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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Regularized Differentiation for Bioburden Density Estimation in Planetary Protection

In this paper, we propose and investigate the performance of two novel shrinkage estimators for bioburden density estimation in planetary protection. The estimators are based on the regularized differentiation of a cumulative count of colony forming units collected throughout the data collecting session or the life cycle of the entire mission. The regularized differentiation recasts the problem of bioburden density estimation as a linear least squares problem. The least squares problem is then solved through regularization techniques, such as truncated singular value decomposition and penalized least squares. The regularization is necessary to avoid noise amplification during the differentiation of noisy data. The two regularization estimators are compared with four other commonly used estimators to simultaneously evaluate the means of multivariable independent Poisson distributions: the maximum likelihood, noninformative Bayes estimator with Jeffreys prior, Empirical Bayes using conjugate gamma-Poisson model with gamma parameters selected by method of moments, and the Clevenson-Zidek estimator. It is shown through computer-simulated data that the regularized differentiation based on ridge regression has the smallest mean-squared error among all estimators. The analysis of shrinkage mechanism implemented by regularized differentiation is performed, and it is shown that the regularized differentiation amounts to performing a weighted averaging of all the samples. The weights are determined by the regularization parameter automatically selected by the L-curve technique. Since the method of least squares makes no distributional assumptions about the data, it presents an attractive technique for bioburden density estimation when there are concerns about the misspecification of the distributional model. The paper concludes with the analysis of the bioburden data collected during InSight mission and directions for future work.

97 - MATHEMATICS AND COMPUTING↗
NASA NTRS2016

The IPAC Image Subtraction and Discovery Pipeline for the Intermediate Palomar Transient Factory

We describe the near real-time transient-source discovery engine for the intermediate Palomar Transient Factory (iPTF), currently in operations at the Infrared Processing and Analysis Center (IPAC), Caltech. We coin this system the IPAC/iPTF Discovery Engine (or IDE). We review the algorithms used for PSF-matching, image subtraction, detection, photometry, and machine-learned (ML) vetting of extracted transient candidates. We also review the performance of our ML classifier. For a limiting signal-to-noise ratio of 4 in relatively unconfused regions, bogus candidates from processing artifacts and imperfect image subtractions outnumber real transients by approximately equal to 10:1. This can be considerably higher for image data with inaccurate astrometric and/or PSF-matching solutions. Despite this occasionally high contamination rate, the ML classifier is able to identify real transients with an efficiency (or completeness) of approximately equal to 97% for a maximum tolerable false-positive rate of 1% when classifying raw candidates. All subtraction-image metrics, source features, ML probability-based real-bogus scores, contextual metadata from other surveys, and possible associations with known Solar System objects are stored in a relational database for retrieval by the various science working groups. We review our efforts in mitigating false-positives and our experience in optimizing the overall system in response to the multitude of science projects underway with iPTF.

methods: analytical – methods: data analysis –↗
DOE OSTI2013

Quality Research in Radiation Oncology Analysis of Clinical Performance Measures in the Management of Gastric Cancer

Background: The specific aim was to determine national patterns of radiation therapy (RT) practice in patients treated for stage IB-IV (nonmetastatic) gastric cancer (GC). Methods and Materials: A national process survey of randomly selected US RT facilities was conducted which retrospectively assessed demographics, staging, geographic region, practice setting, and treatment by using on-site record review of eligible GC cases treated from 2005 to 2007. Three clinical performance measures (CPMs), (1) use of computed tomography (CT)-based treatment planning; (2) use of dose volume histograms (DVHs) to evaluate RT dose to the kidneys and liver; and (3) completion of RT within the prescribed time frame; and emerging quality indicators, (i) use of intensity modulated RT (IMRT); (ii) use of image-guided tools (IGRT) other than CT for RT target delineation; and (iii) use of preoperative RT, were assessed. Results: CPMs were computed for 250 eligible patients at 45 institutions (median age, 62 years; 66% male; 60% Caucasian). Using 2000 American Joint Committee on Cancer criteria, 13% of patients were stage I, 29% were stage II, 32% were stage IIIA, 10% were stage IIIB, and 12% were stage IV. Most patients (43%) were treated at academic centers, 32% were treated at large nonacademic centers, and 25% were treated at small to medium sized facilities. Almost all patients (99.5%) underwent CT-based planning, and 75% had DVHs to evaluate normal tissue doses to the kidneys and liver. Seventy percent of patients completed RT within the prescribed time frame. IMRT and IGRT were used in 22% and 17% of patients, respectively. IGRT techniques included positron emission tomography (n=20), magnetic resonance imaging (n=1), respiratory gating and 4-dimensional CT (n=22), and on-board imaging (n=10). Nineteen percent of patients received preoperative RT. Conclusions: This analysis of radiation practice patterns for treating nonmetastatic GC indicates widespread adoption of CT-based planning with use of DVH to evaluate normal tissue doses. Most patients completed adjuvant RT in the prescribed time frame. IMRT and IGRT were not routinely incorporated into clinical practice during the 2005-2007 period. These data will be a benchmark for future Quality Research in Radiation Oncology GC surveys.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Chlamydomonas reinhardtii LFO1 Is an IsdG Family Heme Oxygenase

Heme is essential for respiration across all domains of life. However, heme accumulation can lead to toxicity if cells are unable to either degrade or export heme or its toxic by-products. Under aerobic conditions, heme degradation is performed by heme oxygenases, enzymes which utilize oxygen to cleave the tetrapyrrole ring of heme. The HO-1 family of heme oxygenases has been identified in both bacterial and eukaryotic cells, whereas the IsdG family has thus far been described only in bacteria. We identified a hypothetical protein in the eukaryotic green alga Chlamydomonas reinhardtii, which encodes a protein containing an antibiotic biosynthesis monooxygenase (ABM) domain consistent with those associated with IsdG family members. This protein, which we have named LFO1, degrades heme, contains similarities in predicted secondary structures to IsdG family members, and retains the functionally conserved catalytic residues found in all IsdG family heme oxygenases. These data establish LFO1 as an IsdG family member and extend our knowledge of the distribution of IsdG family members beyond bacteria. To gain further insight into the distribution of the IsdG family, we used the LFO1 sequence to identify 866 IsdG family members, including representatives from all domains of life. These results indicate that the distribution of IsdG family heme oxygenases is more expansive than previously appreciated, underscoring the broad relevance of this enzyme family. This work establishes a protein in the freshwater alga Chlamydomonas reinhardtii as an IsdG family heme oxygenase. This protein, LFO1, exhibits predicted secondary structure and catalytic residues conserved in IsdG family members, in addition to a chloroplast localization sequence. Additionally, the catabolite that results from the degradation of heme by LFO1 is distinct from that of other heme degradation products. Using LFO1 as a seed, we performed phylogenetic analysis, revealing that the IsdG family is conserved in all domains of life. Also, C. reinhardtii contains two previously identified HO-1 family heme oxygenases, making C. reinhardtii the first organism shown to contain two families of heme oxygenases. These data indicate that C. reinhardtii may have unique mechanisms for regulating iron homeostasis within the chloroplast.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

SeaWiFS Technical Report Series. Volume 8: Proceedings of the First SeaWiFS Science Team Meeting

The first meeting of the SeaWiFS Science Team was held in preparation for a launch of the SeaStar satellite carrying the SeaWiFS ocean color scanner in the October 1993 time frame. The primary goals of the meeting were: (1) to brief Science Team members, agency representatives, and international collaborators on the status of the mission by representatives from the SeaWiFS Project, the prime contractor Orbital Sciences Corporation (OSC), and the Goddard Distributed Active Archive Center (DAAC); (2) to provide for briefings on the science investigations undertaken by Science Team members and to solicit comments and recommendations from meeting attendees for improvements; and (3) to improve coordination of research and validation activities both inter- and intra-nationally with respect to collection, validation, and application of ocean color data from the SeaWiFS mission. Presentations and recommendations are summarized.

Hooker, Stanford B.↗
NASA NTRS2020

NASA ESDS Citizen Science Data Working Group

This document provides guidelines for legal, policy, and ethical issues; standards for citizen science data collection and management; information on ensuring usability of citizen science data and communication regarding its use; and best practices for long-term archival of citizen science data.Section1 contains a detailed discussion of policy, ethical, and legal considerations influencing citizen science data collection. Section 2 considers standards for documentation, including documentation of instrumentation, procedures, and the data itself. It concludes with a discussion of how citizen science data should be attributed. Section 3 provides guidance about how to ensure citizen science data are collected and stored in a useable way. It also considers how NASA and data producers should notify the scientific community, including citizen scientists and the public, about citizen science datasets and the scientific conclusions reached using them. Finally, Section 4 provides detailed information regarding what should be archived from projects using a citizen science approach, including data and code. It provides guidance about archive location, process, and timeframe, as well as information about data access and distribution services provided by NASA that may be relevant to data producers working with citizen scientists.

Citizen Science↗
DOE OSTI2016

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QC outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.

MENG, XIANWEI↗
DOE OSTI2012

Qualification of the Savannah River National Laboratories Coulometer, Model SRNL-Rev. 2 (Serial # SRNL-003 Coulometer) for use in Process 3401a, Plutonium Assay by Controlled Coulometer

This report discusses the process used to prove in the SRNL-Rev.2 coulometer for isotopic data analysis used in the special plutonium material project. In May of 2012, the PAR 173 coulometer system that had been the workhorse of the Plutonium Assay team since the early 1970s became inoperable. A new coulometer system had been purchased from Savannah River National Laboratory (SRNL) and installed in August of 2011.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2019

NOAA-20 ATMS Status: ATMS SDR Team

Data quality looks better than Suomi-NPP (Suomi National Polar-orbiting Partnership): similar biases. Smaller standard deviation of first guess departures and diagnosed observation errors. Weaker striping signal than Suomi-NPP ATMS (Advanced Technology Microwave Sounder). Improved first guess fits to: temperature observations (AMSU-A (Advanced Microwave Sounding Unit-A), CrIS (Cross-track Infrared Sounder), GPSRO (Global Positioning System Radio Occultation)); Humidity observations (MHS (Microwave Humidity Sounder), GEO CSRs (Geostationary Orbit Clear Sky Radiances)). Indicates improved accuracy of short range temperature and humidity forecasts. Neutral to slightly positive forecast scores.

Sensor Data Record (SDR)↗
DOE OSTI2023

Sensitivity-Driven Experimental Design to Facilitate Control of Dynamical Systems

Control of nonlinear dynamical systems is a complex and multifaceted process. Essential elements of many engineering systems include high-fidelity physics-based modeling, offline trajectory planning, feedback control design, and data acquisition strategies to reduce uncertainties. Here this article proposes an optimization-centric perspective which couples these elements in a cohesive framework. We introduce a novel use of hyper-differential sensitivity analysis to understand the sensitivity of feedback controllers to parametric uncertainty in physics-based models used for trajectory planning. These sensitivities provide a foundation to define an optimal experimental design which seeks to acquire data most relevant in reducing demand on the feedback controller. Our proposed framework is illustrated on the Zermelo navigation problem and a hypersonic trajectory control problem using data from NASA’s X-43 hypersonic flight tests.

42 ENGINEERING↗
DOE OSTI2016

Updated kinematic constraints on a dark disk

We update the method of the Holmberg and Flynn study, including an updated model of the Milky Way’s interstellar gas, radial velocities, an updated reddening map, and a careful statistical analysis, to bound the allowed surface density and scale height of a dark disk. We pay careful attention to the self-consistency of the model, including the gravitational influence of the dark disk on other disk components, and to the net velocity of the tracer stars. We find that the data set exhibits a non-zero bulk velocity in the vertical direction as well as a displacement from the expected location at the Galactic midplane. If not properly accounted for, these features would bias the bound toward low dark disk mass. We therefore perform our analysis two ways. In the first, using the traditional method, we subtract the mean velocity and displacement from the tracers’ phase space distributions. In the second method, we perform a non-equilibrium version of the HF method to derive a bound on the dark disk parameters for an oscillating tracer distribution. Despite updates in the mass model and reddening map, the traditional method results remain consistent with those of HF2000. The second, non-equilibrium technique, however, allows a surface density as large as 14 M{sub ⊙} pc{sup −2} (and as small as 0 M{sub ⊙} pc{sup −2}), demonstrating much weaker constraints. For both techniques, the bound on surface density is weaker for larger scale height. In future analyses of Gaia data it will be important to verify whether the tracer populations are in equilibrium.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1994

Convective flow effects on protein crystal growth

A high-resolution microscopic interferometric setup for the monitoring of protein morphologies has been developed. Growth or dissolution of a crystal can be resolved with a long-term depth resolution of 200 A and a lateral resolution of 2 microns. This capability of simultaneously monitoring the interfacial displacement with high local depth resolution has yielded several novel results. We have found with lysozyme that (1) the normal growth rate is oscillatory, and (2) depending on the impurity content of the solution, the growth step density is either greater or lower at the periphery of a facet than in its center. The repartitioning of Na plus and Cl minus ions between lysozyme solutions and crystals was studied for a wide range of crystallization conditions. A nucleation-growth-repartitioning model was developed, to interpret the large body of data in unified way. The results strongly suggest that (1) the ion to lysozyne ratio in the crystal depends mostly on kinetic rather than crystallographic parameters, and (2) lysozyme crystals possess a salt-rich core with a diameter electron microscopy results appear to confirm this finding, which could have far-reaching consequences for x-ray diffraction studies. A computational model for diffusive-convective transport in protein crystallization has been applied to a realistic growth cell geometry, taking into account the findings of the above repartitioning studies and our kinetics data for the growth of lysozyme. The results show that even in the small cell employed, protein concentration nonuniformities and gravity-driven solutal convection can be significant. The calculated convection velocities are of the same order to magnitude as those found in earlier experiments. As expected, convective transport, i.e., at Og, lysozyme crystal growth remains kinetically limited. The salt distribution in the crystal is predicted to be non-uniform at both 1g and 0g, as a consequence of protein depletion in the solution. Static and dynamic light scattering studies in undersaturated and supersaturated solutions have been performed. Diffusivities in undersaturated solutions, were found to vary with lysozyme concentrations. Depending on the salt concentration, the diffusivities either increase or decrease. Interestingly, the corresponding static scattering intensities behave oppositely, Our current analysis indicates that these changes are inconsistent with aggregation in undersaturated solutions. However, the data are compatible with concentration-dependent changes of the interactions between protein and salt.

Rosenberger, Franz↗
NASA NTRS2008

Understanding Earthquake Fault Systems Using QuakeSim Analysis and Data Assimilation Tools

We are using the QuakeSim environment to model interacting fault systems. One goal of QuakeSim is to prepare for the large volumes of data that spaceborne missions such as DESDynI will produce. QuakeSim has the ability to ingest distributed heterogenous data in the form of InSAR, GPS, seismicity, and fault data into various earthquake modeling applications, automating the analysis when possible. Virtual California simulates interacting faults in California. We can compare output from long time history Virtual California runs with the current state of strain and the strain history in California. In addition to spaceborne data we will begin assimilating data from UAVSAR airborne flights over the San Francisco Bay Area, the Transverse Ranges, and the Salton Trough. Results of the models are important for understanding future earthquake risk and for providing decision support following earthquakes. Improved models require this sensor web of different data sources, and a modeling environment for understanding the combined data.

earthquake simulations↗