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DOE OSTI2023

gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes

High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Equation Discovery Using Fast Function Extraction: a Deterministic Symbolic Regression Approach

Advances in machine learning (ML) coupled with increased computational power have enabled identification of patterns in data extracted from complex systems. ML algorithms are actively being sought in recovering physical models or mathematical equations from data. This is a highly valuable technique where models cannot be built using physical reasoning alone. In this paper, we investigate the application of fast function extraction (FFX), a fast, scalable, deterministic symbolic regression algorithm to recover partial differential equations (PDEs). FFX identifies active bases among a huge set of candidate basis functions and their corresponding coefficients from recorded snapshot data. This approach uses a sparsity-promoting technique from compressive sensing and sparse optimization called pathwise regularized learning to perform feature selection and parameter estimation. Furthermore, it recovers several models of varying complexity (number of basis terms). FFX finally filters out many identified models using non-dominated sorting and forms a Pareto front consisting of optimal models with respect to minimizing complexity and test accuracy. Numerical experiments are carried out to recover several ubiquitous PDEs such as wave and heat equations among linear PDEs and Burgers, Korteweg–de Vries (KdV), and Kawahara equations among higher-order nonlinear PDEs. Additional simulations are conducted on the same PDEs under noisy conditions to test the robustness of the proposed approach.

42 ENGINEERING↗

DOE OSTI2021

Open Data and Deep Semantic Segmentation for Automated Extraction of Building Footprints

Advances in machine learning and computer vision, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics, cost-effectively, and at scale. These characteristics are relevant to a variety of urban and energy applications, yet are time consuming and costly to acquire with today’s manual methods. Several recent research studies have shown that in comparison to more traditional methods that are based on features engineering approach, an end-to-end learning approach based on deep learning algorithms significantly improved the accuracy of automatic building footprint extraction from remote sensing images. However, these studies used limited benchmark datasets that have been carefully curated and labeled. How the accuracy of these deep learning-based approach holds when using less curated training data has not received enough attention. The aim of this work is to leverage the openly available data to automatically generate a larger training dataset with more variability in term of regions and type of cities, which can be used to build more accurate deep learning models. In contrast to most benchmark datasets, the gathered data have not been manually curated. Thus, the training dataset is not perfectly clean in terms of remote sensing images exactly matching the ground truth building’s foot-print. A workflow that includes data pre-processing, deep learning semantic segmentation modeling, and results post-processing is introduced and applied to a dataset that include remote sensing images from 15 cities and five counties from various region of the USA, which include 8,607,677 buildings. The accuracy of the proposed approach was measured on an out of sample testing dataset corresponding to 364,000 buildings from three USA cities. The results favorably compared to those obtained from Microsoft’s recently released US building footprint dataset.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2011

Development of the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) Process for Cesium Removal from High-Level Tank Waste

This paper describes the chemical performance of the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process in its current state of development for removal of cesium from the alkaline high-level tank wastes at the Savannah River Site (SRS) in the US Department of Energy (USDOE) complex. Overall, motivation for seeking a major enhancement in performance for the currently deployed CSSX process stems from needs for accelerating the cleanup schedule and reducing the cost of salt-waste disposition. The primary target of the NG-CSSX development campaign in the past year has been to formulate a solvent system and to design a corresponding flowsheet that boosts the performance of the SRS Modular CSSX Unit (MCU) from a current minimum decontamination factor of 12 to 40,000. The chemical approach entails use of a more soluble calixarene-crown ether, called MaxCalix, allowing the attainment of much higher cesium distribution ratios (DCs) on extraction. Concurrently decreasing the Cs-7SB modifier concentration is anticipated to promote better hydraulics. A new stripping chemistry has been devised using a vitrification-friendly aqueous boric acid strip solution and a guanidine suppressor in the solvent, resulting in sharply decreased DCs on stripping. Results are reported herein on solvent phase behavior and batch Cs distribution for waste simulants and real waste together with a preliminary flowsheet applicable for implementation in the MCU. The new solvent will enable MCU to process a much wider range of salt feeds and thereby extend its service lifetime beyond its design life of three years. Other potential benefits of NG-CSSX include increased throughput of the SRS Salt Waste Processing Facility (SWPF), currently under construction, and an alternative modular near-tank application at Hanford.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2011

SOLVENT EXTRACTION RESEARCH AND DEVELOPMENT IN THE U.S. FUEL CYCLE PROGRAM

Treatment or processing of used nuclear fuel to recycle uranium and plutonium has historically been accomplished using the well known PUREX process. The PUREX process has been used on an industrial scale for over 60 years in the nuclear industry. Research is underway to develop advanced separation methods for the recovery of other used fuel components, such as the minor actinides (Np, Am, Cm) for possible transmutation in fast spectrum reactors, or other constituents (e.g. Cs, Sr, transition metals, lanthanides) to help facilitate effective waste management options. This paper will provide an overview of new solvent extraction processes developed for advanced nuclear fuel cycles, and summarize recent experimental results. This will include the utilization of new extractants for selective separation of target metals and new processes developed to selectively recover one or more elements from used fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2014

Automatic Labeling for Entity Extraction in Cyber Security

Timely analysis of cyber-security information necessitates automated information extraction from unstructured text. While state-of-the-art extraction methods produce extremely accurate results, they require ample training data, which is generally unavailable for specialized applications, such as detecting security related entities; moreover, manual annotation of corpora is very costly and often not a viable solution. In response, we develop a very precise method to automatically label text from several data sources by leveraging related, domain-specific, structured data and provide public access to a corpus annotated with cyber-security entities. Next, we implement a Maximum Entropy Model trained with the average perceptron on a portion of our corpus (~750,000 words) and achieve near perfect precision, recall, and accuracy, with training times under 17 seconds.

Automatic Labeling↗

DOE OSTI2013

LL/ILW: Post-Qualification of Old Waste through Non-Destructive Extraction of Barrels from Cement Shields - 13535

Currently there is a large number of radioactive waste drums entombed in cement shields at German nuclear power plants. These concrete containers used in the past for the waste are not approved for the final repository. Compliance with current acceptance criteria of the final repository has to be proven by qualification measures on the waste. To meet these criteria, a new declaration and new packing is necessary. A simple non-destructive extraction of about 2000 drums from their concrete shields is not possible. So different methods were tested to find a way of non-destructive extraction of old waste drums from cement shields and therefore reduce the final repository volume and final repository costs by using a container accepted and approved for Konrad. The main objective was to build a mobile system to offer this service to nuclear plant stations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2013

Peculiarities of highly burned-up NPP SNF reprocessing and new approach to simulation of solvent extraction processes

Substantiation, general description and performance characteristics of a reprocessing flowsheet for WWER-1000 spent fuel with burn-up >60 GW*day/t U is given. Pu and U losses were <0.1%, separation factor > 10{sup 4}; their decontamination factor from γ-emitting fission products was 4*10{sup 4} and 3*10{sup 7}, respectively. Zr, Tc, Np removal was >98% at U and Pu losses <0.05%. A new approach to simulation of extraction equilibrium has been developed. It is based on a set of simultaneous chemical reactions characterized by apparent concentration constants. A software package was created for simulation of spent fuel component distribution in multistage countercurrent extraction processes in the presence of salting out agents. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2013

Gadolinium speciation with Tetradentate, N-donor extractants for minor actinide/lanthanide separation: an XRD, mass spectrometry and EPR study

The hydrophobic organic molecules CyMe{sub 4}-BTPhen (1) and CyMe{sub 4}-BTBP (2) have been developed and tuned over many years to be able to separate the trivalent actinides from the trivalent lanthanides (Ln) selectively in bi-phasic solvent extraction processes for the separation of the long-lived radio-toxic minor actinides from spent nuclear fuel. The ability of these N-donor ligands to perform this separation is poorly understood, as is their speciation with the metal ions when extracted into the organic phase. Our previous work has shown Ln{sup 3+} speciation to be largely 1:2 Ln:L in nature with another small molecule, either water or nitrate, occupying a cavity between the tetradentate bound N-donor ligands. The identity of the small molecule changes across the lanthanide series, and here we continue investigations into this speciation. Complexes of these N-donor ligands with Gd{sup 3+} have been synthesised and characterised by X-ray crystallography, mass spectrometry and EPR spectroscopy. We show that the N-donor ligands have no effect on the electronic configuration of Gd{sup 3+} and that the lanthanide contraction with the steric rigidity of the N-donor ligand appears to determine the size of the cavity between the coordinated ligands. This in turn appears to control the identity of the small molecule on the ninth site in the 1:2 Gd:L species. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2013

New method of uranium and plutonium extraction in reprocessing of the spent nuclear fuel

It is shown that a two-stage process of uranium and plutonium extraction during the reprocessing of spent nuclear fuel solves the problem of obtaining a high-concentrated extract without increasing the loss risk with raffinate and avoids the accumulation of plutonium in the unit. A possible further optimization of the process would be the creation of steps inside the stages.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2012

Assessing Soil Vapor Extraction Remediation Performance and Closure: A Review - 12188

Soil vapor extraction (SVE) is a baseline remediation approach for volatile contaminants. While SVE is generally effective for removal of contaminants from higher permeability portions of the vadose zone, contamination in low-permeability zones can persist due to mass transfer processes that limit the removal effectiveness. Thus, a diminishing rate of contaminant extraction over time is typically observed, yet contamination may remain in low-permeability zones. Under these conditions, SVE performance needs to be evaluated to determine whether the system should be optimized, terminated, or transitioned to another technology to replace or augment SVE. Methodologies have been developed to quantify SVE performance over time and to evaluate the impact of persistent vadose zone contamination sources on groundwater quality. Recently, these methods have applied mass flux/discharge concepts to quantify contaminant source strength. Methods include field measurement techniques using the SVE system to quantify source strength and predictive analyses with analytical and numerical models to evaluate the impact of the contaminant source on groundwater. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Efforts to Improve Efficiency of Extraction Well Operation at the Fernald Preserve, Harrison, Ohio - 16177

The Fernald Preserve, a former uranium processing facility that produced high-purity uranium metal products during the Cold War, is located in southwest Ohio. The facility became a US Department of Energy Office of Legacy Management (LM) site in November 2006, following completion of the Comprehensive Environmental Response, Compensation, and Liability Act environmental remediation and site restoration (with the exception of groundwater). When the site was turned over to LM, approximately 76.5 ha of the Great Miami Aquifer remained contaminated with uranium above the final remediation level of 30 μg/L. Here, uranium contamination is being removed from groundwater in the Great Miami Aquifer through a pump-and-treat operation, which is predicted to continue until 2033. Twenty extraction wells pump about 30 million liters per day. Operation of the system is impacted by iron in the groundwater that promotes iron fouling of the well pumps, motors, and screens. The design of the well field evolved over 21 years and reflected a conservative system that could respond to a wide range of pumping conditions. For instance, some of the extraction wells were sized with pumps and motors that would allow the well to pump up to 1890 L/min (500 gpm) if warranted. The added flexibility, though, came at the cost of operational efficiency. We describe the efforts that have been taken by LM since the Fernald site was transferred to LM to mitigate the operational impacts from the iron fouling aquifer conditions and improve the efficiency of the well-field operation. Variable-frequency drives were installed at six wells to replace flow control valves. Several wells with oversized pumps and motors were changed from 24-hour per day operation to 8-hour per day operation to allow the pumps to operate closer to their design flow rates. Pumps and motors were 'right-sized' at many wells to improve pumping efficiency. The process used to rehabilitate (or clean) well screens was improved, and a process was developed to clean pumps without having to pull them from the well. To reduce pressure drops, improvements were also made to the configuration of the discharge piping. A new control system was installed for each well to allow local control and local tracking of energy used. The amount of energy used daily compared to number of gallons pumped provides a method to assess pump performance and determine when action is necessary to restore well pump efficiency. Additionally, the metrics being employed to help quantify well-field efficiency improvements are described, and the benefits achieved by proactively managing the pump-and-treat operation are presented. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Uranium extraction by apricot shell - 16501

In this paper, use of highly contaminated mine and drainage waters by local residents which lead to increase of doses is described. Uranium concentration in this water is studied. Possibilities of uranium extraction by cheap and local sorbent (almonds, peach and apricot shells) were investigated. It is revealed that apricot shell has very good sorption properties for uranium extraction. Detailed sorption parameters of apricot shell are described. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Complexation and Solvent Extraction Studies of High Valency Actinides by Hard/Soft Donor Schiff Base Ligands

Successful separation of the mid actinides (U, Np, Pu, Am) from other elements is imperative for drastically lowering the long term radiotoxicity of SNF. Ubiquitous to these mid actinides is a wide range of oxidation states (+III, +IV, +V, +VI) where the +V and +VI oxidation states exist in a linear dioxo actinyl cation AnO{sub 2}{sup n+} (O=An=O){sup n+} guaranteeing unique ligand coordination about the equatorial plane. Multidentate Schiff base ligands which possess nitrogen and oxygen donor groups can accommodate the steric demands of the actinyl cations as well as providing selectivity for actinides in a separation process. Group extraction or retention of the mid actinides in a biphasic solvent extraction process can be achieved by complexation of their actinyl species by Schiff base ligands in one phase while all other non actinyl cations are complexed in the other phase. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Causality Extraction from Nuclear Licensee Event Reports Using a Hybrid Framework

In this paper, we proposed a hybrid framework for causality detection and extraction in LER documents. The main contributions are summarized below. We 1) built an LER corpus with 20,129 text samples for causality analysis, 2) developed an interactive tool was developed for labeling cause-effect pairs, 3) built a deep learning-based approach for causal relation detection, and 4) built a knowledge-based cause-effect extraction approach.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

An Overview in the Development of a Multi-Sensor Data Science System for Monitoring a Solvent Extraction Process

To enhance nuclear nonproliferation stewardship, Idaho National Laboratory is building the Beartooth nuclear fuel cycle processing test bed. The Beartooth test bed will allow researchers the opportunity to study nuclear fuel processing operations including the use of centrifugal contactors in solvent extraction processes. The test bed is designed to support data collection and machine learning to monitor process operations. As part of this project, researchers will study data collected from a host of sensors that have not been typically used to monitor solvent extraction processes such as vibration, acoustic, colormetric, and thermal measurement data. The goal of this research is to employ machine learning and data analytics to study the confluence of signals collected from both traditionally and non-traditionally used sensors to provide operator process awareness and discover process anomalies. An overview of planned sensors and experiments that will focus on signal discovery will be presented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

An Overview in the Development of a Multi-Sensor Data Science System for Monitoring a Solvent Extraction Process

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Development of a Multi Sensor Data Science System for Monitoring a Solvent Extraction Process

Idaho National Laboratory is designing and constructing a solvent extraction test bed, Beartooth, as part of a nuclear fuel cycle stewardship initiative. The test bed will provide facilities and equipment for testing novel extraction processes and give early career scientists opportunities to gain skills in performing separations chemistry. The test bed is being uniquely designed to enable machine learning capabilities for the characterization of chemical process operations. One of the intentions of incorporating machine learning methods is to provide process operators with enhanced situational awareness for the optimization of separations techniques and possible detection of a diversion event. As a result, the objective of this Laboratory Directed Research and Development project is to develop a multi-sensor data collections system and implement machine learning techniques on signals from an existing centrifugal contactor cascade to identify equipment usage and process events. This presentation will provide an overview of sensors used and experiments conducted to date.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗