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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil and Water Chemistry and Trace Metal Extractability and Speciation in Wetland Soils from Illinois and South Carolina and Stream Sediments from Tennessee

Dataset revised on October 15, 2021. This revision adds sulfur and iron X-ray absorption near-edge structure spectra for the wetland soils and stream sediments from the field areas. It also renames the sample locations in a way that is more intuitive to readers of the companion paper that is under review. Finally, the data filenames and organization have been updated in their labeling to parallel the data sources in the associated paper. The abstract text and methods were also revised to reflect the data that was added to the dataset.Trace metals are essential for microbially-mediated biogeochemical processes occurring in anoxic wetland soils and stream bed sediments, such as denitrification, methanogenesis, and mercury methylation. Low availability of these elements may potentially inhibit key components of anaerobic carbon and nitrogen cycling and contaminant transformation. The solid-phase speciation of trace metals likely plays an important role in controlling their bioavailability. Metal speciation is well studied in contaminated soils and sediments as well as those naturally elevated in trace metals. However, less is known regarding the chemical forms of trace metals in systems having concentrations similar to geological background levels, the very settings where metal limitations may be most prevalent. We have investigated trace metal concentrations, extractability, and solid-phase speciation in three freshwater subsurface aquatic systems: marsh wetland soils, riparian wetland soils, and the sediments of a streambed.Data are provided for marsh wetland soils at Argonne National Laboratory, riparian wetland soils in the Tims Branch watershed at Savannah River National Laboratory, and stream bed sediments from East Fork Poplar Creek near Oak Ridge National Laboratory. Soil and sediment elemental abundances, mineralogy, and extractable nutrients as well as dissolved major elements, anions, trace metals, and nutrients in the overlying surface waters are provided. In addition, the results of sequential chemical extraction for the trace metals cobalt, nickel, copper, and zinc from the soils and sediment are reported as well as X-ray absorption near-edge structure (XANES) spectra in these materials are reported. To aid interpretation of these data, XANES spectra of sulfur in the soils and sediments as well as both XANES and extended X-ray absorption fine structure (EXAFS) spectra of iron in these materials are reported. The data package also includes the XANES spectra of reference standards and a potential interferent in the measurements. All data are provided in text-based CSV format with header sections indicating the data contained in each file and the corresponding units. Note that "u" is used in place of Greek lower case mu to indicate the micro prefix on units.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Optimization of Diffuser (Pre-Scatterer) Configurations for Slow Extraction Loss Reduction at Electrostatic Septa

Uncontrolled beam loss at the electrostatic septum is a performance limit for several existing or planned high power hadron accelerators delivering slow-extracted spills to fixed targets. A passive diffuser, or pre-scatterer, in a suitable configuration has been shown to reduce such beamloss significantly, with the actual gain factor depending on the parameters and details of the extraction process and hardware. In this paper, the optimization of diffuser configurations is investigated for a range of beam energies and extraction conditions, and the sensitivity to the available parameters explored via simulation results. The advantages and limitations of the diffuser are discussed and conclusions drawn concerning the specific case studies of the 8 GeV Fermilab debuncher ring and 400 GeV CERN SPS.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

Higher Multipoles in 3rd Integer Resonance Extraction

The efficiency of slow extraction is becoming a limiting factor, as the demand for delivered beam power is constantly growing. New methods for improving extraction efficiency include folding the extraction separatrix using the higher multipoles. In this report we discuss a simple and effective approach to determine an optimal placement of those multipoles in the storage ring. This allows reduction of the beam losses and therefore, the level of prompt and residual radioactivity in the accelerator components and surrounding buildings by as much as 40% or more. We also explore here manipulating the higher order effects produced in the pure sextupole configurations for the same purpose and demonstrate that similar results can be achieved by only rearranging the sextupole magnets in the lattice.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Extracting Material Property Measurement Data from Scientific Articles

Machine learning-based prediction of material properties is often hampered by the lack of sufficiently large training datasets. The majority of such measurement data is embedded in scientific literature and the ability to automatically extract these data is essential to support the development of reliable property prediction methods. In this work, we describe a methodology for an automatic property extraction framework using material solubility as the target property. We create an annotated dataset containing tags for solubility-related entities using a combination of regular expressions and manual tagging. We then compare five entity recognition models leveraging both token-level and span-level architectures on the task of classifying solute names, solubility values, and solubility units. Additionally, we explore a novel pretraining approach that leverages automated chemical name and quantity extraction tools to generate large datasets that do not rely on intensive manual effort. Finally, we perform an analysis to identify the causes of classification errors.

Panapitiya, Gihan U.↗
DOE OSTI2019

An Investigation of Plume Response to Soil Vapor Extraction and Hypothetical Drum Failure

Core Ideas Soil vapor extraction (SVE) wells are an effective interim remediation technique. Flow and transport modeling assists in evaluation of vapor plume behavior. Plume simulations assuming drum failure and SVE provide a framework for remediation planning. A small borehole subset could be monitored for detection of VOC releases due to drum failure. Soil vapor extraction (SVE) has been used at sites across the Department of Energy complex, including sites where legacy subsurface wastes represent a potential source of groundwater contamination. At Los Alamos National Laboratory (LANL), leakage from waste drums buried at an inactive chemical waste site has created a subsurface vapor plume of volatile organic compounds (VOCs). Soil vapor extraction operation in 2015 and rebound testing through 2017 were successful in reducing the plume's mass and mitigating VOC migration toward the water table. However, the possibility that waste drums could fail and release VOCs could pose a challenge in the future. To explore the impacts of drum failure, as well as the capabilities of SVE remediation, we simulated hypothetical contaminant release scenarios and subsequent SVE remediation. Three‐dimensional subsurface VOC behavior, including advection, diffusion, and plume interactions with topography, were simulated using the porous flow simulator Finite Element Heat and Mass Transfer. Simulations of future site conditions have allowed identification of “sentry” boreholes that can be monitored for early detection in case of drum failure. Sentry boreholes can also be used to set concentration thresholds above which SVE should be initiated. For the LANL site, simulations show that SVE can be started 3 yr following drum failure and remain a viable remediation tool. More broadly, the principles outlined in this work can be used to support remediation planning at other subsurface waste sites. Predictive models of future releases can be analyzed to set concentration threshold values, guide selection of sentry boreholes, and increase operational efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Development of Novel Method for Rapid Extract of Radionuclides from Solution using Polymer Ligand Film [Dissertation]

Accurate and fast determination of the activity of radionuclides in a sample is critical for nuclear forensics and emergency response. Radioanalytical techniques are well established for radionuclides measurement, however, they are slow and labor intensive, requiring extensive radiochemical separations and purification prior to analysis. With these limitations of current methods, there is great interest for a new technique to rapidly process samples. This dissertation describes a new analyte extraction medium called Polymer Ligand Film (PLF) developed to rapidly extract radionuclides. Polymer Ligand Film is a polymer medium with ligands incorporated in its matrix that selectively and rapidly extract analytes from a solution. The main focus of the new technique is to shorten and simplify the procedure necessary to chemically isolate radionuclides for determination by alpha spectrometry or beta counting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or D Cs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction D Cs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.

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

Results of Hg Speciation Testing on 2Q15 Tank 50 and Tank 21 TCLP Extraction Fluid Samples and Tank 49 Material

The Savannah River National Laboratory (SRNL) was tasked with preparing and shipping samples for Hg speciation by Eurofins Frontier Global Sciences, Inc. in Seattle, WA on behalf of the Savannah River Remediation (SRR) Mercury Task Team. The sixth shipment of samples was designated to include SRNL Toxicity Characteristic Leaching Procedure (TCLP) extraction fluids from the 2Q15 Tank 50 and Tank 21 saltstone waste forms as well as Tank 49 material (HTF-49-15-45) collected on May 7, 2015. The TCLP extraction fluid samples were collected from duplicate extractions of two crushed saltstone fractions, one designated as “large” and one designated as “normal”. Both fractions of 2Q15 Tank 50 and Tank 21 saltstones (eight samples) were collected with the minimum possible free headspace and refrigerated prior to final dilution. The Tank 49 sample was left in its stainless steel dip bottle until it was opened and an aliquot diluted 1:100 with Eurofins deionized water on May 21, 2015. Following initial dilution in the Shielded Cells, the diluted Tank 49 sample was immediately moved to refrigeration and kept in the dark until prepared for shipment to Eurofins.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Extractant Design by Covalency

This project aims to provide an electronic structure-to-function understanding of extractants for actinide selective separation processes. The research entails a multi-disciplinary approach that integrates chemical syntheses, structural determination, K-edge X-ray Absorption Spectroscopy (XAS), and Density Functional Theory (DFT) calculations. In FY15, the project reached the final stage of testing the extraction performance of a new ligand design and preparing an americium-extractant complex for analysis.

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

Development of Solvent Extraction Approach to Recycle Enriched Molybdenum Material

Argonne National Laboratory, in cooperation with Oak Ridge National Laboratory and NorthStar Medical Technologies, LLC, is developing a recycling process for a solution containing valuable Mo-100 or Mo-98 enriched material. Previously, Argonne had developed a recycle process using a precipitation technique. However, this process is labor intensive and can lead to production of large volumes of highly corrosive waste. This report discusses an alternative process to recover enriched Mo in the form of ammonium heptamolybdate by using solvent extraction. Small-scale experiments determined the optimal conditions for effective extraction of high Mo concentrations. Methods were developed for removal of ammonium chloride from the molybdenum product of the solvent extraction process. In large-scale experiments, very good purification from potassium and other elements was observed with very high recovery yields (~98%).

36 MATERIALS SCIENCE↗
DOE OSTI2015

Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames

This dissertation presents research on addressing some of the contemporary challenges in the analysis of vector fields—an important type of scientific data useful for representing a multitude of physical phenomena, such as wind flow and ocean currents. In particular, new theories and computational frameworks to enable consistent feature extraction from vector fields are presented. One of the most fundamental challenges in the analysis of vector fields is that their features are defined with respect to reference frames. Unfortunately, there is no single “correct” reference frame for analysis, and an unsuitable frame may cause features of interest to remain undetected, thus creating serious physical consequences. This work develops new reference frames that enable extraction of localized features that other techniques and frames fail to detect. As a result, these reference frames objectify the notion of “correctness” of features for certain goals by revealing the phenomena of importance from the underlying data. An important consequence of using these local frames is that the analysis of unsteady (time-varying) vector fields can be reduced to the analysis of sequences of steady (timeindependent) vector fields, which can be performed using simpler and scalable techniques that allow better data management by accessing the data on a per-time-step basis. Nevertheless, the state-of-the-art analysis of steady vector fields is not robust, as most techniques are numerical in nature. The residing numerical errors can violate consistency with the underlying theory by breaching important fundamental laws, which may lead to serious physical consequences. This dissertation considers consistency as the most fundamental characteristic of computational analysis that must always be preserved, and presents a new discrete theory that uses combinatorial representations and algorithms to provide consistency guarantees during vector field analysis along with the uncertainty visualization of unavoidable discretization errors. Together, the two main contributions of this dissertation address two important concerns regarding feature extraction from scientific data: correctness and precision. The work presented here also opens new avenues for further research by exploring more-general reference frames and more-sophisticated domain discretizations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Towards a method of rapid extraction of strontium-90 from urine: urine pretreatment and alkali metal removal

A technical program to support the Centers of Disease Control and Prevention is being developed to provide an analytical method for rapid extraction of Sr-90 from urine, with the intent of assessing the general population’s exposure during an emergency response to a radiological terrorist event. Results are presented on the progress in urine sample preparation and chemical separation steps that provide an accurate and quantitative detection of Sr-90 based upon an automated column separation sequence and a liquid scintillation assay. Batch extractions were used to evaluate the urine pretreatment and the column separation efficiency and loading capacity based upon commercial, extractant-loaded resins. An efficient pretreatment process for decolorizing and removing organics from urine without measurable loss of radiostrontium from the sample was demonstrated. In addition, the Diphonix® resin shows promise for the removal of high concentrations of common strontium interferents in urine as a first separation step for Sr-90 analysis.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2011

Extraction of GEN at Q 2 = 1 (GeV/c) 2 from Measurements of polarized He(pol. e, e')

The neutron electric form factor, GEN , is extracted for the first time at Q 2 = 1 (GeV/c) 2 from polarized 3 $\vec{He}$ ($\vec{e}$ ,e ') measurements in Hall A at Jefferson Lab. By getting the ratio of asymmetries in longitudinal and transverse quasi-elastic 3 $\vec{He}$($\vec{e}$,e ' ), the electric and magnetic contributions can be separated. The proton and neutron contributions to the 3 He quasi-elastic response functions are calculated in PWIA by Salme? et al., and the neutron electric form factor can be extracted. This method of inclusive scattering becomes feasible for the first time due to the falloff of the other form factors at high Q 2 while G$n\atop{E}$ keeps increasing in units of the dipole form factor. Approximately, 20% uncertainty is achieved in the extraction largely contributed by the statistical uncertainties from 3 days of data-taking. All aspects of the measurement will be discussed in this thesis including theoretical model, experiment setup and the details in the analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Extraction, -scrub, -strip test results from the interim salt disposition program macrobatch 10 tank 21H qualification samples

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Macrobatch (Salt Batch) 10 for the Interim Salt Disposition Program (ISDP). The Salt Batch 10 characterization results were previously reported.ii,iii An Extraction, -Scrub, -Strip (ESS) test was performed to determine cesium distribution ratios (D(Cs)) and cesium concentration in the strip effluent (SE) and decontaminated salt solution (DSS) streams; this data will be used by Tank Farm Engineering to project a cesium decontamination factor (DF). This test used actual Tank 21H material, and a sample of the NGS Blend solvent currently being used at the Modular Caustic-Side Solvent Extraction Unit (MCU). The ESS test showed acceptable performance with an extraction D(Cs) value of 110. This value is consistent with results from previous salt batch ESS tests using similar solvent formulations. This is better than the predicted value of 39.8 from a recently created D(Cs) model.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2019

Extraction, Scrub, and Strip Test Results from The Interim Salt Disposition Program Macrobatch 11 Tank 21H Qualification Samples

Savannah River National Laboratory (SRNL) analyzed samples from Tank 21H in support of qualification of Macrobatch (Salt Batch) 11 for the Interim Salt Disposition Program (ISDP). The Salt Batch 11 characterization results were previously reported. An Extraction, Scrub, and Strip (ESS) test was performed to determine cesium distribution ratios (D(Cs)) and cesium concentration in the strip effluent (SE) and decontaminated salt solution (DSS) streams; this data will be used by Tank Farm Engineering to project a cesium decontamination factor (DF). This test used actual Tank 21H material, and a sample of the Next Generation Solvent (NGS) Blend solvent currently being used at the Modular Caustic-Side Solvent Extraction Unit (MCU). The ESS test showed acceptable performance with an extraction D(Cs) value of 117. This value is consistent with results from previous salt batch ESS tests using similar solvent formulations. This cesium removal efficiency is better than the predicted value of 50.8 from a recently created D (Cs) model.

Peters, T.↗
DOE OSTI2019

Enhanced Light Extraction from Low Cost White OLEDs Fabricated on Novel Patterned Substrates” (Final Report)

Organic LEDs (OLEDs) are a very attractive emerging solid state lighting (SSL) technology. Currently, one of the main challenges is to increase the extraction of the light generated inside the OLED into the forward (viewing) hemisphere. In conventional OLEDs fabricated on a transparent flat anode coated on glass the outcoupling factor is only about 20%. About 50% of the light is lost at the metal cathode (surface plasmon excitation), and waveguided internally in the organic layers and the transparent anode. Another ~30% is waveguided in the substrate to its edges. The research addressed this issue of outcoupling by evaluating OLEDs fabricated on corrugated plastic substrates manufactured in a cost-effective approach. It demonstrated that the outcoupling from such OLEDs can exceed 50% by mitigating plasmon–related loss and internal waveguiding, even without the addition of a microlens array or a hemispherical lens, either of which extracts the light trapped in the substrate. Simulations conducted in parallel with the experimental effort demonstrated how the corrugation assists in the outcoupling. The project also evaluated the role of the corrugation pitch and height in determining the outcoupling factor and other properties of the OLEDs. The technical effectiveness and economic feasibility of the project lie in the patterning of the extracting plastic substrates in an approach that is scalable to roll-to-roll (R2R) manufacturing. R2R processes are drastically lower-cost than batch or single-unit fabrication. The corrugated plastic substrates studied are part of an integrated substrate that includes also a microlens array at the air-side of the substrate and a conductive electrode. The project that was a university-industry collaboration is of major benefit to the public as it demonstrates the feasibility of manufacturing highly efficient OLEDs for SSL in a R2R process, which would drastically reduce the manufacturing cost and increase production in the USA. SSL is efficient and environmentally-friendly. It reduces electricity consumption, and hence lighting cost.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data

Standard of practice approaches to time series cluster analysis involve careful feature engineering, often utilizing expert input to tune and select features by hand. In many cases, expert input may not be readily available, or there may not yet exist a community consensus on the ideal features for a given application. This paper compares the results of several cluster analysis methods, using both hand selected features and those extracted automatically, when applied to large geospatial time series telematics data from commercial trucking fleets. The impacts of feature selection, dimensionality reduction, and choice of clustering algorithm on the quality of clustering results are explored. Results from this analysis confirm prior results that domain agnostic features are competitive with the hand engineered features with respect to clustering quality metrics. These results also provide new insight into the most successful strategies for identifying structure in large unstructured vehicle telematics data, and suggest that time series clustering using automatic feature extraction can be an effective approach to extract structure from large scale geospatial time series data in cases when hand selected features are not available.

33 ADVANCED PROPULSION SYSTEMS↗