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DOE OSTI2022

Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures

Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.

mass spectrometry, FTICR, FTMS, ultrahigh mass res↗

DOE OSTI2021

ClimateNet: an expert-labeled open dataset and deep learning architecture for enabling high-precision analyses of extreme weather

Abstract. Identifying, detecting, and localizing extreme weather events is a crucial first step in understanding how they may vary under different climate change scenarios. Pattern recognition tasks such as classification, object detection, and segmentation (i.e., pixel-level classification) have remained challenging problems in the weather and climate sciences. While there exist many empirical heuristics for detecting extreme events, the disparities between the output of these different methods even for a single event are large and often difficult to reconcile. Given the success of deep learning (DL) in tackling similar problems in computer vision, we advocate a DL-based approach. DL, however, works best in the context of supervised learning – when labeled datasets are readily available. Reliable labeled training data for extreme weather and climate events is scarce. We create “ClimateNet” – an open, community-sourced human-expert-labeled curated dataset that captures tropical cyclones (TCs) and atmospheric rivers (ARs) in high-resolution climate model output from a simulation of a recent historical period. We use the curated ClimateNet dataset to train a state-of-the-art DL model for pixel-level identification – i.e., segmentation – of TCs and ARs. We then apply the trained DL model to historical and climate change scenarios simulated by the Community Atmospheric Model (CAM5.1) and show that the DL model accurately segments the data into TCs, ARs, or “the background” at a pixel level. Further, we show how the segmentation results can be used to conduct spatially and temporally precise analytics by quantifying distributions of extreme precipitation conditioned on event types (TC or AR) at regional scales. The key contribution of this work is that it paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data using a curated expert-labeled dataset – ClimateNet. ClimateNet and the DL-based segmentation method provide several unique capabilities: (i) they can be used to calculate a variety of TC and AR statistics at a fine-grained level; (ii) they can be applied to different climate scenarios and different datasets without tuning as they do not rely on threshold conditions; and (iii) the proposed DL method is suitable for rapidly analyzing large amounts of climate model output. While our study has been conducted for two important extreme weather patterns (TCs and ARs) in simulation datasets, we believe that this methodology can be applied to a much broader class of patterns and applied to observational and reanalysis data products via transfer learning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Machine learning and deep learning tools for the automated capture of cancer surveillance data

The National Cancer Institute and the Department of Energy strategic partnership applies advanced computing and predictive machine learning and deep learning models to automate the capture of information from unstructured clinical text for inclusion in cancer registries. Applications include extraction of key data elements from pathology reports, determination of whether a pathology or radiology report is related to cancer, extraction of relevant biomarker information, and identification of recurrence. With the growing complexity of cancer diagnosis and treatment, capturing essential information with purely manual methods is increasingly difficult. These new methods for applying advanced computational capabilities to automate data extraction represent an opportunity to close critical information gaps and create a nimble, flexible platform on which new information sources, such as genomics, can be added. This will ultimately provide a deeper understanding of the drivers of cancer and outcomes in the population and increase the timeliness of reporting. These advances will enable better understanding of how real-world patients are treated and the outcomes associated with those treatments in the context of our complex medical and social environment.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

New Constraints on the Melting Temperature and Phase Stability of Shocked Iron up to 270 GPa Probed by Ultrafast X-Ray Absorption Spectroscopy

Studying the properties and phase diagram of iron at high-pressure and high-temperature conditions has relevant implications for Earth’s inner structure and dynamics and the temperature of the inner core boundary (ICB) at 330 GPa. Also, a hexagonal-closed packed to body-centered cubic (bcc) phase transition has been predicted by many theoretical works but observed only in a few experiments. The recent coupling of high-power laser with advanced x-ray sources from synchrotrons allows for novel approaches to address these issues. Here, we present a study on shock compressed iron up to 270 GPa and 5800 K probed by single-pulse (100 ps FWHM) x-ray absorption spectroscopy (XAS). Based on the analysis of the XAS spectra, we provide structural identification and bulk temperature measurements along the Hugoniot up to the melting. These results rule out the predicted transition to a high-temperature bcc phase and allow one to discriminate among existing equations of state models and melting curves. In particular, we report the first bulk temperature measurement in shock compressed iron on the melting plateau at 240(20) GPa and 5345(600) K. The melting curve resulting from our work extrapolates to a temperature of 6202(514) K at 330 GPa and represents a refined upper bound for the ICB temperature. Published by the American Physical Society 2024

Balugani, S.↗

DOE OSTI2021

Mapathons versus automated feature extraction: a comparative analysis for strengthening immunization microplanning

Background: Social instability and logistical factors like the displacement of vulnerable populations, the difficulty of accessing these populations, and the lack of geographic information for hard-to-reach areas continue to serve as barriers to global essential immunizations (EI). Microplanning, a population-based, healthcare intervention planning method has begun to leverage geographic information system (GIS) technology and geospatial methods to improve the remote identification and mapping of vulnerable populations to ensure inclusion in outreach and immunization services, when feasible. We compare two methods of accomplishing a remote inventory of building locations to assess their accuracy and similarity to currently employed microplan line-lists in the study area. Methods: The outputs of a crowd-sourced digitization effort, or mapathon, were compared to those of a machine-learning algorithm for digitization, referred to as automatic feature extraction (AFE). The following accuracy assessments were employed to determine the performance of each feature generation method: (1) an agreement analysis of the two methods assessed the occurrence of matches across the two outputs, where agreements were labeled as “befriended” and disagreements as “lonely”; (2) true and false positive percentages of each method were calculated in comparison to satellite imagery; (3) counts of features generated from both the mapathon and AFE were statistically compared to the number of features listed in the microplan line-list for the study area; and (4) population estimates for both feature generation method were determined for every structure identified assuming a total of three households per compound, with each household averaging two adults and 5 children. Results: The mapathon and AFE outputs detected 92,713 and 53,150 features, respectively. A higher proportion (30%) of AFE features were befriended compared with befriended mapathon points (28%). The AFE had a higher true positive rate (90.5%) of identifying structures than the mapathon (84.5%). The difference in the average number of features identified per area between the microplan and mapathon points was larger (t = 3.56) than the microplan and AFE (t = -2.09) (alpha = 0.05). Conclusions: Our findings indicate AFE outputs had higher agreement (i.e., befriended), slightly higher likelihood of correctly identifying a structure, and were more similar to the local microplan line-lists than the mapathon outputs. These findings suggest AFE may be more accurate for identifying structures in high-resolution satellite imagery than mapathons. However, they both had their advantages and the ideal method would utilize both methods in tandem.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Joint Survey Processing. I. Compact Oddballs in the COSMOS Field—Low-luminosity Quasars at z > 6?

The faint-end slope of the quasar luminosity function at z ~ 6 and its implication on the role of quasars in reionizing the intergalactic medium at early times has been an outstanding problem for some time. The identification of faint high-redshift quasars with luminosities of <10 44.5 erg s –1 is challenging. They are rare (few per square degree), and the separation of these unresolved quasars from late-type stars and compact star-forming galaxies is difficult from ground-based observations alone. In addition, source confusion becomes significant at >25 mag, with ~30% of sources having their flux contaminated by foreground objects when the seeing resolution is ~0''.7. We mitigate these issues by performing a pixel-level joint processing of ground and space-based data from Subaru/Hyper-SuprimeCam (HSC) and Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS). We create a deconfused catalog over the 1.64 deg 2 of the COSMOS field, after accounting for spatial varying point-spread functions and astrometric differences between the two data sets. We identify twelve low-luminosity (M UV ~ –21 mag) z > 6 quasar candidates through (i) their red color measured between ACS/F814W and HSC/i band and (ii) their compactness in the space-based data. Nondetections of our candidates in Hubble DASH data argues against contamination from late-type stars. Our constraints on the faint end of the quasar luminosity function at z ~ 6.4 suggest a negligibly small contribution to reionization compared to the star-forming galaxy population. The confirmation of our candidates and the evolution of number density with redshift could provide better insights into how supermassive galaxies grew in the first billion years of cosmic time.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

PyFLEXTRKR: a flexible feature tracking Python software for convective cloud analysis

Abstract. This paper describes the new open-source framework PyFLEXTRKR (Python FLEXible object TRacKeR), a flexible atmospheric feature tracking software package with specific capabilities to track convective clouds from a variety of observations and model simulations. This software can track any atmospheric 2D objects and handle merging and splitting explicitly. The package has a collection of multi-object identification algorithms, scalable parallelization options, and has been optimized for large datasets including global high-resolution data. We demonstrate applications of PyFLEXTRKR on tracking individual deep convective cells and mesoscale convective systems from observations and model simulations ranging from large-eddy resolving (∼100s m) to mesoscale (∼10s km) resolutions. Visualization, post-processing, and statistical analysis tools are included in the package. New Lagrangian analyses of convective clouds produced by PyFLEXTRKR applicable to a wide range of datasets and scales facilitate advanced model evaluation and development efforts as well as scientific discovery.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Web-based Preprocessing and Visualization of 3D FIB Tomography Data for Nuclear Fuel Characterization

Three-dimensional (3D) focused ion beam (FIB) tomography enables reconstruction of internal nuclear fuel features that can't be fully evaluated through surface imaging alone. This capability supports characterization of fuel constituents and defects under thermal and irradiation conditions relevant to microreactor development. However, large tomography datasets can create data-handling, loading, and visualization challenges, especially when image-stack preparation and file conversion must be completed with separate tools. The Computational Ultraspatial Tomography Toolkit for High-Resolution Object Analysis Tools (CUTTRHOAT) is an open-source web application being developed to display FIB tomography datasets available through the Nuclear Research Data System (NRDS). The current alpha version requires prepared HDF5 datasets and has limited integrated data-preparation capabilities. This project improves CUTTHROAT by adding dataset-folder selection, automatic input detection, dataset scanning, missing-slice identification, blank-slice insertion, and image-stack-to-HDF5 conversion. Two applications will be compared: the baseline CUTTHROAT alpha workflow and the updated application containing the integrated data-handling and preprocessing functions. Evaluation will consider dataset detection accuracy, conversion success, loading time, rendering responsiveness, application stability, and user interaction. Preliminary results demonstrate successful loading of existing HDF5 files and converted image stacks, while testing also identified performance reductions caused by excessive blank-slice generation. The updated workflow reduces reliance on external preparation tools and supports more direct movement from image stacks to color-code 3D visualization. Future work includes refining missing-slice handling, integrating additional preprocessing functions, like a denoising feature, parsing TIFF metadata for automatic voxel scaling, and adding manual X, Y, and Z voxel-spacing inputs for PNG and JPEG.

36 - MATERIALS SCIENCE↗

DOE OSTI2021

Phase effects from strong gravitational lensing of gravitational waves

Assessing the probability that two or more gravitational wave (GW) events are lensed images of the same source requires an understanding of the properties of the lensed images. For short enough wavelengths where wave effects can be neglected, lensed images will generically have a fixed relative phase shift that needs to be taken into account in the lensing hypothesis. For non-precessing, circular binaries dominated by quadrupole radiation these lensing phase shifts are degenerate with either a shift in the coalescence phase or a detector and inclination dependent shift in the orientation angle. This degeneracy is broken by the presence of higher harmonic modes with |m| ≠ 2 in the former and |m| ≠ l in the latter. The presence of precession or eccentricity will also break this degeneracy. This implies that a lensed GW image will not necessarily be consistent with (unlensed) predictions from general relativity (GR). Therefore, unlike the conventional scenario of electromagnetic waves, strong lensing of GWs can lead to images with a modified phase evolution that can be observed. However, we find that templates with a shifted orientation angle remain a good approximation, with signal-to-noise ratio differences of less than 1% for mass ratios up to 1/18, and less than 5% for precession parameters up to 0.5 and eccentricities up to 0.4. We conclude that an optimal strong lensing search strategy would incorporate phase information in all stages of the identification of strong-lensing, with an exact treatment in the final assessment of the probability of multiple lensed events. Here, this work clarifies the role that strong lensing plays in the phase evolution of GWs: how it can lead to apparent deviations from GR, how it can affect the detectability of GW events, and how it can be exploited to help identify cases of strong gravitational lensing of gravitational wave sources.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Fermi -LAT follow-up observations in seven years of real-time high-energy neutrino alerts

The realtime program for high-energy neutrino track events detected by the IceCube South Pole Neutrino Observatory releases alerts to the astronomical community with the goal of identifying electromagnetic counterparts to astrophysical neutrinos. Gamma-ray observations from theFermi-Large Area Telescope (LAT) enabled the identification of the flaring gamma-ray blazar TXS 0506+056 as a likely counterpart to the neutrino event IC-170922A. By continuously monitoring the gamma-ray sky,Fermi-LAT plays a key role in the identification of candidate counterparts to realtime neutrino alerts. In this paper, we present theFermi-LAT strategy for following up high-energy neutrino alerts applied to seven years of IceCube data. Right after receiving an alert, a search is performed in order to identify gamma-ray activity from known and newly detected sources that are positionally consistent with the neutrino localization. In this work, we study the population of blazars found in coincidence with high-energy neutrinos and compare them to the full population of gamma-ray blazars detected byFermi-LAT. We also evaluate the relationship between the neutrino and gamma-ray luminosities, finding different trends between the two blazar classes BL Lacs and flat-spectrum radio quasars.

Astronomy & Astrophysics↗

DOE OSTI2024

Estimating Critical Customer Outages Resulting from Extreme Hurricanes

US power outage data has been collected by organizations such as Oak Ridge National Laboratory (ORNL) through Environment for Analysis Geo-Located Energy Infrastructure (EAGLE-I: freely available) and poweroutage.us (commercial data: available to purchase). However, these sources do not provide information specific to outages of critical customers. Critical customers include entities, facilities, and individuals whose continuous access to electricity is essential for public safety, emergency response, disaster recovery, the well-being of vulnerable populations, public safety and order, and public utilities such as natural gas, communications, water and sanitation. Identification and geolocation of critical customers is crucial for understanding and addressing the effects of power outages on essential services and ensuring that necessary measures are taken to maintain their operations during power disruptions. This work is a first step towards estimating the occurrences of critical customer outages and developing a critical customer power outage data repository. This work estimates outage incidents of critical customers through spatiotemporal mapping of power outage data, weather data, building data, and critical infrastructure network data. Our results show that critical customer effects vary across different counties. We provide appropriate mathematical explanations and simplifications to define and systematize the proposed approach.

Bhusal, Narayan [ORNL] (ORCID:0000000222752145)↗

DOE OSTI2024

Rare Neutrino Interaction and $\pi^0$ Production Cross Sections with MicroBooNE

MicroBooNE is a Liquid Argon Time Projection Chamber, able to image neutrino interactions with excellent spatial and timing resolution, enabling the identification of complex final states resulting from neutrino-nucleus interactions. This poster will provide an overview of measurements for rare final states, such as and η production. These processes both provide unique sensitivities to the interplay between nucleon-level cross-section physics and nuclear-level physics, as well as account for sources of background in proton decay experiments. Furthermore, this poster showcases MicroBooNE’s measurements of total and first-order differential cross-sections on argon for muon neutrino interactions producing neutral pions in the final-state. These interactions will dominate the event rates observed at forthcoming high-precision neutrino experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Development of a Multi-Sensor Data Science System Used for Signature Development on Solvent Extraction Processes in support of safeguards- an overview

A new nuclear fuel cycle test bed is being built at Idaho National Laboratory to support the purification of special nuclear material recovered from used fuel. The test bed provides an opportunity to research process flow and the application of computational tools in solvent extraction processes. A deeper understanding of process and equipment behavior coupled with real time data collection can indicate whether a process failure is accidental or purposeful. The goal of this project is to develop a system that utilizes non-traditional measurement sources such as vibration, acoustics, current, light, flow, and temperature in conjunction with data-based, machine learning techniques that will allow for signal discovery. This multi-sensor data can support the development of safeguards by design and security by design measures for such a facility. Additionally, it can aid in early detection and identification of removed materials indicating diversion, which is essential for initiating material recovery and actor identification. This overview encompasses the current research and testing of sensors to develop a spectrum of process signatures. To be followed by planned experiments aimed to characterize said signatures and study potential feature extraction techniques to identify a fault in the system (i.e. flow diversion).

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2024

Rare Neutrino Interaction and $\pi^0$ Production Cross Sections with MicroBooNE

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Calibration of the DUNE Far Detector Using Cosmic-ray Muon Events

The Deep Underground Neutrino Experiment (DUNE) aims to set new limits on parameters associated with neutrino oscillations, neutrino astrophysics, and beyond the Standard Model (SM) searches such as nucleon decay. DUNE will quantify the magnitude of CP violation in the lepton sector, and determine the neutrino mass ordering. These benefit highly from the large target mass and excellent imaging, tracking, and particle identification capabilities of Liquid Argon Time Projection Chambers (LArTPCs). Detector calibration is essential to make precise physics measurements. For instance, accurate energy reconstruction is necessary for measuring many of the aforementioned quantities with the precision required for discovering new physics and fully exploiting the capabilities of the detector. Cosmic muons are a freely available natural source of calorimetric data and can be used for calibrating various detector parameters. This thesis provides an analysis of simulated cosmic-ray muon events generated with the Muon Simulation Underground (MUSUN) generator in the DUNE horizontal drift (HD) far detector (FD). The study focuses on analysing the energy and angular distribution of various classes of muon events, as well as characterising the different particles produced by cosmic muon interactions. The analysis of π0 → 2γ events within the cosmic-ray muon sample is presented in this thesis with a detailed study of reconstructing electromagnetic showers. The π0 mass is reconstructed within the DUNE FD, yielding a value of (136 ± 7) MeV/c2. Additionally, the thesis introduces methods for dE/dx calibration using simulated and reconstructed muon tracks. A calibration constant Ccal = (5.469 ± 0.003) × 10−3 ADC × tick/e is obtained through a model-dependent calibration process, where 1 tick corresponds to 500 ns of sampling time of an ADC. Furthermore, a calibration technique is presented, demonstrating precise translation from dQ/dx to dE/dx. This calibration method is applied to stopping muons, charged pions, and protons in the DUNE FD, addressing the measurement of energy loss in the detector volume. These are important calibrations of the DUNE FD and will contribute to achieving the exciting physics goals of the experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

ChemEnv : a fast and robust coordination environment identification tool

Coordination or local environments have been used to describe, analyze and understand crystal structures for more than a century. Here, a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner, is presented. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can also be used through a web app available on http://crystaltoolkit.org through the Materials Project.

42 ENGINEERING↗

DOE OSTI2022

Inverse Method for Noninvasive Material Discrimination with Multienergy X-Ray Radiography

Active x-ray inspections have great potential for noninvasive detection of illicit materials. Dual-energy x-ray radiography, in particular, has been used to determine material composition by utilizing the energy-dependence of the x-ray attenuation coefficients. However, current implementations of this method are limited in their ability to determine the material composition of composite objects. Here, in this paper, we present an inverse algorithm that uses multienergy x-ray radiography data to noninvasively reconstruct the contents of a container. A critical feature of the current contribution is that material identification can be performed using conventional detectors and x-ray spectra with different endpoint energies produced by varying nothing more than the tube voltage. Adaptive regularization is used to increase the accuracy of material estimations from multienergy data sets. The utility of these methods is demonstrated with experimentally acquired radiographs obtained using a tunable x-ray source that produces spectra with endpoint energies of 100–450 keV. The object inspected is a scale model of a nuclear materials storage container composed of three-dimensional printed plastic and stainless-steel spheres inside a thin-walled steel container. Reconstructions of the steel sphere thicknesses are within a root-mean-square error of 0.37 cm.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Using Systems Theoretic Process Analysis and Causal Analysis to Map and Manage Organizational Information to Enable Digitalization and Information Automation

The overarching goal of this Light Water Reactor Sustainability Program–supported research and development project is to provide planning tools and comprehensive guidance to utilities considering or undertaking full nuclear plant modernization. The results of this research will provide the nuclear industry with a comprehensive and usable solution, including guidance, lessons learned, methods, and planning tools. This research is currently working to provide guidance on digitalization and information automation to enable the evolution of data to information, insight, and action—thereby allowing utilities to operate safely and cost-competitively with all other electrical generation sources. Light Water Reactor Sustainability Program researchers have also recently started investigating how human and technology integration principles, information automation, and digitalization enable data evolution. These researchers are currently in the process of validating the use of System-Theoretic Process Analysis to define high-level safety constraints in the United States Nuclear Regulatory Commission’s problem identification and resolution process (i.e., a plant compliance information gathering activity). The next step in this research, which is described in the following sections of this report, is to map out data evolution in a use case to identify inefficiencies in another aspect of plant compliance information gathering and communication activities—event investigations and root cause analyses.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗