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All sourcesNASA NTRSDOE OSTI
NASA NTRS1995

SeaWiFS technical report series. Volume 31: Stray light in the SeaWiFS radiometer

Some of the measurements from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) will not be useful as ocean measurements. For the ocean data set, there are procedures in place to mask the SeaWiFS measurements of clouds and ice. Land measurements will also be masked using a geographic technique based on each measurment's latitude and longitude. Each of these masks involves a source of light much brighter than the ocean. Because of stray light in the SeaWiFS radiometer, light from these bright sources can contaminate ocean measurements located a variable number of pixels away from a bright source. In this document, the sources of stray light in the sensor are examined, and a method is developed for masking measurements near bright targets for stray light effects. In addition, a procedure is proposed for reducing the effects of stray light in the flight data from SeaWiFS. This correction can also reduce the number of pixels masked for stray light. Without these corrections, local area scenes must be masked 10 pixels before and after bright targets in the along-scan direction. The addition of these corrections reduces the along-scan masks to four pixels before and after bright sources. In the along-track direction, the flight data are not corrected, and are masked two pixels before and after. Laboratory measurements have shown that stray light within the instrument changes in a direct ratio to the intensity of the bright source. The measurements have also shown that none of the bands show peculiarities in their stray light response. In other words, the instrument's response is uniform from band to band. The along-scan correction is based on each band's response to a 1 pixel wide bright sources. Since these results are based solely on preflight laboratory measurements, their successful implementation requires compliance with two additional criteria. First, since SeaWiFS has a large data volume, the correction and masking procedures must be such that they can be converted into computationally fast algorithms. Second, they must be shown to operate properly on flight data. The laboratory results, and the corrections and masking procedures that derive from them, should be considered as zeroeth order estimates of the effects that will be found on orbit.

Hooker, Stanford B.↗
NASA NTRS2019

Improving the AVHRR Long Term Data Record BRDF Correction

The Long Term Data Record (LTDR) project has the goal of developing a quality and consistent surface reflectance product from coarse resolution optical sensors. This paper focuses on the Advanced Very High Resolution Radiometer (AVHRR) part of the record, using the Moderate Resolution Imaging Spectrometer (MODIS) instrument as a reference. When a surface reflectance time series is acquired from satellites with variable observation geometry, the directional variation generates an apparent noise which can be corrected by modeling the bidirectional reflectance distribution function (BRDF). The VJB (Vermote, Justice and Bréon, 2009) method estimates a target’s BRDF shape using 5 years of observation and corrects for directional effects maintaining the high temporal resolution of the measurement using the instantaneous Normalized Difference Vegetation Index (NDVI). The method was originally established on MODIS data but its viability and optimization for AVHRR data have not been fully explored. In this study we analyze different approaches to find the most robust way of applying the VJB correction to AVHRR data, considering that high noise in the red band (B1) caused by atmospheric effect makes the VJB method unstable. Firstly, our results show that for coarse spatial resolution, where the vegetation dynamics of the target don’t change significantly, deriving BRDF parameters from 15+ years of observations reduces the average noise by up to 7% in the Near Infrared (NIR) band and 6% in the NDVI, in comparison to using 3-year windows. Secondly, we find that the VJB method can be modified for AVHRR data to improve the robustness of the correction parameters and decrease the noise by an extra 8% and 9% in the red and NIR bands with respect to using the classical VJB inversion. We do this by using the Stable method, which obtains the volumetric BRDF parameter (V) based on its NDVI dependency, and then obtains the geometric BRDF parameter (R) through the inversion of just one parameter.

LTDR↗
NASA NTRS2019

Hydrogen Recovery by Methane Pyrolysis to Elemental Carbon

Use of a Sabatier reactor to recover the oxygen from the carbon dioxide exhaled by the crew on the International Space Station has been limited by the loss of the hydrogen contained in the methane it generates. Maximizing the oxygen recovered requires the hydrogen to be recovered from the methane product and recycled back to the Sabatier reactor. We describe the use of a tailored methane pyrolysis reactor to completely recover this hydrogen. The carbon-containing byproduct is elemental carbon, which is generated in the form of easily handled, non-sooty material that may have various uses. The process of creating this tailored carbon vapor deposition process involved exploration of the effects of temperature, pressure, substrate design and other variables to develop a high yield process that cleanly generates the desired products. Reaction kinetics and kinetics modelling were used to specify the temperature, pressure and reactor volume required to achieve the target conversion and to assure that the final average density was as high as possible. Reactor design included the selection of materials that will survive the high temperatures and environment in the pyrolysis reactor, and thermal modeling to achieve the required temperatures with minimum power consumption. The successful construction and demonstration of a brassboard prototype will allow the results of the chemical, thermal and mechanical models to be validated and should provide a useful alternative for a completely closed loop ECLS system. Integration of this technology with state-of-the-art (SOA) Sabatier hardware on ISS requires a complete understanding of the effects of impurities in the product hydrogen on the Sabatier catalyst. SOA Sabatier catalyst was evaluated over short and long-term exposure to anticipated contaminants to identify effects.

Yates, Stephen F.↗
NASA NTRS2019

Hydrogen Recovery by Methane Pyrolysis to Elemental Carbon

Use of a Sabatier reactor to recover the oxygen from the carbon dioxide exhaled by the crew on the International Space Station has been limited by the loss of the hydrogen contained in the methane it generates. Maximizing the oxygen recovered requires the hydrogen to be recovered from the methane product and recycled back to the Sabatier reactor. We describe the use of a tailored methane pyrolysis reactor to completely recover this hydrogen. The carbon-containing byproduct is elemental carbon, which is generated in the form of easily handled, non-sooty material that may have various uses. The process of creating this tailored carbon vapor deposition process involved exploration of the effects of temperature, pressure, substrate design and other variables to develop a high yield process that cleanly generates the desired products. Reaction kinetics and kinetics modelling were used to specify the temperature, pressure and reactor volume required to achieve the target conversion and to assure that the final average density was as high as possible. Reactor design included the selection of materials that will survive the high temperatures and environment in the pyrolysis reactor, and thermal modeling to achieve the required temperatures with minimum power consumption. The successful construction and demonstration of a brassboard prototype will allow the results of the chemical, thermal and mechanical models to be validated and should provide a useful alternative for a completely closed loop ECLS system. Integration of this technology with state-of-the-art (SOA) Sabatier hardware on ISS requires a complete understanding of the effects of impurities in the product hydrogen on the Sabatier catalyst. SOA Sabatier catalyst was evaluated over short and long-term exposure to anticipated contaminants to identify effects.

Yates, Stephen F.↗
DOE OSTI2023

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/μl to 0.1 pg/μl (10 –1 to 10 –4 ). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10 –1 (mean Ct value: 20.3) and 10 –2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2022

Foraging with MUSHROOMS: A Mixed-integer Linear Programming Scheduler for Multimessenger Target of Opportunity Searches with the Zwicky Transient Facility

Electromagnetic follow-up of gravitational-wave detections is very resource intensive, taking up hours of limited observation time on dozens of telescopes. Creating more efficient schedules for follow-up will lead to a commensurate increase in counterpart location efficiency without using more telescope time. Widely used in operations research and telescope scheduling, mixed-integer linear programming is a strong candidate to produce these higher-efficiency schedules, as it can make use of powerful commercial solvers that find globally optimal solutions to provided problems. We detail a new target-of-opportunity scheduling algorithm designed with Zwicky Transient Facility in mind that uses mixed-integer linear programming. We compare its performance to gwemopt, the tuned heuristic scheduler used by the Zwicky Transient Facility and other facilities during the third LIGO–Virgo gravitational-wave observing run. This new algorithm uses variable-length observing blocks to enforce cadence requirements and to ensure field observability, along with having a secondary optimization step to minimize slew time. We show that by employing a hybrid method utilizing both this scheduler and gwemopt, the previous scheduler used, in concert, we can achieve an average improvement in detection efficiency of 3%–11% over gwemopt alone for a simulated binary neutron star merger data set consistent with LIGO–Virgo's third observing run, highlighting the potential of mixed-integer target of opportunity schedulers for future multimessenger follow-up surveys.

B Parazin↗
DOE OSTI2021

Unsupervised learning for identifying events in active target experiments

This article presents novel applications of unsupervised machine learning methods to the problem of event separation in an active target detector, the Active-Target Time Projection Chamber (AT-TPC). The overarching goal is to group similar events in the early stages of the data analysis, thereby improving efficiency by limiting the computationally expensive processing of unnecessary events. The application of unsupervised clustering algorithms to the analysis of two-dimensional projections of particle tracks from a resonant proton scattering experiment on 46 Ar is introduced. We explore the performance of autoencoder neural networks and a pre-trained VGG16 Simonyan and Zisserman (2015) convolutional neural network. We study clustering performance on both data from a simulated 46 Ar experiment, and real events from the AT-TPC detector. We find that a -means algorithm applied to simulated data in the VGG16 latent space forms almost perfect clusters. Additionally, the VGG16+-means approach finds high purity clusters of proton events for real experimental data. Here, we also explore the application of clustering the latent space of autoencoder neural networks for event separation. While these networks show strong performance, they suffer from high variability in their results.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Dual Targeting Factors Are Required for LXG Toxin Export by the Bacterial Type VIIb Secretion System

Bacterial type VIIb secretion systems (T7SSb) are multisubunit integral membrane protein complexes found in Firmicutes that play a role in both bacterial competition and virulence by secreting toxic effector proteins. The majority of characterized T7SSb effectors adopt a polymorphic domain architecture consisting of a conserved N-terminal Leu-X-Gly (LXG) domain and a variable C-terminal toxin domain. Recent work has started to reveal the diversity of toxic activities exhibited by LXG effectors; however, little is known about how these proteins are recruited to the T7SSb apparatus. In this work, we sought to characterize genes encoding domains of unknown function (DUFs) 3130 and 3958, which frequently cooccur with LXG effector-encoding genes. Using coimmunoprecipitation-mass spectrometry analyses, in vitro copurification experiments, and T7SSb secretion assays, we found that representative members of these protein families form heteromeric complexes with their cognate LXG domain and in doing so, function as targeting factors that promote effector export. Additionally, an X-ray crystal structure of a representative DUF3958 protein, combined with predictive modeling of DUF3130 using AlphaFold2, revealed structural similarity between these protein families and the ubiquitous WXG100 family of T7SS effectors. Interestingly, we identified a conserved FxxxD motif within DUF3130 that is reminiscent of the YxxxD/E “export arm” found in mycobacterial T7SSa substrates and mutation of this motif abrogates LXG effector secretion. Overall, our data experimentally link previously uncharacterized bacterial DUFs to type VIIb secretion and reveal a molecular signature required for LXG effector export.

24 antibacterial toxins↗
DOE OSTI2019

Imaging post-stereotactic body radiation therapy responses for hepatocellular carcinoma: typical imaging patterns and pitfalls

Stereotactic body radiation therapy (SBRT) has increased utility in the management of hepatocellular carcinoma (HCC) ranging from local therapy in early-stage HCC not suitable for other focal therapies to end-stage HCC. As the indications for the use of SBRT in HCC expand, diagnostic imaging is being increasingly used to assess response to treatment. The imaging features of tumor response do not parallel those of other focal therapies such as radiofrequency ablation or trans-arterial chemoembolization that immediately devascularize the tumor. The tumor response to SBRT on imaging takes much longer and often shows gradual changes including the reduction of enhancement and size over several months. It is essential to recognize the typical imaging patterns of response, as well as the appearance of focal liver reaction in the non-target liver that can confound image interpretation. The timing of treatment response assessment imaging is fundamental to minimize the potential for false negative response. The purpose of this article is to review the variable post-SBRT imaging features of HCC and adjacent liver parenchyma and discuss the potential pitfalls of imaging evaluation after SBRT for HCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Application of real‐time nonlinear model predictive control for wave energy conversion

Abstract This article presents an approach to implement a Nonlinear Model Predictive Controller (NMPC) in real‐time with a non‐standard cost index. The proposed technique's applications are presented to maximize the energy produced by a Wave Energy Converter (WEC) when the cost index is a non‐quadratic piecewise discontinuous functional of some design variables. The presented framework is based on pseudo‐quadratisation and weight scheduling, which is implemented using the ACADO toolkit for MATLAB/Simulink. The proposed strategy features code generation and deployment on the real‐time target machines for industrial applications. The simulations and experiments confirm the success of the proposed approach in achieving the feasible operation of the NMPC and an optimal power capture by the wave energy converters.

16 TIDAL AND WAVE POWER↗
DOE OSTI2020

Moisture availability mediates the relationship between terrestrial gross primary production and solar-induced chlorophyll fluorescence: Insights from global-scale variations

Effective use of solar-induced chlorophyll fluorescence (SIF) to estimate and monitor gross primary production (GPP) in terrestrial ecosystems requires a comprehensive understanding and quantification of the relationship between SIF and GPP. To date, this understanding is incomplete and somewhat controversial in the literature. Here we derived the GPP/SIF ratio from multiple data sources as a diagnostic metric to explore its global-scale patterns of spatial variation and potential climatic dependence. We found that the growing season GPP/SIF ratio varied substantially across global land surfaces, with the highest ratios consistently found in boreal regions. Spatial variation in GPP/SIF was strongly modulated by climate variables. The most striking pattern was a consistent decrease in GPP/SIF from cold-and-wet climates to hot-and-dry climates. We propose that the reduction in GPP/SIF with decreasing moisture availability may be related to stomatal responses to aridity. Furthermore, we show that GPP/SIF can be empirically modeled from climate variables using a machine learning (random forest) framework, which can improve the modeling of ecosystem production and quantify its uncertainty in global terrestrial biosphere models. Finally, our results point to the need for targeted field and experimental studies to better understand the patterns observed and to improve the modeling of the relationship between SIF and GPP over broad scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

SU-C-19A-07: Influence of Immobilization On Plan Robustness in the Treatment of Head and Neck Cancer with IMPT

Purpose: We evaluated the effect of interposing immobilization devices into the beam's path on the robustness of a head and neck plan. Methods: An anthropomorphic head phantom was placed into a preliminary prototype of a specialized head and neck immobilization device for proton beam therapy. The device consists of a hard low density shell, a custom mold insert, and thermoplastic mask to immobilize the patient's head in the shell. This device was provided by CIVCO Medical Solutions for the purpose of evaluation of suitability for proton beam therapy. See Figure 1. Two pairs of treatment plans were generated. The first plan in each pair was a reference plan including only the anthropomorphic phantom, and the second plan in each pair included the immobilization device. In all other respects the plans within the pair were identical. Results: In the case of the simple plan the degradation of plan robustness was found to be clinically insignificant. In this case, target coverage in the worst case scenario was reduced from 95% of the target volume receiving 96.5% of prescription dose to 95% of the target volume receiving 96.3% of prescription dose by introducing the immobilization device. In the case of the complex plan, target coverage of the boost volume in the worst case scenario was reduced from 95% of the boost target volume receiving 97% of prescription dose to 95% of the boost target volume receiving 83% of prescription dose by introducing the immobilization device. See Figure 2. Conclusion: Immobilization devices may have a deleterious effect on plan robustness. Evaluation of the preliminary prototype revealed a variable impact on the plan robustness depending of the complexity of the case. Brian Morse is an employee of CIVCO Medical Solutions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Online adaptation and verification of VMAT

Purpose: This work presents a method for fast volumetric modulated arc therapy (VMAT) adaptation in response to interfraction anatomical variations. Additionally, plan parameters extracted from the adapted plans are used to verify the quality of these plans. The methods were tested as a prostate class solution and compared to replanning and to their current clinical practice. Methods: The proposed VMAT adaptation is an extension of their previous intensity modulated radiotherapy (IMRT) adaptation. It follows a direct (forward) planning approach: the multileaf collimator (MLC) apertures are corrected in the beam’s eye view (BEV) and the monitor units (MUs) are corrected using point dose calculations. All MLC and MU corrections are driven by the positions of four fiducial points only, without need for a full contour set. Quality assurance (QA) of the adapted plans is performed using plan parameters that can be calculated online and that have a relation to the delivered dose or the plan quality. Five potential parameters are studied for this purpose: the number of MU, the equivalent field size (EqFS), the modulation complexity score (MCS), and the components of the MCS: the aperture area variability (AAV) and the leaf sequence variability (LSV). The full adaptation and its separate steps were evaluated in simulation experiments involving a prostate phantom subjected to various interfraction transformations. The efficacy of the current VMAT adaptation was scored by target mean dose (CTV{sub mean}), conformity (CI{sub 95%}), tumor control probability (TCP), and normal tissue complication probability (NTCP). The impact of the adaptation on the plan parameters (QA) was assessed by comparison with prediction intervals (PI) derived from a statistical model of the typical variation of these parameters in a population of VMAT prostate plans (n = 63). These prediction intervals are the adaptation equivalent of the tolerance tables for couch shifts in the current clinical practice. Results: The proposed adaptation of a two-arc VMAT plan resulted in the intended CTV{sub mean} (Δ ≤ 3%) and TCP (ΔTCP ≤ 0.001). Moreover, the method assures the intended CI{sub 95%} (Δ ≤ 11%) resulting in lowered rectal NTCP for all cases. Compared to replanning, their adaptation is faster (13 s vs 10 min) and more intuitive. Compared to the current clinical practice, it has a better protection of the healthy tissue. Compared to IMRT, VMAT is more robust to anatomical variations, but it is also less sensitive to the different correction steps. The observed variations of the plan parameters in their database included a linear dependence on the date of treatment planning and on the target radius. The MCS is not retained as QA metric due to a contrasting behavior of its components (LSV and AAV). If three out of four plan parameters (MU, EqFS, AAV, and LSV) need to lie inside a 50% prediction interval (3/4—50%PI), all adapted plans will be accepted. In contrast, all replanned plans do not meet this loose criterion, mainly because they have no connection to the initially optimized and verified plan. Conclusions: A direct (forward) VMAT adaptation performs equally well as (inverse) replanning but is faster and can be extended to real-time adaptation. The prediction intervals for the machine parameters are equivalent to the tolerance tables for couch shifts in the current clinical practice. A 3/4—50%PI QA criterion accepts all the adapted plans but rejects all the replanned plans.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1974

A new adaptive classifier using iterative filtering

To cope with signature variability, an algorithm has been defined which will adaptively classify remotely sensed data in the visible and near infrared band. The signal is divided into a space-dependent component and a target-dependent component. The target-dependent component is assumed fixed across the image for each target type. The space-dependent component is estimated iteratively by a weighted, least-squares algorithm. Included are the derivations of the sensor model and the two-dimensional, estimation algorithm.

Actkinson, A. L.↗
NASA NTRS1992

Radar determination of Mars surface properties

Radar studies of Mars have provided measurements of surface texture on scales of centimeters to hundreds of meters and measurements of surface material properties. Texture (rms surface tilts and estimates of small-scale roughness) may be inferred from dispersion and/or polarization of the radar echo; material properties (reflectivity of dielectric constant) are derived from echo strength. Mars is a diverse target; depending on location, rms surface tilts have been found to vary over the range 0.25 to 10 deg while reflectivity covers at least 3 to 13 percent. Plains units are the most variable, having both the smoothest and roughest surfaces, cratered terrain can be considered predictable and 'average' by comparison. Recent data identify scattering by small structures (perhaps rocks on or near the surface) as playing a more important role than previously recognized. Scattering by the residual ice cap near Mars' south pole is particularly unusual. The present state of radar surface studies is summarized.

Simpson, Richard A.↗
NASA NTRS1989

Effect of structured visual environments on apparent eye level

Each of 12 subjects set a binocularly viewed target to apparent eye level; the target was projected on the rear wall of an open box, the floor of which was horizontal or pitched up and down at angles of 7.5 degrees and 15 degrees. Settings of the target were systematically biased by 60% of the pitch angle when the interior of the box was illuminated, but by only 5% when the interior of the box was darkened. Within-subjects variability of the settings was less under illuminated viewing conditions than in the dark, but was independent of box pitch angle. In a second experiment, 11 subjects were tested with an illuminated pitched box, yielding biases of 53% and 49% for binocular and monocular viewing conditions, respectively. The results are discussed in terms of individual and interactive effects of optical, gravitational, and extraretinal eye-position information in determining judgements of eye level.

NASA Center ARC↗
NASA NTRS2016

Point Source Polarimetry with the Gemini Planet Imager: Sensitivity Characterization with T5.5 Dwarf Companion HD 19467 B

Detecting polarized light from self-luminous exoplanets has the potential to provide key information about rotation, surface gravity, cloud grain size, and cloud coverage. While field brown dwarfs with detected polarized emission are common, no exoplanet or substellar companion has yet been detected in polarized light. With the advent of high contrast imaging spectro-polarimeters such as GPI and SPHERE, such a detection may now be possible with careful treatment of instrumental polarization. In this paper, we present 28 minutes of H-band GPI polarimetric observations of the benchmark T5.5 companion HD 19467 B. We detect no polarization signal from the target, and place an upper limit on the degree of linear polarization of pCL99:73% less than 1:7%. We discuss our results in the context of T dwarf cloud models and photometric variability.

Gemini Planet Imager↗