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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Report on progress in physics: observation of the Breit–Wheeler process and vacuum birefringence in heavy-ion collisions

This report reviews the effort over several decades to observe the linear Breit–Wheeler process ($\gamma\gamma \rightarrow e^+e^-$) and vacuum birefringence (VB) in high-energy particle and heavy-ion collider experiment. This report, motivated by the STAR collaboration's recent observations, attempts to summarize the key issues related to the interpretation of polarized $\gamma\gamma \rightarrow l^+l^-$ measurements in high-energy experiments. To that end, we start by reviewing the historical context and essential theoretical developments, before focusing on the decades of progress made in high-energy collider experiments. Special attention is given to the evolution in experimental approaches in response to various challenges, to the demanding detector capabilities required to unambiguously identify the linear Breit–Wheeler process, and to the connections with VB. Finally, we close the report with a discussion, followed by a look at near-future opportunities for utilizing these discoveries and for testing quantum electrodynamics in previously unexplored regimes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Using ensembles and distillation to optimize the deployment of deep learning models for the classification of electronic cancer pathology reports

One of the goals of the Surveillance, Epidemiology, and End Results (SEER) program is to estimate incidence, prevalence, and mortality of all cancers. To that end, cancer registries across the country maintain a massive database of cancer pathology reports which contain rich information to understand cancer trends. However, these reports are stored in the form of unstructured text, and human annotators are required to read and extract relevant information. In this article, we show that existing deep learning models for automating information extraction from cancer pathology reports can be significantly improved by using ensemble model distillation. We found that by training multiple predictive models and transferring their knowledge to a single, low-resource model, we can reduce the number of highly confident wrong predictions. Our results show that our implemented methods could save 1000s of manual annotation hours.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Live-cell Imaging of Pol II Promoter Activity to Monitor Gene expression with RNA IMAGEtag reporters

We describe a ribonucleic acid (RNA) reporter system for live-cell imaging of gene expression to detect changes in polymerase II activity on individual promoters in individual cells. The reporters use strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags) that can be expressed from a promoter of choice. For imaging, the cells are incubated with their ligands that are separately conjugated with one of the FRET pair, Cy3 and Cy5. The IMAGEtags were expressed in yeast from the GAL1, ADH1 or ACT1 promoters. Transcription from all three promoters was imaged in live cells and transcriptional increases from the GAL1 promoter were observed with time after adding galactose. Expression of the IMAGEtags did not affect cell proliferation or endogenous gene expression. Advantages of this method are that no foreign proteins are produced in the cells that could be toxic or otherwise influence the cellular response as they accumulate, the IMAGEtags are short lived and oxygen is not required to generate their signals. The IMAGEtag RNA reporter system provides a means of tracking changes in transcriptional activity in live cells and in real time.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Coarse-to-Fine Multi-Task Training of Convolutional Neural Networks for Automated Information Extraction from Cancer Pathology Reports

Information extraction and coding of free-text pathology reports is an important activity for cancer registries to support national cancer surveillance. Cancer registrars must process high volumes of pathology reports on an annual basis. In this study, we investigated an automated approach using a coarse-to-fine training of convolutional neural networks (CNNs) for extracting the primary site, histological grade and laterality from unstructured cancer pathology text reports. Our proposed training scheme consists of two stages. In the first stage, the multi-task learning (MTL) with hard parameter sharing approach is used to train a multi-task MT-CNN model for all the tasks. Then, the TM-CNN parameters are used to initialize a CNN model for each task to be fine trained individually using its corresponding dataset. The performance of our proposed model was compared against a state-of-the-art CNN and the commonly used SVM classifier. We observed that the proposed model consistently outperformed the base line models, especially for the less prevalent classes. Specifically, the proposed training approach achieved a micro-F score of 0.7749 over 12 ICD- O-3 topography codes which is a significant improvement as compared with state-of-the-art CNN (0.7101) and the SVM (0.6019) classifiers. Also, the results demonstrate the potential of the proposed method for handling class imbalance within each task. It significantly improves macro-F score by 24% and 12% of the primary site and histology grade tasks, respectively.

Alawad, Mohammed↗
DOE OSTI2026

Global Explainability of A Deep Abstaining Classifier for Cancer Pathology Reports

We present a global explainability method to characterize sources of errors in a real-world multitask deep abstaining classifier (DAC), in the context of cancer histology prediction. Our multitask classifier, currently deployed for automated annotation of cancer pathology reports from NCI-SEER registries, was trained and evaluated on 1.04 million hand-annotated samples and makes simultaneous predictions of cancer site, subsite, histology, laterality, and behavior for each report. The DAC framework enables the model to abstain on ambiguous reports and confusing classes to achieve the target accuracy on the retained (non-abstained) samples, but at the cost of decreased coverage. Requiring 97% accuracy on the histology task caused our model to retain only 22% of all samples, mostly the less ambiguous and common classes. Local explainability with the GradInp technique provided a computationally efficient way of obtaining contextual reasoning for hundreds of thousands of individual predictions. Our method, involving dimensionality reduction of approximately 13000 aggregated local explanations (ALE), offers a tractable path to true global explainability. It enabled identification of sources of errors in histology classification, globally, as hierarchical complexity among classes, label noise, insufficient information, and conflicting evidence. This suggests several strategies for iterative improvement of our DAC, including well-designed exclusion criteria, focused annotation, and reduced penalties for errors involving hierarchically related classes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Insufficient reporting of x-ray photoelectron spectroscopy instrumental and peak fitting parameters (metadata) in the scientific literature

This study was motivated by earlier observations. It is a systematic examination of the adequacy of reporting of information (metadata) necessary to understand x-ray photoelectron spectroscopy (XPS) data collection and data analysis in the scientific literature. The information for this study was obtained from papers published in three high-quality journals over a six-month period in 2019 and throughout 2021. Each paper was evaluated to determine whether the authors had reported (percentages of the papers properly providing the information are given in parentheses) the spectrometer (66%), fitting software (15%), x-ray source (40%), pass energy (10%), spot size (5%), synthetic peak shapes in fits (10%), backgrounds in fits (10%), whether the XPS data are shown in the main body of the paper or in the supporting information (or both), and whether fitted or unfitted spectra were shown (80% of published spectra are fit). The Shirley background is the most widely used background in XPS peak fitting. The Al Kα source is the most widely used x-ray source for XPS data collection. CASAXPS is the most widely used fitting program for XPS data analysis. Further, there is good agreement between the results gathered during the two years of our survey. There are some hints the situation may be improving. This study also provides a list of the information/parameters that should be reported when XPS is performed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2015

SU-E-T-142: Automatic Linac Log File: Analysis and Reporting

Purpose: End to end QA for IMRT/VMAT is time consuming. Automated linac log file analysis and recalculation of daily recorded fluence, and hence dose, distribution bring this closer. Methods: Matlab (R2014b, Mathworks) software was written to read in and analyse IMRT/VMAT trajectory log files (TrueBeam 1.5, Varian Medical Systems) overnight, and are archived on a backed-up network drive (figure). A summary report (PDF) is sent by email to the duty linac physicist. A structured summary report (PDF) for each patient is automatically updated for embedding into the R&V system (Mosaiq 2.5, Elekta AG). The report contains cross-referenced hyperlinks to ease navigation between treatment fractions. Gamma analysis can be performed on planned (DICOM RTPlan) and treated (trajectory log) fluence distributions. Trajectory log files can be converted into RTPlan files for dose distribution calculation (Eclipse, AAA10.0.28, VMS). Results: All leaf positions are within +/−0.10mm: 57% within +/−0.01mm; 89% within 0.05mm. Mean leaf position deviation is 0.02mm. Gantry angle variations lie in the range −0.1 to 0.3 degrees, mean 0.04 degrees. Fluence verification shows excellent agreement between planned and treated fluence. Agreement between planned and treated dose distribution, the derived from log files, is very good. Conclusion: Automated log file analysis is a valuable tool for the busy physicist, enabling potential treated fluence distribution errors to be quickly identified. In the near future we will correlate trajectory log analysis with routine IMRT/VMAT QA analysis. This has the potential to reduce, but not eliminate, the QA workload.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-511: Inter-Rater Variability in Classification of Incidents in a New Incident Reporting System

Purpose To determine how consistent the results of different raters are when reviewing the same cases within the Radiation Oncology Incident Learning System (ROILS). Methods Three second-year medical physics graduate students filled out incident reports in spreadsheets set up to mimic ROILS. All students studied the same 33 cases and independently entered their assessments, for a total of 99 reviewed cases. The narratives for these cases were obtained from a published International Commission on Radiological Protection (ICRP) report which included shorter narratives selected from the Radiation Oncology Safety Information System (ROSIS) database. Each category of questions was reviewed to see how consistent the results were by utilizing free-marginal multirater kappa analysis. The percentage of cases where all raters shared full agreement or full disagreement was recorded to show which questions were answered consistently by multiple raters for a given case. The consistency among the raters was analyzed between ICRP and ROSIS cases to see if either group led to more reliable results. Results The categories where all raters agreed 100 percent in their choices were the event type (93.94 percent of cases 0.946 kappa) and the likelihood of the event being harmful to the patient (42.42 percent of cases 0.409 kappa). The categories where all raters disagreed 100 percent in their choices were the dosimetric severity scale (39.39 percent of cases 0.139 kappa) and the potential future toxicity (48.48 percent of cases 0.205 kappa). ROSIS had more cases where all raters disagreed than ICRP (23.06 percent of cases compared to 15.58 percent, respectively). Conclusion Despite reviewing the same cases, the results among the three raters was widespread. ROSIS narratives were shorter than ICRP, which suggests that longer narratives lead to more consistent results. This study shows that the incident reporting system can be optimized to yield more consistent results.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-516: Investigation of a Novel Radiochromic Radiation Reporting System Utilizing the Reduction of Ferric Ion

Purpose To introduce and characterize a new “reverse-Fricke” radiation reporting system utilizing the reduction of ferric ions (Fe{sup 3+}) to ferrous ions (Fe{sup 2+}). Methods Two formulations of the radiochromic reporting system, referred to as A and B, were prepared for investigation. Formulation-A consisted of 14 mM 1,10-phenanthroline, 42 mM ethanol, and 57 mM ammonium ferric oxalate in water. Formulation-B consisted of 27 mM 1,10-phenanthroline, 42 mM ethanol, and 28 mM ammonium ferric oxalate in water. Solutions were prepared immediately prior to irradiation with a Cobalt-60 unit with radiation doses of 0, 1, 5, 10, 15, 20, and 25 Gy. The change in optical density over the visible range of 450–650 nm was measured using a spectrophotometer immediately after irradiation. The effective atomic numbers of the formulations were calculated using Mayneord’s formula. Results Ionizing radiation energy absorbed in the solutions causes the reduction of ferric ions (Fe{sup 3+}) into ferrous ions (Fe{sup 2+}), which then forms a 1:3 red colored complex with 1,10-phenanthroline ([(C{sub 1} {sub 2}H{sub 8}N{sup 2}){sub 3}Fe]{sup 2+}) that can be measured spectrophotometrically. The absorbance spectra of the resulting complex displayed a peak maximum at 512 nm with a greater change in absorbance for Formulation-B after receiving comparable radiation doses. The change in absorbance relative to dose exhibited a linear response up to 25 Gy for both Formulation-A (R{sup 2} = 0.98) and Formulation-B (R{sup 2} = 0.97). The novel formulations were also nearly water equivalent (Zeff = 7.42) with effective atomic numbers of 7.65 and 7.52 and mass densities within 0.2% of water. Conclusion Both formulations displayed visible Fe{sup 2+} complex formation with 1,10-phenanthroline after irradiation using a Cobalt-60 source. The higher sensitivity measured for Formulation-B is attributed to the increase in 1,10-phenanthroline concentration and the increase in the 1,10-phenanthroline to ammonium ferric oxalate ratio. Further investigation of this radiation reporting system in a 3D matrix material is encouraged. NSF GRFP Grant Award #LH-102SPS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Monte Carlo reference data sets for imaging research: Executive summary of the report of AAPM Research Committee Task Group 195

The use of Monte Carlo simulations in diagnostic medical imaging research is widespread due to its flexibility and ability to estimate quantities that are challenging to measure empirically. However, any new Monte Carlo simulation code needs to be validated before it can be used reliably. The type and degree of validation required depends on the goals of the research project, but, typically, such validation involves either comparison of simulation results to physical measurements or to previously published results obtained with established Monte Carlo codes. The former is complicated due to nuances of experimental conditions and uncertainty, while the latter is challenging due to typical graphical presentation and lack of simulation details in previous publications. In addition, entering the field of Monte Carlo simulations in general involves a steep learning curve. It is not a simple task to learn how to program and interpret a Monte Carlo simulation, even when using one of the publicly available code packages. This Task Group report provides a common reference for benchmarking Monte Carlo simulations across a range of Monte Carlo codes and simulation scenarios. In the report, all simulation conditions are provided for six different Monte Carlo simulation cases that involve common x‐ray based imaging research areas. The results obtained for the six cases using four publicly available Monte Carlo software packages are included in tabular form. In addition to a full description of all simulation conditions and results, a discussion and comparison of results among the Monte Carlo packages and the lessons learned during the compilation of these results are included. This abridged version of the report includes only an introductory description of the six cases and a brief example of the results of one of the cases. This work provides an investigator the necessary information to benchmark his/her Monte Carlo simulation software against the reference cases included here before performing his/her own novel research. In addition, an investigator entering the field of Monte Carlo simulations can use these descriptions and results as a self‐teaching tool to ensure that he/she is able to perform a specific simulation correctly. Finally, educators can assign these cases as learning projects as part of course objectives or training programs.

Sechopoulos, Ioannis↗
DOE OSTI2019

HE-LHC: The High-Energy Large Hadron Collider

Particle physics has arrived at an important moment of its history. The discovery of the Higgs boson, with a mass of 125 GeV, completes the matrix of particles and interactions that has constituted the “Standard Model” for several decades. This model is a consistent and predictive theory, which has so far proven successful at describing all phenomena accessible to collider experiments. However, several experimental facts do require the extension of the Standard Model and explanations are needed for observations such as the abundance of matter over antimatter, the striking evidence for dark matter and the non-zero neutrino masses. Theoretical issues such as the hierarchy problem, and, more in general, the dynamical origin of the Higgs mechanism, do likewise point to the existence of physics beyond the Standard Model. This report contains the description of a novel research infrastructure based on a high-energy hadron collider, which extends the current energy frontier by almost a factor 2 (27 TeV collision energy) and an integrated luminosity of at least a factor of 3 larger than the HL-LHC. In connection with four experimental detectors, this infrastructure will deepen our understanding of the origin of the electroweak symmetry breaking, allow a first measurement of the Higgs self-coupling, double the HL-LHC discovery reach and allow for in-depth studies of new physics signals arising from future LHC measurements. This collider would directly produce particles at significant rates at scales up to 12 TeV. The project re-uses the existing LHC underground infrastructure and large parts of the injector chain at CERN. This particle collider would succeed the HL-LHC directly and serve the world-wide physics community for about 20 years beyond the middle of the 21st century. The European Strategy for Particle Physics (ESPP) update 2013 stated “To stay at the forefront of particle physics, Europe needs to be in a position to propose an ambitious post-LHC accelerator project at CERN by the time of the next Strategy update”. The FCC study has implemented the ESPP recommendation by developing a vision for an “accelerator project in a global context”. This document describes the detailed design and preparation of a construction project for a post-LHC circular high-energy hadron collider “in collaboration with national institutes, laboratories and universities worldwide”, and enhanced by a strong participation of industrial partners. Now, a coordinated preparation effort can be based on a core of an ever-growing consortium of already more than 135 institutes worldwide. The technology for constructing a High-Energy LHC can be brought to the technology readiness level required for construction within the coming ten years through a committed and focused R&D programme. The concept comprises a power-saving, low-temperature superconducting magnet system based on an evolution of the Nb3Sn technology pioneered at the HL-LHC, an energy-efficient cryogenic refrigeration infrastructure based on a neon-helium (Nelium) light gas mixture, a high-reliability and low loss cryogen distribution infrastructure based on Invar, high-power distributed beam transfer using superconducting elements and local magnet energy recovery and re-use technologies that are already gradually introduced at other CERN accelerators. Re-use of the LHC underground civil infrastructure worth about 500 million CHF at the time of its construction, extension of the surface sites and use of the existing injector chain that also serve for a concurrently running physics programme are levers to come to a sustainable research infrastructure at the energy frontier. Strategic R&D for HE-LHC aims at minimising construction cost and energy consumption, while maximising the socio-economic impact. It needs to mitigate technology-related risks and ensure that industry can benefit from an acceptable economic utility. Concerning the implementation, a preparatory phase of about eight years is both necessary and adequate to establish the project governance and organisation structures, to build the international machine and experiment consortia, to develop a territorial implantation plan considering the constraints emerging from using the existing infrastructure and the host states’ requirements, optimising the use of land, resources and preparing the construction project. Such a large-scale, international fundamental research infrastructure, tightly involving industrial partners and providing training at all education levels, will be a strong motor of economic and societal development in all participating nations. The FCC study has implemented a set of actions towards a coherent vision for the world-wide high-energy and particle physics community, providing a collaborative framework for topically complementary and geographically well-balanced contributions. This conceptual design report lays the foundation for a subsequent infrastructure preparatory and technical design phase.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

Application Reporting and Termination Utility for Windows

The Application Reporting and Termination Utility for Windows (terminate.exe) is a simple diagnostics and recovery tool designed to help LANDesk system administrators manage hung client applications on Windows systems. Terminate can either report on (tag) or stop (kill) a specified process on computers on which it is run. If KILL is specified, all processes that match the specified name and have a start time older than the specified minutes will be force stopped. If TAG is specified, all processes that match the name and have a start time older than the specified minutes will be reported to LANDesk inventory via the miniscan LANDesk client component.

Frye, DavidJ.↗
DOE OSTI2015

LucY: A versatile new fluorescent reporter protein

We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble FAD. LucY displays excitation and emission spectra characteristic of FAD, with 3 excitation peaks at 276nm, 377nm, and 460nm and a single emission peak at 530nm. These excitation and emission maxima provide the large Stokes shift beneficial to fluorescence experimentation. LucY belongs to the MurB family of UDP-N-acetylenolpyruvylglucosamine reductases. The high resolution crystal structure shows that in contrast to other structurally resolved MurB enzymes, LucY does not contain a potentially quenching aromatic residue near the FAD isoalloxazine ring, which may explain its increased fluorescence over related proteins. Using E. coli as a system in which to develop LucY as a reporter, we show that it is amenable to circular permutation and use as a reporter of protein-protein interaction. Fragmentation between its distinct domains renders LucY non-fluorescent, but fluorescence can be partially restored by fusion of the fragments to interacting protein domains. Thus, LucY may find application in Protein-fragment Complementation Assays for evaluating protein-protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Testing biasedness of self-reported microbusiness innovation in the annual business survey

This study tests for potential bias in self-reported innovation due to the inclusion of a research and development (R&D) module that only microbusinesses (less than 10 employees) receive in the Annual Business Survey (ABS). Previous research found that respondents to combined innovation/R&D surveys reported innovation at lower rates than respondents to innovation-only surveys. A regression discontinuity design is used to test whether microbusinesses, which constitute a significant portion of U.S. firms with employees, are less likely to report innovation compared to other small businesses. In the vicinity of the 10-employee threshold, the study does not detect statistically significant biases for new-to-market and new-to-business product innovation. Statistical power analysis confirms the nonexistence of biases with a high power. Comparing the survey design of ABS to earlier combined innovation/R&D surveys provides valuable insights for the proposed integration of multiple Federal surveys into a single enterprise platform survey. The findings also have important implications for the accuracy and reliability of innovation data used as an input to policymaking and business development strategies in the United States.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2016

Magnetic Nanofluid Rare Earth Element Extraction Process Report, Techno Economic Analysis, and Results for Geothermal Fluids

This GDR submission is an interim technical report and raw data files from the first year of testing on functionalized nanoparticles for rare earth element extraction from geothermal fluids. The report contains Rare Earth Element uptake results (percent removal, mg Rare Earth Element/gram of sorbent, distribution coefficient) for the elements of Neodymium, Europium, Yttrium, Dysprosium, and Cesium. A detailed techno economic analysis is also presented in the report for a scaled up geothermal rare earth element extraction process. All rare earth element uptake testing was done on simulated geothermal brines with one rare earth element in each brine. The rare earth element uptake testing was conducted at room temperature.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Dataset for report: Non-Technical Barriers to Geothermal Development in California and Nevada

In California and Nevada, geothermal projects are subject to non-technical barriers, which may create development delays leading to higher project costs and risks and decreased competitiveness with other electricity generation technologies. These non-technical barriers may include federal and state permits, authorizations, environmental reviews, and other regulatory requirements that are applicable throughout different phases of geothermal project development. The 2022 National Renewable Energy Laboratory (NREL) report, "Non-Technical Barriers to Geothermal Development in California and Nevada" presents findings of a study on non-technical barriers that may influence geothermal project development. The set of data resources relied upon for the report includes: 1) interviews conducted with relevant geothermal stakeholders including regulators and project developers, 2) federal and state environmental review documents developed for specific projects, 3) a techno-economic analysis conducted using the NREL Annual Technology Baseline (ATB) framework, and 4) an analysis of the impacts of site-specific land access and permitting considerations on project development readiness conducted using the Geothermal Resource Portfolio Optimization and Reporting Technique (GeoRePORT) Socioeconomic Assessment Tool (SEAT).

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

Utah FORGE 5-2557: Trixial Shear and Wellbore Breakout Tests Report and Data

Included are a report and data from triaxial shear tests on simulated Sierra White fault gouge and a borehole stimulation experiment. This serves as a progress report for the Role of Fluid and Temperature in Fracture Mechanics and Coupled Thermo-Hydro-Mechanical-Chemical (THMC) Processes for Enhanced Geothermal Systems project by Purdue University (Utah FORGE R&D project 5-2557). Tests were done with Sierra White granite (SWG) to investigate slip mechanisms and to evaluate the fracture initiation and propagation from a geothermal borehole. Raw data is provided alongside a report on all experimental testing protocols, experimental design, and results.

15 GEOTHERMAL ENERGY↗
DOE OSTI2019

Recent advances in analysis of trace elements in environmental samples by X-ray based techniques (IUPAC Technical Report)

Trace elements analysis is a foundational challenge in environmental sciences. Scientists measure trace elements in environmental media in order to assess the quality and safety of ecosystems and to quantify the burden of anthropogenic pollution. Among the available analytical techniques, X-ray based methods are particularly powerful, as they can quantify trace elements in situ . Chemical extraction is not required, as is the case for many other analytical techniques. In the last few years, the potential for X-ray techniques to be applied in the environmental sciences has dramatically increased due to developments in laboratory instruments and synchrotron radiation facilities with improved sensitivity and spatial resolution. In this report, we summarize the principles of the X-ray based analytical techniques most frequently employed to study trace elements in environmental samples. We report on the most recent developments in laboratory and synchrotron techniques, as well as advances in instrumentation, with a special attention on X-ray sources, detectors, and optics. Lastly, we inform readers on recent applications of X-ray based analysis to different environmental matrices, such as soil, sediments, waters, wastes, living organisms, geological samples, and atmospheric particulate, and we report examples of sample preparation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗