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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from its nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WLN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for proteomics, metabolomics, and lipidomics expression analysis. See Experiment WLN002 for corresponding transcriptome analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, and lipidomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The role of polymer films on the oxidation of magnetite nanoparticles

A detailed investigation about the role of polymer films on the oxidation process of magnetite nanoparticles (∼7 nm diameter), under laser irradiation is performed employing micro Raman spectroscopy. To support this investigation, Fe{sub 3}O{sub 4}-np are synthesized by the co-precipitation method and assembled layer-by-layer with sodium sulfonated polystyrene (PSS). Polymer films (Fe{sub 3}O{sub 4}-np/PSS){sub n} with n=2,3,5,7,10 and 25 bilayers are employed as a model system to study the oxidation process under laser irradiation. Raman data are further processed by principal component analysis. Our findings suggest that PSS protects Fe{sub 3}O{sub 4}-np from oxidation when compared to powder samples, even for the sample with the greater number of bilayers. Further, the oxidation of magnetite to maghemite occurs preferably for thinner films up to 7 bilayers, while the onset for the formation of the hematite phase depends on the laser intensity for thicker films. Water takes part on the oxidation processes of magnetite, the oxidation/phase transformation of Fe{sub 3}O{sub 4}-np is intensified in films with more bilayers, since more water is included in those films. Encapsulation of Fe{sub 3}O{sub 4}-np by PSS in layer-by-layer films showed to be very efficient to avoid the oxidation process in nanosized magnetite. - Graphical abstract: Encapsulation of Fe{sub 3}O{sub 4}-np by PSS in layer-by-layer films avoids the oxidation and phase transformation of nanosized magnetite. - Highlights: • (Fe{sub 3}O{sub 4}-np/PSS){sub n} nanofilms, with n=2 up to 25, where layer-by-layer assembled. • The influence of film architecture on the Fe{sub 3}O{sub 4}-np oxidation was investigated through Raman spectroscopy. • Encapsulation of Fe{sub 3}O{sub 4}-np by PSS showed to be very efficient to avoid the Fe{sub 3}O{sub 4}-np oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Conversion of Nuclear Waste to Molten Glass: Cold-Cap Reactions in Crucible Tests

The feed-to-glass conversion, which comprises complex chemical reactions and phase transitions, occurs in the cold-cap zone during nuclear waste vitrification. Knowledge of the chemistry and physics of feed-to-glass conversion will help us control the conversion path by changing the melter feed makeup to maximize the glass production rate. To investigate the conversion process, we analyzed heat-treated samples of a simulated high-level waste feed using X-ray diffraction, electron probe microanalysis – wavelength dispersive X-ray spectroscopy, leaching tests, and residual anion analysis. Feed dehydration, gas evolution, and borate phase formation occurred at temperatures below 700 °C before the emerging glass-forming melt was completely connected. Above 800 °C, intermediate aluminosilicate phases and quartz particles were gradually dissolving in the continuous borosilicate melt, which expanded into transient foam. Knowledge of the chemistry and physics of feed-to-glass conversion will help us control the conversion path by changing the melter feed makeup to maximize the glass production rate.

Cold-cap↗
DOE OSTI2019

AP-105 Melter Offgas Condensate and EMF Evaporator Concentrate Raman and LIBS Qualitative Evaluation for the use of In-Line Monitoring (Rev. 0)

The Pacific Northwest National Laboratory (PNNL) was tasked to perform Raman spectroscopy and laser induced breakdown spectroscopy (LIBS) testing on the melter off-gas condensate generated during low-activity waste process testing of a sample from Hanford Site tank AP-105 and/or evaporate from evaporation of the condensate. This was a proof-of-principle demonstration that Raman spectroscopy and LIBS have the potential to be used as analytical tools for in-line process analysis of key aqueous phase analytes in radioactive process streams associated with the Hanford Waste Treatment and Immobilization Plant. The work completed under this project complements work completed for WRPS with the development of in-line monitoring systems to characterize and quantify constituents of tank waste following Cs removal and filtration. The WRPS work is currently limited to Raman sensors and utilizes chemometric models for quantification of several anionic species in the sample system. It should be noted that while this approach can be applied to off-gas condensate streams, new chemometric models are needed to accurately quantify analytes under off-gas condensate conditions. The work completed under this project makes timely use of available samples and equipment at PNNL. The project utilized the opportunity to collect off-gas samples from planned AP-105 processing work and included the direct condensate and the evaporate from the DFLAW Radioactive Waste Test Platform. Samples were characterized by instruments already in place at PNNL including a Raman spectrometer optimized for in-line monitoring of flowing and stationary samples as well as a LIBS instrument, which was optimized for static liquid droplet analysis. The ultimate objective was to determine if these techniques could be used to qualitatively characterize analytes present within the off-gas samples. The testing confirmed the use of the Raman as an in-line monitoring system was able to qualitatively observe NO 3 - , NO 2 - , aluminum (as aluminate, Al(OH) 4 - ), SO 4 2- , CrO 4 2- , CO 3 2- , and PO 4 3- in the AP-105 melter feed evaporator condensate samples. The testing also confirmed LIBS as a potential useful technique for in-line monitoring, able to qualitatively detect Na, N, Al, and tentatively Cr and Cl in a simulant stock evaporate solution.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2013

Analysis Of 2H-Evaporator Scale Pot Bottom Sample [HTF-13-11-28H]

Savannah River Remediation (SRR) is planning to remove a buildup of sodium aluminosilicate scale from the 2H-evaporator pot by loading and soaking the pot with heated 1.5 M nitric acid solution. Sampling and analysis of the scale material from the 2H evaporator has been performed so that the evaporator can be chemically cleaned beginning July of 2013. Historically, since the operation of the Defense Waste Processing Facility (DWPF), silicon in the DWPF recycle stream combines with aluminum in the typical tank farm supernate to form sodium aluminosilicate scale mineral deposits in the 2H-evaporator pot and gravity drain line. The 2H-evaporator scale samples analyzed by Savannah River National Laboratory (SRNL) came from the bottom cone sections of the 2H-evaporator pot. The sample holder from the 2H-evaporator wall was virtually empty and was not included in the analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

Impact of residual carbon impurities and gallium vacancies on trapping effects in AlGaN/GaN metal insulator semiconductor high electron mobility transistors

Effects of residual C impurities and Ga vacancies on the dynamic instabilities of AlN/AlGaN/GaN metal insulator semiconductor high electron mobility transistors are investigated. Secondary ion mass spectroscopy, positron annihilation spectroscopy, and steady state and time-resolved photoluminescence (PL) measurements have been performed in conjunction with electrical characterization and current transient analyses. The correlation between yellow luminescence (YL), C- and Ga vacancy concentrations is investigated. Time-resolved PL indicating the C{sub N} O{sub N} complex as the main source of the YL, while Ga vacancies or related complexes with C seem not to play a major role. The device dynamic performance is found to be significantly dependent on the C concentration close to the channel of the transistor. Additionally, the magnitude of the YL is found to be in agreement with the threshold voltage shift and with the on-resistance degradation. Trap analysis of the GaN buffer shows an apparent activation energy of ∼0.8 eV for all samples, pointing to a common dominating trapping process and that the growth parameters affect solely the density of trap centres. It is inferred that the trapping process is likely to be directly related to C based defects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

High-Resolution Mass Spectrometry Quantification: Impact of Differences in Data Processing of Centroid and Continuum Data

High-resolution mass spectrometry (HRMS) in full scan mode acquires all ions present in the sample of interest offering a lot of qualitative information. This, in combination with the improved performance of the new generation HRMS systems, triggers more (bio) analysts to switch from triple quad MS systems to HRMS for quantitative analysis. Quantitative processing of HRMS data is performed based on narrow mass extraction windows rather than on nominal mass product ion chromatograms (SRM or MRM). Optimal processing of HRMS data requires different considerations and software tools and can have an impact on data processing and final results. The selection of centroid versus continuum/profile data for processing, selection of the optimal narrow mass extraction window, using theoretical versus measured accurate mass for the extraction of the ion chromatograms as well as differences in calculations and data handling residing in the different vendor software packages are tackled in the presented manuscript. These differences are illustrated on HRMS data acquired for the same plasma samples on three different platforms, i.e., a Sciex QToF, a Waters QToF, and a Thermo Orbitrap system, and processed in four different software packages, i.e., Sciex Analyst® TF, Waters Masslynx, Waters Unifi, and Thermo Xcalibur. The impact of these differences on quantitative HRMS performance was evaluated on calibration curves of eight small molecule compounds in plasma using four different ways of processing. Simple guidelines are provided for the selection of an optimal mass extraction window for continuum and centroided data. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Multi-Model and Multi-Scale Global Sensitivity Analysis for Identifying Controlling Processes of Complex Systems

An environmental model consists of multiple process level sub-models, and each sub-model represents a process that is key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing hypotheses about one or more processes. To address this problem, this project develops a new method to probe model output sensitivity to competing process models by integrating model averaging methods with variance-based global sensitivity analysis to address uncertainty in process models and parameters. The new method yields three process sensitivity indices. The first one is called first-order process sensitivity index, and it is derived as a single summary measure of relative process importance. Evaluating the index is computationally expensive, because it relies in a Monte Carlo scheme that requires thousands and even millions of model executions. To reduce computational cost, this project develops a computationally efficient, quasi Monte Carlo method, and this method is presented in Chapter 2 of this report with and a numerical example for demonstration. The numerical example shows that the results of the quasi Monte Carlo method are substantially close to those of the full Monte Carlo method, but the computational cost of the quasi Monte Carlo method is only 0.7% of that of the full Monte Carlo method. The second index is called total-effect process sensitivity index, and it measures interactions between different processes. Therefore, this sensitivity index includes the first-order process sensitivity index, and can be used to identify influential processes. On the other hand, the total-effect process sensitivity index can also be used to screen non-influential processes. This is demonstrated by two numerical examples using the Sobol-G* functions and groundwater flow models that consider recharge process, geological process, and snowmelt process. The numerical examples shows that the total-effect process sensitivity index is more informative than the first-order process sensitivity. The derivation of the process sensitivity index and the numerical examples are discussed in Chapter 3. Chapter 4 presents two computationally efficient methods for screening non-influential processes to exclude them from further investigation. The two methods are the multi-model difference-based sensitivity (MMDS) analysis method, which can be implemented using the Latin Hypercube Sampling. The second one is the implementation of MMDS method using a binning method. The numerical example for the Sobol-G* function indicates the two methods are capable of identifying non-influential models, and the numerical examples for the groundwater flow and reactive transport show that the two methods are effective for groundwater problems. However, it should be noted that the two methods are numerical approximations, and they can only be used for screening non-influential processes, not for ranking importance of system processes. All the sensitivity analysis methods are implemented by developing python codes, and the codes are in a software called SAMMPY: a python package for process sensitivity analysis under multiple models. The SAMMPY design and structure are discussed in Chapter 5, and the package is released to the public for free download.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Atom Probe Tomography for Catalysis Applications: A Review

Atom probe tomography is a well-established analytical instrument for imaging the 3D structure and composition of materials with high mass resolution, sub-nanometer spatial resolution and ppm elemental sensitivity. Thanks to recent hardware developments in Atom Probe Tomography (APT), combined with progress on site-specific focused ion beam (FIB)-based sample preparation methods and improved data treatment software, complex materials can now be routinely investigated. From model samples to complex, usable porous structures, there is currently a growing interest in the analysis of catalytic materials. APT is able to probe the end state of atomic-scale processes, providing information needed to improve the synthesis of catalysts and to unravel structure/composition/reactivity relationships. This review focuses on the study of catalytic materials with increasing complexity (tip-sample, unsupported and supported nanoparticles, powders, self-supported catalysts and zeolites), as well as sample preparation methods developed to obtain suitable specimens for APT experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Pr{sup 3+}–Yb{sup 3+} codoped Y{sub 2}O{sub 3} phosphor for display devices

Graphical abstract: Concentration dependence of UC emission intensity for (a) Pr{sup 3+} ions and (b) Yb{sup 3+} ions in doped/codoped Y{sub 2}O{sub 3} phosphors. - Highlights: • Upconversion emission bands with their enhanced emission intensity have been observed on codoping of Yb{sup 3+} ions. • By using Scherrer’s formula and Hall–Williamson plot, the presence of nano-structured crystallites have been identified. • The decay curve analysis for the emitting level has been performed. • The codoped phosphor proves its suitability in making the visible upconverter and display devices. - Abstract: Efficient green colour emitting Pr{sup 3+}–Yb{sup 3+} codoped Y{sub 2}O{sub 3} phosphor prepared by low temperature solution combustion process has been investigated under the excitation with a 980 nm diode laser. Several upconversion emission bands from Pr{sup 3+} ions with their enhanced upconversion emission intensity have been observed on codoping of Yb{sup 3+} ions in the Y{sub 2}O{sub 3}:Pr{sup 3+} system. To identify the phase formation, size of crystallites and strain present in synthesized sample, X-ray diffraction pattern has been recorded. The decay curve analysis for the emitting level has also been performed along with power dependence study to clear the upconversion process. The tunability of colour emitted from the codoped phosphor has been examined which proves its suitability for display devices.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Headspace analysis of foams and fixatives

In the process of decontaminating and decommissioning (D&D) older nuclear facilities, special precautions must be taken with removable or airborne contamination. One possible strategy utilizes foams and fixatives to affix these loose contaminants. Many foams and fixatives are already commercially available, either generically or sold specifically for D&D. However, due to a lack of revelant testing in a radioactive environment, additional verification is needed to confirm that these products not only affix contamination to their surfaces, but also will function in a D&D environment. Several significant safety factors, including flammability and worker safety, can be analyzed through the process of headspace analysis, a technique that analyzes the off gas formed before or during the curing process of the foam/fixative, usually using gas chromatography-mass spectrometry (GC-MS). This process focuses on the volatile components of a chemical, which move freely between the solid/liquid form within the sample and the gaseous form in the area above the sample (the headspace). Between possibly hot conditions in a D&D situation and heat created in a foaming reaction, the volatility of many chemicals can change, and thus different gasses can be released at different times throughout the reaction. This project focused on analysis of volatile chemicals involved in the process of using foams and fixatives to identify any potential hazardous or flammable compounds.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2017

Laser‐ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia

Summary Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen‐fixing ability). The symbiotic interaction between legumes and nitrogen‐fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser‐ablation electrospray ionization mass spectrometry ( LAESI ‐ MS ) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI ‐ MS to explore the well characterized symbiosis between soybean ( Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum . The utilization of ion mobility separation ( IMS ) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI – IMS – MS for the rapid analysis of intact root nodules, uninfected root segments, and free‐living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI – IMS – MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean‐rhizobial symbiosis.

Stopka, Sylwia A.↗
DOE OSTI2016

Global sensitivity analysis in stochastic simulators of uncertain reaction networks

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol’s decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. Here, a sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Omics-Lethal Human Viruses, Ebola Experiment EHUH002

The purpose of this experiment was to evaluate the human host response to Zaire Ebola wild-type virus and mutant virus infection. Samples were obtained from human hepatoma carcinoma cells (HUH-7) infected with Zaire Ebola ΔVP30-WT background for proteome, metabolome, and lipidome expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, and lipidomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Ebola virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Cytogenetic analysis of oral mucosa cells, induced by chlorhexidine, essential oils in ethanolic solution and triclosan mouthwashes

Objectives: The aim of this study was to evaluate DNA damage and cytokinetic defects, proliferative potential and cell death caused by the frequent use of mouthrinses containing chlorhexidine, triclosan and essential oils in ethanolic solution, compared to a placebo mouthwash. Study design: This double-blind, prospective, randomized clinical trial included 80 Caucasian patients. Subjects were divided into four groups: Group I used a mouthrinse, Triclosan; Group II used physiological saline; Group III used chlorhexidine; Group IV a mouthrinse with essential oils in ethanolic solution. All subjects used the mouthrinses for two weeks (15 ml, twice a day, rinsing for 30 s). Two cell samples per subject were collected, before and after mouthrinse use (on day 0 and day 15). Samples were processed as follows: cell collection from cheeks with a cytobrush; cell centrifuge; slide preparation, fixation and staining; and fluorescent microscope analysis. 2000 exfoliated cells were screened for nuclear abnormalities, particularly the presence of micronuclei by means of cytome assay. Results: No significant differences between study times (before and after use of mouthwash) were identified for any of the variables studied (p>0.05). Differences between mouthrinse groups were also compared but no significant differences were found (p>0.05). Conclusions: This study did not observe any genotoxic effect resulting from mouthrinse use. - Highlights: • Mouthrinses are used widely, mainly for their capacity to control dental plaque. • No genotoxic effects from the mouthrinses triclosan, chlorhexidine essential oils solution. • The buccal cytome assay is a sensitive, non-invasive, and low cost technique.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Helioseismology of pre-emerging active regions. III. Statistical analysis

The subsurface properties of active regions (ARs) prior to their appearance at the solar surface may shed light on the process of AR formation. Helioseismic holography has been applied to samples taken from two populations of regions on the Sun (pre-emergence and without emergence), each sample having over 100 members, that were selected to minimize systematic bias, as described in Paper I. Paper II showed that there are statistically significant signatures in the average helioseismic properties that precede the formation of an AR. This paper describes a more detailed analysis of the samples of pre-emergence regions and regions without emergence based on discriminant analysis. The property that is best able to distinguish the populations is found to be the surface magnetic field, even a day before the emergence time. However, after accounting for the correlations between the surface field and the quantities derived from helioseismology, there is still evidence of a helioseismic precursor to AR emergence that is present for at least a day prior to emergence, although the analysis presented cannot definitively determine the subsurface properties prior to emergence due to the small sample sizes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗