmittance distribution. We perform finite-size decoy-state Bennett-Brassard 1984 QKD in a laboratory setting where we simulate the atmospheric turbulence using an acousto-optical modulator. We show that P-RTS can yield considerably higher secure key rates for a wide range of the atmospheric channel parameters. In addition, we evaluate the performance of the P-RTS method for a realistically finite sample size. We demonstrate that a near-optimal selection threshold can be predetermined even with imperfect knowledge of the channel transmittance distribution parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1973

A technique to eliminate false lock in PCM demodulation

One loop provides error signal which adjusts voltage controlled oscillator. Second loop multiplies input signal with generated in-phase signal. Both signals are integrated over bit period. First loop detects null which indicates lockup, and second loop emphasizes impact signal information.

Kobayashi, H. S.↗

NASA NTRS1977

A model of the 1.6 GHz scatterometer

The performance was studied of the 1.6 GHz airborne scatterometer system which is used as one of several Johnson Space Center (JSC) microwave remote sensors to detect moisture content of soil. The system is analyzed with respect to its antenna pattern and coupling, the signal flow in the receiver data channels, and the errors in the signal outputs. The operational principle and the sensitivity of the system, as well as data handling are also described. The finite cross-polarized gains of all four 1.6 GHz scatterometer antennae are found to have profound influence on the cross-polarized backscattered signal returns. If these signals are not analyzed properly, large errors could result in the estimate of the cross-polarized coefficient. It is also found necessary to make corrections to the variations of the aircraft parameters during data reduction in order to minimize the error in the coefficient estimate. Finally, a few recommendations are made to improve the overall performance of the scatterometer system.

Wang, J. R.↗

NASA NTRS1981

Near optimum delay-line detection filters for serial detection of MSK signals

A method for designing transversal delay-line filter approximations to the matched filter for the serial detection of minimum-shift keyed (MSK) modulated signals is given. Two configurations are characterized in terms of signal-to-noise ratio degradation at a bit error rate (BER) of 10 to the -6th. One is shown to depart less than 0.3 dB from the ideal matched filter performance when its parameter values are optimized. A lumped-element equivalent is also given and shown to provide a degradation of less than 0.4 dB at a BER of 10 to the -6th

Ziemer, R. E.↗

NASA NTRS1984

A Model for the Effectiveness of Aircraft Alerting and Warning Systems

The effectiveness of an alerting system with a single alert was analyzed. The pilot's decision behavior is modeled by the theory of signal detection and therefore accounts for different strengths of cross check information and different pilot criteria. The model includes the effects of the alerting and warning system (CAWS) error rate; the pilot's past experience with the CAWS accuracy; his reliance on the CAWS rather than independent monitoring; missed alerts; and adoption of a minimum error or Neyman-Pearson objective rather than minimum cost objective. It is showwn that for rare events: (1) the expected cost is greatly increased if the pilot ignores the a posteriori information in the existence of an alert; (2) the expected cost is insensitive to CAWS Type 1 errors; and (3) the expected cost is sensitive to CAWS type 2 errors only when the cross check information is ambiguous.

Curry, R. E.↗

NASA NTRS1987

The LAGEOS Lense-Thirring precession and the LAGEOS non-gravitational nodal perturbations. I

After a brief description of the experiment to detect the gravitomagnetic field using high altitude laser ranged artificial satellites, several nongravitational perturbations that affect the LAGEOS nodal longitude are studied. It is shown that the error in the calculated value of the secular nodal precession or the value of the secular nodal precession itself is, for each perturbation, less than 1 percent of the gravitomagnetic drag.

Ciufolini, Ignazio↗

NASA NTRS1994

Telecommunications end-to-end systems monitoring on TOPEX/Poseidon: Tools and techniques

The TOPEX/Poseidon Project Satellite Performance Analysis Team's (SPAT) roles and responsibilities have grown to include functions that are typically performed by other teams on JPL Flight Projects. In particular, SPAT Telecommunication's role has expanded beyond the nominal function of monitoring, assessing, characterizing, and trending the spacecraft (S/C) RF/Telecom subsystem to one of End-to-End Information Systems (EEIS) monitoring. This has been accomplished by taking advantage of the spacecraft and ground data system structures and protocols. By processing both the received spacecraft telemetry minor frame ground generated CRC flags and NASCOM block poly error flags, bit error rates (BER) for each link segment can be determined. This provides the capability to characterize the separate link segments, determine science data recovery, and perform fault/anomaly detection and isolation. By monitoring and managing the links, TOPEX has successfully recovered approximately 99.9 percent of the science data with an integrity (BER) of better than 1 x 10(exp 8). This paper presents the algorithms used to process the above flags and the techniques used for EEIS monitoring.

Calanche, Bruno J.↗

NASA NTRS1994

Comptel measurements of the gamma-ray burst GRB 930131

On 1993 January 31 at 1857:12 Universal Time (UT), the Imaging Compton Telescope COMPTEL onboard the Compton Gamma Ray Observatory (CGRO) detected the cosmic gamma-ray burst GRB 930131. COMPTEL's MeV imaging capability was employed to locate the source to better than 2 deg (1 sigma error radius) within 7 hr of the event, initiating a world-wide search for an optical and radio counterpart. The maximum likelihood position of the burst from the COMPTEL data is alpha(sub 2000) = 12h 18m, delta(sub 2000) = -9 deg 42 min, consistent with independent CGRO-Burst and Transient Source Experiment (CGRO-BATSE) and Energetic Gamma Ray Experiment Telescope (EGRET) locations as well as with the triangulation annulus constructed using BATSE and Ulysses timing data. The combined COMPTEL and EGRET burst data yield a better estimate of the burst location: alpha(sub 2000) = 12h 18m and delta(sub 2000) = -10 deg 21 min, with a 1 sigma error radius of 32 min. In COMPTEL's energy range, this burst was short, consisting of two separate spikes occurring within a approximately 1 s interval with a low intensity tail for approximately 1 s after the second spike. No statistically significant flux is present for a 30 s period after the main part of the burst. This is consistent with the EGRET data. The COMPTEL telescope events indicate a hard, power-law emission extending to beyond 10 MeV with a spectral index of -1.8 +/- 0.4. The rapid fluctuations and high intensities of the gamma-ray flux greater than 10 MeV place the burst object no farther than 250 pc if the burst emission is not beamed.

Ryan, J.↗

NASA NTRS2003

Coronagraphic Amplitude and Phase Correction for Detecting Planets

Detection of earth-like planets around other stars using coronagraphy requires the optical beam into the coronagraph to be extremely uniform in both phase and amplitude. Errors in phase can be corrected using a deformable mirror, and error in amplitude can be corrected using a spatial light modulator, both in the pupil plan,a. These corrections can be combined using a Michelson interferometer. If amplitude corrections of only a few percent range are needed, the required accuracy of 10 (circumflex) -4 can be obtained with spatial light modulators with the modest dynamic range of 8 bits.

Woodgate, Bruce E.↗

NASA NTRS2006

Terrestrial Planet Finder Interferometer Technology Status and Plans

A viewgraph presentation on the technology status and plans for Terrestrial Planet Finder Interferometer is shown. The topics include: 1) The Navigator Program; 2) TPF-I Project Overview; 3) Project Organization; 4) Technology Plan for TPF-I; 5) TPF-I Testbeds; 6) Nulling Error Budget; 7) Nulling Testbeds; 8) Nulling Requirements; 9) Achromatic Nulling Testbed; 10) Single Mode Spatial Filter Technology; 11) Adaptive Nuller Testbed; 12) TPF-I: Planet Detection Testbed (PDT); 13) Planet Detection Testbed Phase Modulation Experiment; and 14) Formation Control Testbed.

Terrestrial Planet Finder (TPF)↗

NASA NTRS2018

Real-Time Parameter Estimation for Flexible Aircraft

A method for estimating aeroelastic stability and control derivatives for flexible aircraft is developed and demonstrated using flight test data for the X-56A subscale demonstrator. The method uses the equation-error approach with frequency-domain data, and can be applied post-flight or in real time during flight. The non-dimensional aeroelastic forces and moments and the explanatory variables (including generalized displacement, rate, and acceleration states for the vibration modes) are estimated using a finite element model and onboard sensor measurements in both a least squares and Kalman filtering framework. The data are then transformed into the frequency domain for parameter estimation using equation error. This method can result in a more efficient analysis than with other iterative methods, and can leverage existing statistical tools for model structure determination, data collinearity detection, combining multiple maneuvers or prior information, and others to improve model quality.

Grauer, Jared A.↗

NASA NTRSDate not supplied

Assessment of Near-Angle Scatter on Exo-Earth Coronagraphy

A first order single surface analysis indicates that, to enable coronagraphic detection and characterization of exo-Earth planets, near angle scatter must be considered when specifying optical surfaces for a potential Habitable World Observatory. Based on arbitrary error budget allocations and using Rayleigh-Rice Vector Scatter Theory, Generalized Harvey-Shack Scalar Scatter Theory, and Greynolds Approximation, ‘placeholder’ specifications for the primary mirror are derived: Static Surface Roughness < 1 nm rms, and Dynamic Surface Roughness < 1 pm PV. These specifications will change once error budget allocations are defined. Analysis does not include scatter from more than just the primary mirror, coating structure, edges, contamination, micrometeoroid impacts, etc.

H. Philip Stahl↗