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At least 487 records · Page 27
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 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 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↗
DOE OSTI2020

Development of a Cost-Effective Extraction Process for the Recovery of Heavy and Critical Rare Earth Elements from the Clays and Shales Associated with Coal

The primary objective of the project was to investigate and develop a novel process technology that can extract and concentrate rare earth elements (REE) from coal refuse material, namely shales and clays, to a concentration of greater than or equal to 2% by weight. The extraction and recovery technologies developed in this project leverage the low-cost ion-exchange leaching techniques that are currently applied for commercial heavy rare earth production in South China. In addition to the ion-exchange extraction technology, the project also investigated a novel method of solution concentration and recovery based on ion and/or precipitate flotation.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Pulse Detonation Engine for Advanced Oxy-Combustion of Coal-Based Fuel for Direct Power Extraction Applications

Pressure gain combustion and magnetohydrodynamic (MHD) systems have the potential to provide a step increase in the efficiency of combined-cycle power plants. Specific advantages include a net pressure increase to the system instead of a pressure drop, the high temperature of the detonation waves can increase the efficiency of power extraction compared to other processes, significant thermal energy can be released in a compact region, and the high velocities of the flow increase extraction of electrical power. In summary, a pressure gain combustor coupled with a MHD has the potential to be transformative. Despite the potential advantages, relatively little research has been conducted considering coupled pressure gain combustion systems with MHD systems. With this background and motivation, the overall goal of this effort was to advance the knowledge, technology, and computational tools associated with coupled detonation and MHD systems. A joint experimental and computational approach was used while seeking to accomplish the goals of this work. Specifically, two pulse detonation engines were developed and used for the experiments to produce detonations. Detonation speeds were measured for a variety of flow and fuel conditions (e.g., methane, propane, with coal particles). Preliminary electrical conductivity measurements were collected. An extensive amount of research was performed to identify sensitivities of detonation behaviors to the presence of combustion products. Computationally, a twofold approach was used in this work. First, a solver was developed for solving the governing equations for a reactive flow with coupled detonation and ionization chemistry. The solver was applied to study the impacts of seed material ionization on detonation. Second, a conservation element-solution element (CE-SE) based numerical solver for detonation studies with a reduced reaction mechanism for oxy-methane combustion was developed and verified on standard test cases. Key findings and contributions from this work are as follows. A system was developed for injecting powderized coal, or other seeding material, into a pulse-detonation system. The influence of a combustion product (i.e., CO 2 ) on detonation behavior was identified. Knowledge gained from this work is applicable to devices such as rotating detonation engines, where combustion products mix with fresh reactants. A system for measuring the electrical conductivity of the exhaust from a pulse-detonation engine was developed. The open-source solver, Clawpack, was extended to solve the reactive Euler equations for simulating detonations. A coupled combustion and ionization chemistry was developed in a single chemical kinetic model for methane oxidation. This model can be used to solve coupled MHD and detonation simulations. It was found that parasitic interactions from ionization chemistry with the magnetic field can reduce the detonation velocity by up to 8%, with a potential impact on power extraction of 15%. It is recommended that interactions between the detonation front and MHD field be considered. Higher gas temperatures and velocities were achieved owing to oxy-fuel detonations. Use of radical dissociation reactions in the reduced reaction mechanism, was found to be critical in predicting detonation temperature and velocity accurately.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Diagnostic Testing for COVID-19 Bridging Study for QIAamp Viral RNA Extraction vs Beckman RNAdvance vs Thermofisher MagMAX

This report describes testing that was performed by LANL’s Biological Agent Testing Lab (BATL) to validate modifications to the CDC EUA 2019-Novel Coronavirus (2019- nCoV) Real-Time RT-PCR Diagnostic Panel (EUA-CDC-nCoV-IFU). BATL intends to implement the modifications to increase thoughput for daily testing . BATL validated the viral RNA extraction process, using the orignial component, QIAamp Viral RNA Mini Kit (Cat # 52906) and the new components, Beckman Coulter magnetic 96-well plate RNAdvance Viral kit (Cat # C63510), Thermofisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit (Cat # A48310). Equivalency was demonstrated between the original component and the Beckman Coulter magnetic 96-well plate RNAdvance Viral kit (Cat # C63510). Equivalency was also demonstrated between the original component and the Thermofisher MagMAX Viral/Pathogen Nucleic Acid Isolation Kit (Cat # A48310). Subsequently, substitution of the original component with either of these kits for viral RNA extraction increased BATL’s extraction capability from 100 samples per day to 279 samples per day.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Techno-Economic Analysis of Lithium Extraction from Geothermal Brines

The United States has a large, domestic source of lithium in geothermal fluids, especially at the Salton Sea region of southern California, where estimates of lithium pass-through at geothermal plants exceed 24,000 metric tons per year, based on 2019 geothermal plant operations. Lithium extraction from geothermal brines offers the potential to provide the United States with a secure, domestic supply of lithium to meet the increasing demands of electric vehicles, grid energy storage, portable electronics, and other end-use applications. Additionally, the use of direct extraction technologies allows for a more sustainable lithium supply relative to current evaporative brine and hardrock mining operations in terms of land use, water use, time to market with lithium products, and carbon intensity of operations. This report is part of an effort to assess geothermal brines as a source of commercial lithium supply for the United States. In this study, the National Renewable Energy Laboratory (NREL) reviews and summarizes public technoeconomic analyses of lithium extraction technologies. The work was coordinated with the Critical Minerals Institute at the Colorado School of Mines who focused on supply chain analysis of lithium.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Investigation of Rare Earth Element Extraction from North Dakota Coal-Related Feedstocks (Phase 2 Final Technical Report)

There were four major goals of this project: i) identify promising lignite or lignite-related feedstocks with total rare earth element content above 300 parts per million (ppm), ii) evaluate at the lab and bench-scale the extractability of the REE from the material, iii) determine the processing required to generate REE concentrates in excess of 2 wt%, iv) evaluate the economic feasibility of the process and develop a pathway for commercialization. In the Phase 1 study, work was primarily focused upon resource evaluation and labscale extractability of the REE, with a preliminary techno-economic assessment (TEA) conducted, whereas in the Phase 2 work, the extraction process was conducted at the bench scale, a method for cost-effective generation of higher purity mixed REE concentrates (up to 65%) was developed, and a refined TEA on the bench-scale data for a 1,000 kg coal processing test was conducted.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

A Lithium Feedstock Pathway: Coupled Electrochemical Saltwater Extraction and Direct Battery Materials Manufacturing

Lithium (Li) is one of the critical industrial materials and an indispensable component in manufacturing Li batteries. However, Li resource is limited and geographically uneven in earth’s crust and its mining is not sustainable due to the low efficiency and complicated separation and refining processes. In this work, we develop a one-step technology to electrochemically extract Li from low concentration solutions (brines, seawater or used Li-ion batteries) into a form to directly produce commercial battery materials, eliminating the costly Li separation/purification steps. By using this approach, Li was selectively extracted and converted into battery cathodes (e.g., spinel LiMn 2 O 4 and layered LiNi x Mn y Co z O 2 ) through heat treatment. With the importance of Li-ion batteries to the overall decarbonization strategy, the demonstration of a one-step Li-extraction to a ready-to-use material could expand the access to Li resources at a lower cost by eliminating processing steps.

25 ENERGY STORAGE↗
DOE OSTI2023

Extending Magnetic Core Shell Nanoparticle Extraction Technology to Cesium and Antimony Removal from Geothermal Brines in New Zealand

Our industrial client (Geo40) has developed and deployed a process to remove silica from geothermal fluids and produce a high-margin specialty colloidal silica product comparable to those of market leaders. Geo40 now wishes to explore opportunities to extend their mineral extraction operations to other elements that are present in these brines. Geo40 has identified cesium (Cs) that is present in Ohaaki brines (pH ~8–8.5) at parts per million levels and could be sold to customers if it could be produced at an attractive price. With support from the Department of Energy’s (DOE’s) Geothermal Technologies Office, a simple and highly cost-effective magnetic nanofluid method for extraction of rare earth elements (REEs) from geothermal brine solutions has been developed and demonstrated at the laboratory bench scale at Pacific Northwest National Laboratory (PNNL). Core shell sorbent particles are produced using an iron oxide core particle, which is used to anchor and grow a surrounding adsorbent shell functionalized with a chelating ligand that selectively binds REEs. We extended PNNL’s work by exploring new sorbent shells that are highly selective for Cs. Uptake of Cs was measured as a function of exposure time by analyzing solution samples extracted from batch sorption tests.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

An Evaluation of Main Content Extraction Libraries in Java and Python

Main content extraction is a method to isolate the relevant content from a webpage and remove extraneous content such as advertisements and sidebars. There are many different Python and Java libraries that attempt to perform main content extraction through various algorithms. Due to the differing structures between web pages, there is no “perfect” way to accomplish this task, motivating an evaluation of different main content extraction libraries.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Enhanced PDV waveform search and analysis method using parallel circular-convolution / cross-correlation for improved dynamic surface velocity extraction [Poster]

Previous work on exhaustive search methodologies for extracting best-match parameters pertaining to dynamic surface quantities from PDV was done by cross-correlating synthetically generated PDV waveforms with observed counterparts using the circular-convolution theorem. This work was further developed into an open-source PDV analysis toolkit called CCPDVANALYSIS which expands upon and enhances the previously tested methods by parallelizing serial algorithmic components and incorporating a comprehensive script library for different flavors of instantaneous frequency functions utilized in generating synthetic PDV waveforms. Results of these enhancements have been shown to markedly decrease execution times of exhaustive search and extraction algorithms and produce improved velocity recoveries for low-velocity and dynamically varying velocity signals. The CCPDVANALYSIS script library demonstrates an advanced method for extracting velocities from low-velocity and non-constant velocity signals further extending and improving the methods beyond capabilities of traditional frequency domain tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Surrogate Modelling of 3rd Integer Resonant Extraction at Fermilab Delivery Ring

We present an ongoing work in which a surrogate model is being developed to reproduce the response dynamics of the third-integer resonant extraction process in the Delivery Ring (DR) at Fermilab. This effort is in pursuit of smoothly extracting circulating beam to the Mu2e Experiment s production target, wherein the goal is to extract a uniform slice of the circulating $1e12$ protons in the DR over 25,000 turns (43~ms). The DR contains 3 harmonic sextupoles which excite a third-integer resonance as well as three fast, tune-ramping quadrupole magnets which drive the horizontal tune towards the $29/3$ resonance. In our initial work the surrogate model trains on a semi-analytical simulation provided in the same format as live data. Using Reinforcement Learning (and other potential ML methods), the trained surrogate acts as the environment in which a simple ML control agent could learn to dynamically adjust the quadrupole ramp at 430 break points within the 43 microsecond spill window. The control agent will be hosted on a dedicated Arria 10 FPGA, introducing its own requirements on control agent architecture. In this work we report the accuracy and fidelity of surrogate models in comparison to the response dynamics of the physics simulator.

Narayanan, Aakaash [Fermilab] (ORCID:0000000157944↗