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At least 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

ABSTRACT Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences. IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Simultaneous Sensing Error Recovery and Tomographic Inversion Using an Optimization-Based Approach

Tomography can be used to reveal internal properties of a 3D object using any penetrating wave. Advanced tomographic imaging techniques, however, are vulnerable to both systematic and random errors associated with the experimental conditions, which are often beyond the capabilities of the state-of-the-art reconstruction techniques such as regularizations. Because they can lead to reduced spatial resolution and even misinterpretation of the underlying sample structures, these errors present a fundamental obstacle to full realization of the capabilities of next-generation physical imaging. In this work, we develop efficient and explicit recovery schemes of the most common experimental error: movement of the center of rotation during the experiment. We formulate new physical models to capture the experimental setup, and we devise new mathematical optimization formulations for reliable inversion of complex samples. We demonstrate and validate the efficacy of our approach on synthetic data under known perturbations of the center of rotation.

Nonlinear optimization↗
DOE OSTI2025

A Survey on Error-Bounded Lossy Compression for Scientific Datasets

Error-bounded lossy compression has been effective in significantly reducing the data storage/transfer burden while preserving the reconstructed data fidelity very well. Many error-bounded lossy compressors have been developed for a wide range of parallel and distributed use cases for years. They are designed with distinct compression models and principles, such that each of them features particular pros and cons. In this article, we provide a comprehensive survey of emerging error-bounded lossy compression techniques. The key contribution is fourfold. (1) We summarize a novel taxonomy of lossy compression into six classic models. (2) We provide a comprehensive survey of 10 commonly used compression components/modules. (3) We summarized pros and cons of 47 state-of-the-art lossy compressors and present how state-of-the-art compressors are designed based on different compression techniques. (4) We discuss how customized compressors are designed for specific scientific applications and use-cases. We believe this survey is useful to multiple communities including scientific applications, high-performance computing, lossy compression, and big data.

Error-Bounded Lossy Compression↗
DOE OSTI2016

Superdense coding interleaved with forward error correction

Superdense coding promises increased classical capacity and communication security but this advantage may be undermined by noise in the quantum channel. We present a numerical study of how forward error correction (FEC) applied to the encoded classical message can be used to mitigate against quantum channel noise. By studying the bit error rate under different FEC codes, we identify the unique role that burst errors play in superdense coding, and we show how these can be mitigated against by interleaving the FEC codewords prior to transmission. As a result, we conclude that classical FEC with interleaving is a useful method to improve the performance in near-term demonstrations of superdense coding.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Utilizing Adjoint-Based Error Estimates for Surrogate Models to Accurately Predict Probabilities of Events

In thist study, we develop a procedure to utilize error estimates for samples of a surrogate model to compute robust upper and lower bounds on estimates of probabilities of events. We show that these error estimates can also be used in an adaptive algorithm to simultaneously reduce the computational cost and increase the accuracy in estimating probabilities of events using computationally expensive high-fidelity models. Specifically, we introduce the notion of reliability of a sample of a surrogate model, and we prove that utilizing the surrogate model for the reliable samples and the high-fidelity model for the unreliable samples gives precisely the same estimate of the probability of the output event as would be obtained by evaluation of the original model for each sample. The adaptive algorithm uses the additional evaluations of the high-fidelity model for the unreliable samples to locally improve the surrogate model near the limit state, which significantly reduces the number of high-fidelity model evaluations as the limit state is resolved. Numerical results based on a recently developed adjoint-based approach for estimating the error in samples of a surrogate are provided to demonstrate (1) the robustness of the bounds on the probability of an event, and (2) that the adaptive enhancement algorithm provides a more accurate estimate of the probability of the QoI event than standard response surface approximation methods at a lower computational cost.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Measurement Error Variance Estimation in Gamma-Spectroscopy Data using FRAM

The FRAM gamma-ray isotopic analysis code has recently been applied to four Pu data sets and four U data sets, each with relatively well-characterized standard items, in order to estimate the variances of random errors and of item-specific systematic errors. Assay results are available for Pu238, Pu239, Pu240, Pu241, Pu242 (operator entered, not independently measured), Am241, Specific Power, and Pu240eff. For the four U data sets, results are available for the measurands U234, U235, U236 (operator entered, not independently measured), and U238. For example, in Pu data set 1, there are 33 standard reference Pu items, which have well-known nominal/true values (except for a few items). FRAM was used to make approximately 15 repeat measurements for each of the 33 items, so empirical standard deviations can be calculated. In addition, FRAM internally estimates its random error variance using propagation of variance. This paper applies analysis of variance (ANOVA) to separately estimate the repeatability standard deviation and the standard deviation of the item-specific biases δ s in each of the 8 data sets.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

EFCOG Human Performance Improvement Task Group: Task 20-2, Asking Better Error Precursor Questions for Effective Job Planning, Pre-Job Briefs, and Event Investigations

The second principle of human performance states: “error-likely situations are predictable, manageable, and preventable.” An error-likely situation comes into play when task-related factors exceed the capabilities of the individual, creating a mismatch at the point when the individual is “touching” either the physical or the paper plant. The simple presence of adverse conditions cannot be error-likely unless a specific action is to occur within that set of adverse conditions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Implementation Guide for Minimum Required Error Codes in Electric Vehicle Charging Infrastructure

With the growing adoption of Electric Vehicles (EVs), there is an increasing need for a reliable EV charging infrastructure. To help meet this need, the report “Recommendations for Minimum Required Error Codes for Electric Vehicle Charging Infrastructure,” recommends a set of minimum required error codes (MRECs) and their functional and responsibility classification. Charger manufacturers, charging station operators, EV manufacturers, and other stakeholders in the North American market are encouraged to uniformly adopt the MRECs to enhance EV charging error reporting, interpretation, and diagnostics. This document serves as a guide to enable uniform implementation of the MRECs using the Open Charge Point Protocol (OCPP).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Characterizing the Impact of Heliostat Size, Focus Method, and Optical Error on Concentrating Solar Tower Systems

Concentrating Solar Power (CSP) tower systems use heliostat fields to direct solar energy to a central receiver. The efficiency of the heliostat field is crucial for achieving thermal generation targets and is also the largest cost component, making up 30-40% of total project costs. Developers face a tradeoff: reducing heliostat costs may decrease optical performance and increase land use, while improving performance could raise manufacturing costs (through higher precision). The optimal design depends on land, labor, and manufacturing costs. Additionally, inherent performance limitations exist - optical errors result in larger solar images as heliostats move farther from the receiver, increasing spillage and attenuation losses. Ultimately, there exists a point where receiver design power can no longer be achieved at design conditions for a given solar field area. This point depends on key heliostat field design parameters including field layout, heliostats size, focus method, and heliostat optical error. In this work, we explore and characterize the performance trade-offs between heliostat size, focus method, and optical error using Monte Carlo ray-tracing simulations using NREL's high performance computing resources. The goal of this fundamental investigation is to understand practical heliostat design performance impacts that can be used to produce more cost-effective heliostat fields while still achieving plant thermal generation targets.

14 SOLAR ENERGY↗
DOE OSTI2020

Evaluation of the Four-Dimensional Ensemble-Variational Hybrid Data Assimilation with Self-Consistent Regional Background Error Covariance for Improved Hurricane Intensity Forecasts

The feasibility of a hurricane initialization framework based on the Gridpoint Statistical Interpolation (GSI)-based four-dimensional ensemble-variational (GSI-4DEnVar) hybrid data assimilation system for the Hurricane Weather Research and Forecasting model (HWRF) model is evaluated in this study. The system considers the temporal evolution of error covariances via the use of four-dimensional ensemble perturbations that are provided by high-resolution, self-consistent HWRF ensemble forecasts. It is different from the configuration of the GSI-based three-dimensional ensemble-variational (GSI-3DEnVar) hybrid data assimilation system, similar to that used in the operational HWRF, which employs background error covariances provided by coarser-resolution global ensembles from the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS) ensemble Kalman filtering data assimilation system. In addition, our proposed initialization framework discards the empirical intensity correction in the vortex initialization package that is employed by the GSI-3DEnVar initialization framework in operational HWRF. Data assimilation and numerical simulation experiments for Hurricanes Joaquin (2015), Patricia (2015), and Matthew (2016) are conducted during their intensity changes. The impacts of two initialization frameworks on the HWRF analyses and forecasts are compared. It is found that GSI-4DEnVar leads to a reduction in track, minimum sea level pressure (MSLP), and maximum surface wind (MSW) forecast errors in all of the HWRF simulations, compared with the GSI-3DEnVar initialization framework. With assimilating high-resolution observations within the hurricane inner-core region, GSI-4DEnVar can produce the initial hurricane intensity reasonably well without the empirical vortex intensity correction. Further diagnoses with Hurricane Joaquin indicate that GSI-4DEnVar can significantly alleviate the imbalances in the initial conditions and enhance the performance of the data assimilation and subsequent hurricane intensity and precipitation forecasts

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Vetting galactic Leavitt law calibrators using radial velocities: On the variability, binarity, and possible parallax error of 19 long-period cepheids

We investigate the radial velocity (RV) variability and spectroscopic binarity of 19 Galactic long-period (P{sub puls} ≳ 10 days) classical Cepheid variable stars whose trigonometric parallaxes are being measured using the Hubble Space Telescope and Gaia. Our primary objective is to constrain possible parallax error due to undetected orbital motion. Using over 1600 high-precision RVs measured between 2011 and 2016, we find no indication of orbital motion on ≲5 year timescales for 18 Cepheids and determine upper limits on allowed configurations for a range of input orbital periods. The results constrain the unsigned parallax error due to orbital motion to <2% for 16 stars, and <4% for 18. We improve the orbital solution of the known binary YZ Carinae and show that the astrometric model must take into account orbital motion to avoid significant error (∼±100 μarcsec). We further investigate long-timescale (P{sub orb} > 10 years) variations in pulsation-averaged velocity v {sub γ} via a template fitting approach using both new and literature RVs. We discover the spectroscopic binarity of XZ Car and CD Cyg, find first tentative evidence for AQ Car, and reveal KN Cen’s orbital signature. Further (mostly tentative) evidence of time-variable v {sub γ} is found for SS CMa, VY Car, SZ Cyg, and X Pup. We briefly discuss considerations regarding a vetting process of Galactic Leavitt law calibrators and show that light contributions by companions are insignificant for most distance scale applications.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

JWST Noise Floor. II. Systematic Error Sources in JWST NIRCam Time Series

The James Webb Space Telescope (JWST) holds great promise for characterizing atmospheres of transiting exoplanets, potentially providing insights into Earth-sized planets within the habitable zones of M-dwarf host stars if photon-limited performance can be achieved. Here, we discuss the systematic error sources that are expected to be present in grism time-series observations with the NIRCam instrument. We find that pointing jitter and high-gain antenna moves in addition to the detectors’ subpixel crosshatch patterns will produce relatively small variations (less than 6 parts per million, ppm). The time-dependent aperture losses due to thermal instabilities in the optics can also be kept to below 2 ppm. To achieve these low noise values, it is important to employ a sufficiently large (more than 11) extraction aperture. Persistence due to charge-trapping will have a minor (less than 3 ppm) effect on the time series 20 minutes into an exposure and is expected to play a much smaller role than it does for the Hubble Space Telescope WFC3 detectors. We expect detector temperature fluctuations to contribute less than 3 ppm. In total, our estimated noise floor from known systematic error sources is only 9 ppm per visit. We urge caution, however, because unknown systematic error sources could be present in flight and will only be measurable on astrophysical sources such as quiescent stars. We find that reciprocity failure may introduce a perennial instrument offset at the 40 ppm level, so corrections may be needed when a multi-instrument multi-observatory spectrum is stitched together over wide wavelength ranges.

47 OTHER INSTRUMENTATION↗
NASA NTRS2002

Error margin for antenna gain measurements

The specification of measured antenna gain is incomplete without knowing the error of the measurement. Also, unless gain is measured many times for a single antenna or over many identical antennas, the uncertainty or error in a single measurement is only an estimate. In this paper, we will examine in detail a typical error budget for common antenna gain measurements. We will also compute the gain uncertainty for a specific UHF horn test that was recently performed on the Jet Propulsion Laboratory (JPL) antenna range. The paper concludes with comments on these results and how they compare with the 'unofficial' JPL range standard of +/- ?.

error antennas gain↗
NASA NTRS2004

Performance of multi level error correction in binary holographic memory

At the Optical Computing Lab in the Jet Propulsion Laboratory (JPL) a binary holographic data storage system was designed and tested with methods of recording and retrieving the binary information. Levels of error correction were introduced to the system including pixel averaging, thresholding, and parity checks. Errors were artificially introduced into the binary holographic data storage system and were monitored as a function of the defect area fraction, which showed a strong influence on data integrity. Average area fractions exceeding one quarter of the bit area caused unrecoverable errors. Efficient use of the available data density was discussed. .

data storage↗
NASA NTRS2013

Estimating Root Mean Square Errors in Remotely Sensed Soil Moisture over Continental Scale Domains

Root Mean Square Errors (RMSE) in the soil moisture anomaly time series obtained from the Advanced Scatterometer (ASCAT) and the Advanced Microwave Scanning Radiometer (AMSR-E; using the Land Parameter Retrieval Model) are estimated over a continental scale domain centered on North America, using two methods: triple colocation (RMSETC ) and error propagation through the soil moisture retrieval models (RMSEEP ). In the absence of an established consensus for the climatology of soil moisture over large domains, presenting a RMSE in soil moisture units requires that it be specified relative to a selected reference data set. To avoid the complications that arise from the use of a reference, the RMSE is presented as a fraction of the time series standard deviation (fRMSE). For both sensors, the fRMSETC and fRMSEEP show similar spatial patterns of relatively highlow errors, and the mean fRMSE for each land cover class is consistent with expectations. Triple colocation is also shown to be surprisingly robust to representativity differences between the soil moisture data sets used, and it is believed to accurately estimate the fRMSE in the remotely sensed soil moisture anomaly time series. Comparing the ASCAT and AMSR-E fRMSETC shows that both data sets have very similar accuracy across a range of land cover classes, although the AMSR-E accuracy is more directly related to vegetation cover. In general, both data sets have good skill up to moderate vegetation conditions.

Remotely sensed soil moisture validation↗
NASA NTRS2014

Use of an OSSE to Evaluate Background Error Covariances Estimated by the 'NMC Method'

The NMC method has proven utility for prescribing approximate background-error covariances required by variational data assimilation systems. Here, untunedNMCmethod estimates are compared with explicitly determined error covariances produced within an OSSE context by exploiting availability of the true simulated states. Such a comparison provides insights into what kind of rescaling is required to render the NMC method estimates usable. It is shown that rescaling of variances and directional correlation lengths depends greatly on both pressure and latitude. In particular, some scaling coefficients appropriate in the Tropics are the reciprocal of those in the Extratropics. Also, the degree of dynamic balance is grossly overestimated by the NMC method. These results agree with previous examinations of the NMC method which used ensembles as an alternative for estimating background-error statistics.

Data Assimilation↗
NASA NTRS2013

Managing the Risk of Command File Errors

Command File Error (CFE), as defined by the Jet Propulsion Laboratory's (JPL) Mission Operations Assurance (MOA) is, regardless of the consequence on the spacecraft, either: an error in a command file sent to the spacecraft, an error in the process for developing and delivering a command file to the spacecraft, or the omission of a command file that should have been sent to the spacecraft. The risk consequence of a CFE can be mission ending and thus a concern to space exploration projects during their mission operations. A CFE during space mission operations is often the symptom of some kind of imbalance or inadequacy within the system that comprises the hardware & software used for command generation and the human experts involved in this endeavour. As we move into an era of enhanced collaboration with other NASA centers and commercial partners, these systems become more and more complex and hence it is all the more important to formally model and analyze CFEs in order to manage the risk of CFEs. Here we will provide a summary of the ongoing efforts at JPL in this area and also explain some more recent developments in the area of developing quantitative models for the purpose of managing CFE's.

Bayesian Belief Networks↗
NASA NTRS2016

Estimating Model Prediction Error: Should You Treat Predictions as Fixed or Random?

Crop models are important tools for impact assessment of climate change, as well as for exploring management options under current climate. It is essential to evaluate the uncertainty associated with predictions of these models. We compare two criteria of prediction error; MSEP fixed, which evaluates mean squared error of prediction for a model with fixed structure, parameters and inputs, and MSEP uncertain( X), which evaluates mean squared error averaged over the distributions of model structure, inputs and parameters. Comparison of model outputs with data can be used to estimate the former. The latter has a squared bias term, which can be estimated using hindcasts, and a model variance term, which can be estimated from a simulation experiment. The separate contributions to MSEP uncertain (X) can be estimated using a random effects ANOVA. It is argued that MSEP uncertain (X) is the more informative uncertainty criterion, because it is specific to each prediction situation.

model structure uncertainty↗