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At least 1,243 records · Page 69

Updates on MURAVES Project at Mt. Vesuvius

The MUon RAdiography of VESuvius (MURAVES) project aims to employ muography imaging techniques to investigate the internal structure of the summit of Mount Vesuvius, an active volcano located near Naples, Italy. This paper reports recent advancements in data analysis and simulation tools that significantly improve the quality and reliability of the experiment’s results. A new track selection method, referred to as the Golden Selection, has been developed to identify high-quality muon tracks by applying an improved χ 2 -based criterion. This method enhances the signal-to-background ratio and improves the resolution of the resulting muographic images. Moreover, the simulation framework has been upgraded through the integration of the MULDER (MUon simuLation for DEnsity Reconstruction) library, which consolidates the functionalities of previously used libraries into a single, unified platform. MULDER enables efficient and accurate modeling of muon flux variations induced by topographical features. A good agreement is observed between the simulated and measured muon flux maps, validating the effectiveness of the new analysis and simulation approaches.

Cosmic rays↗

Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach

Most classic genetic approaches utilize binary modifications that preclude the identification of key knockdowns for essential genes or other targets that only require moderate modulation. As a complementary approach to these classic genetic methods, we describe a plasmid-based library methodology that affords bidirectional, graded modulation of gene expression enabled by tiling the promoter regions of all 969 genes that comprise the ito977 model of Saccharomyces cerevisiae’s metabolic network. When coupled with a CRISPR-dCas9–based modulation and next-generation sequencing, this method affords a library-based, bidirection titration of gene expression across all major metabolic genes. We utilized this approach in two case studies: growth enrichment on alternative sugars, glycerol and galactose, and chemical overproduction of betaxanthins, leading to the identification of unique gene targets. In particular, we identify essential genes and other targets that were missed by classic genetic approaches.

59 BASIC BIOLOGICAL SCIENCES↗

Sorting for secreted molecule production using a biosensor-in-microdroplet approach

Significance The design–build–test cycle of metabolic engineering is swiftly becoming test limited owing to advances in DNA synthesis and library design. At the same time, improving extracellular production requires high-throughput studies to detect extracellular (not intracellular) content. Traditional approaches that utilize chromatography-based analysis or plate-based fluorescence assays are relatively throughput limited and require a high degree of liquid handling. These limitations are avoided here by creating a generalizable approach for small molecule production screening. Namely, this paradigm combines “off-the-shelf” biosensors with large library screening from producing cells in a cell-type agnostic manner.

Bowman, Emily K.↗

Comparison of Irradiated TRISO Fuel Radioactivity from Multiple Advanced Reactor Designs

The SCALE code system was used to model, deplete, and compare several different TRISO-fueled reactor designs: a helium-cooled prismatic reactor, a helium-cooled pebble-bed reactor (PBR), and a Fluoride-Lithium-Beryllium (FLIBE) molten-salt-cooled PBR. The purpose of this comparison was to understand how differences in the reactor designs affect the radioactivity of the fuel after discharge and whether those differences are significant. First, the various reactor designs were build and depleted in the TRITON module for each design and fuel enrichment. Then, the TRITON outputs were used to create burn-up dependent reactor libraries. These libraries were then used by ORIGEN to determine the activities of discharged fuel for each reactor, which were compared to generic Westinghouse 17x17 fuel. Overall, the results showed that short term decays are dominated by reactors with higher operating powers, and the reactor type, initial fuel enrichment, and maximum burn-up are of only secondary importance. Although this analysis only focuses on activities in becquerels, these dependencies are consistent with the expected behavior of decay heat. However, analysis of long- term time periods post-irradiation shows that the reactor type and maximum burn-up have strong impacts on the activities; initial fuel enrichment has a secondary impact while operating power is inconsequential. These results would be useful for analyses, such as dose assessment and modeling in post- release scenarios; normal fuel handling operations; and spent fuel transport, storage and disposal. Of particular interest, the results in this report show that analyses that focus on spent nuclear fuel of advanced reactors need to consider each parameter carefully. Unsurprisingly, if the correct operating power is not used in short term analyses, the results will not be correct. Perhaps unexpectedly, however, if the correct reactor type is not used, then the long term results will also be incorrect, especially for areas such as permanent disposal. Even though this report focuses on the total activity of nuclear fuel, it provides initial results on the effects of various input parameters and also provides a framework to extend the work into other analyses of spent fuel from advanced reactors, especially those employing TRISO fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Modeling of the Molten Salt Reactor Experiment with SCALE

A SCALE model was developed for the Molten Salt Reactor Experiment (MSRE) benchmark that was recently added to the International Handbook of Evaluated Reactor Physics Benchmark Experiments. This SCALE model served as a basis for criticality calculations and nuclear data sensitivity and uncertainty analyses with the Monte Carlo code Shift and the TSUNAMI computational capabilities in the SCALE code system. The focus of this work is the assessment of the impact of nuclear data on the calculated eigenvalue results in support of the discussion of differences between the calculated and the experimental eigenvalue result. The differences in the eigenvalues obtained using the ENDF/B-VII.0, ENDF/B-VII.1, and ENDF/B-VIII.0 nuclear data libraries cover a relatively small range of ~230 pcm. Since eigenvalue sensitivity of the MSRE is dominated by the neutron multiplicity and neutron capture of 235 U and elastic scattering in graphite, relevant changes in the ENDF/B libraries for nuclear reactions (such as carbon capture) that caused large differences in other graphite-moderated systems did not have a significant impact. Propagation of nuclear data uncertainty results in an eigenvalue uncertainty of ~700 pcm with the major contributors being 235 U neutron multiplicity, graphite elastic scattering, and 7Li neutron capture. All calculations resulted in large differences of ~2000 pcm in eigenvalue compared to the benchmark experimental value. Several potential contributors to this difference—including uncertainties and gaps in the knowledge of the material, geometry, and nuclear data—were identified. Simplified models of the full MSRE core were developed, and similarity assessments were conduced with the full MSRE core model. It was found that simplified models can serve as adequate surrogates of the full-core model such that they can be used for performing selected nuclear data performance assessments with a lower computational burden.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A Machine Learning Method for the Forensics Attribution of Separated Plutonium

Plutonium (Pu) source attribution would be a powerful tool to support nuclear nonproliferation efforts. This capability to find the source of a Pu sample would act as a deterrent to smuggling efforts, and also help regulatory agencies verify declared nuclear activities. Work at Texas A&M University yielded a nuclear forensics methodology, which is capable of determining separated Pu’s reactor of origin, fuel burnup, and the time since irradiation (TSI)—three parameters of interest. The methodology used a set of ten intra-element isotopic ratios found in separated Pu, which was compared to a library of isotopic ratio values produced using neutronics simulations for reactors of interest. By calculating the probability that unknown Pu sample’s isotopic ratio set matched a set in the library, the methodology could predict the three parameters of interest of the sample. One shortcoming of this methodology was an inability to correctly attribute spoofed Pu, where Pu sourced from two different reactors or two different fuel burnup levels are mixed. A new methodology to rectify this vulnerability using machine learning (ML) technique is developed, instead of the maximum likelihood calculation previously used and the results are satisfactory. The ML approach leverages the existing simulated data for training the algorithm, but use them efficiently by only using intra-element isotope ratios that contribute to the attribution one of the three parameters at a time. Previously, all isotope ratios were used to attribute all three parameters together. The new methodology attributes the Pu parameters in three steps, one for each parameter, rather than resolving all of the three parameters simultaneously like the previous maximum likelihood approach. First, a support vector machine classifier with a set of seven isotopic ratios finds the reactor of origin and a set of regression models trained using gaussian process predicts the burnup with a different set of seven isotopes. Finally, TSI is calculated analytically using decay equations. Thus far, the new methodology is capable of attributing pure Pu samples and has been validated using experimental data. The next step will to be augment the classifier training data set with spoofed Pu data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

New Measurements to Resolve Discrepancies in Evaluated Model Parameters of 181 Ta

To resolve discrepancies in evaluated cross sections among major nuclear data libraries, energy-differential neutron transmission and radiative capture yield of 181 Ta were measured from 0.15 to 100 keV using multiple sample thicknesses. The new measurements provide resolution such that the resolved resonance region (RRR) can be evaluated up to at least 2.5 keV and the unresolved resonance region can be evaluated up to at least 100 keV. The transmission and capture yield measurements were modeled using resonance parameters from three major libraries to assess the predictive capability of each. It was found that JENDL-5.0 performed best in the RRR. Because of the poor performance of the U.S. ENDF/B evaluation, it is recommended that ENDF/B be reevaluated for 181 Ta.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Fixed Source Sensitivity Calculations for Inertial Confinement Fusion Applications

A numerical code library was developed for the radiation transport code MCNP6.3 to calculate generalized response sensitivity coefficients for fixed source neutron transport problems with applications to inertial confinement fusion (ICF) experiments. The new MCNP6.3 dependency is used to generate a novel time convolution response that represents a neutron time-of-flight (nToF) signal. The traditional suite of macroscopic cross-section sensitivities and constrained fixed source probability distribution sensitivities are available for both the standard and the new response tallies in this library. However, novel sensitivity coefficients for the constrained hyperparameters of analytic fixed source probability distributions are emphasized in this work for their connection to ICF neutron transport models. Particularly, advanced Monte Carlo methods are developed for calculating the sensitivity of a nToF signal to perturbations in an ICF plasma’s ion temperature and burn history as well as perturbations in the target liner mass density and the shape parameters of the nToF detector’s impulse response function. Together, these capabilities form an advanced suite of computational tools that can be used to analyze and extract information from any ICF experimental platform.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The MUSIC Critical Benchmark and Nuclear Data

The Measurement of Uranium Subcritical and Critical (MUSIC) experiment was a series of measurements of critical and subcritical configurations of bare highly enriched uranium. The goal was to compare measurement methods, analysis techniques, and simulation methods across regimes of criticality and to provide high-quality validation of 235 U nuclear data. A benchmark evaluation of the two critical configurations of the MUSIC experiments will soon be published in the release of the International Criticality Safety Benchmark Evaluation Project Handbook. The recent execution of the experiment aids in proper quantification of model simplifications and all uncertainties associated with the experiment. Historical benchmark evaluations are heavily relied on for uranium nuclear data validation despite the fact that the same level of documentation and comparable uncertainty analysis may not be present. The MUSIC evaluation is less likely to include “unknown unknowns” that could impede accurately modeling the system. Presented are both highly detailed and very simplified models, which represent the experimental configurations accurately, aiding the users of the benchmark for nuclear data or transport code validation. The sensitivities of k eff to nuclear data and nuclear data–related uncertainties are very similar between this experiment and previous bare uranium sphere experiments. In addition, the nuclear data uncertainties to any nuclides other than 235 U are small. For all these reasons, the recently evaluated MUSIC benchmark critical configurations could prove very useful for 235 U nuclear data validation. Currently, major libraries have good agreement with the experimental results, within 200 pcm for all nuclear data libraries, and within one standard deviation of the experimental result for most. Suggested nuclear data adjustments based on MUSIC and Lady Godiva are also presented, with posterior improvements to both the agreement in k eff and the uncertainty associated with the nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Offline Maximizing Minimally Invasive Proper Orthogonal Decomposition for Reduced-Order Modeling of S n Radiation Transport

Deterministic solutions to the Sn radiation transport equation can be computationally expensive to calculate. Reduced-order modeling enables efficient approximation of the full-order model (FOM) solution. We propose a novel method for constructing reduced-order models (ROMs) of the S n radiation transport equation, offline maximizing minimally invasive (OMMI) proper orthogonal decomposition (POD). POD uses the method of snapshots to create a reduced-order basis for constructing an ROM. Minimally invasive POD leverages the sweep infrastructure existing in deterministic transport codes to create a POD-based ROM, even when infeasible by traditional methods. Offline maximizing minimally invasive proper orthogonal decomposition (OMMI-POD) extends minimally invasive POD by performing sweeps offline, therefore maximizing the potential speedup. OMMI-POD does so by creating a library of reduced systems from a training set. This library of reduced systems is then interpolated to provide a rapid approximate solution of the S n radiation transport equation. The model is evaluated on a set of test problems, achieving a low error with a 466 times speedup over the FOM. Also presented is a study of the effect of sampling method on the performance of OMMI-POD, specifically comparing naive uniform sampling to the more accurate and computationally expensive greedy sampling.

97 MATHEMATICS AND COMPUTING↗

Multi-Analytical Investigation of Arsenical Transfer and Remediation on Nineteenth-Century Green Books

Books containing heavy metals, specifically nineteenth-century green arsenical books, have been identified at Northwestern University Libraries, raising health and safety concerns related to handling. Copper acetoarsenite pigments, such as emerald green, were detected on book covers, decorative page edges, labels, and other components using noninvasive analytical techniques including X-ray fluorescence (XRF), Raman spectroscopy, and Fourier-transform infrared (FTIR) spectroscopy. Further examination of selected volumes using synchrotron radiation (SR) techniques revealed pigment migration, degradation, and arsenic transfer to adjacent books. This paper expands on initial findings through two related experiments. The first explored the transfer of arsenic using mechanical friction; Staedtler Mars® white vinyl erasers rubbed on arsenical books generated crumbs which were analyzed via scanning electron microscopy–energy-dispersive X-ray spectroscopy (SEM-EDX). Results confirmed the transfer of arsenic, copper, and lead, with decorative page edges being particularly prone to shedding arsenic onto other materials. The second experiment tested remediation methods on a book contaminated by prolonged exposure to an arsenical neighbor. Surface cleaning using erasers and a vacuum removed flecks of pigment but did not eliminate non-chromophoric arsenic as confirmed by SR analyses, which highlights its presence either as a degradation product embedded within the paper or present in the paper as part of its production process. Findings demonstrate the acute toxicity risk posed by arsenical books and support the need for safe handling protocols. However, materials with only trace levels of arsenic embedded during production may pose a lower risk of transfer. Cross contamination beyond prolonged direct contact appears limited. These results highlight critical considerations for library preservation practices and future research on arsenic in historical materials.

arsenic↗

Performance portability for the CMS Reconstruction with Alpaka

For CMS, Heterogeneous Computing is a powerful tool to face the computational challenges posed by the upgrades of the LHC, and will be used in production at the High Level Trigger during Run 3. In principle, to offload the computational work on non-CPU resources, while retaining their performance, different implementations of the same code are required. This would introduce code-duplication which is not sustainable in terms of maintainability and testability of the software. Performance portability libraries allow to write code once and run it on different architectures with close-to-native performance. The CMS experiment is evaluating performance portability libraries for the near term future.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Improving seasonal precipitation forecasts in the Western United States through statistical downscaling

Abstract Seasonal precipitation forecasts in the western United States are critical resources for water resource management, especially during winter. While current seasonal forecasting systems provide monthly precipitation forecasts operationally, their coarse resolution limits their effectiveness in capturing the localized precipitation patterns and snowpack conditions essential for water resource managers in the mountainous regions. Here, analog statistical downscaling is demonstrated as an effective approach to enhance the spatial resolution of operational seasonal forecasts provided by the North American Multi-Model Ensemble. Downscaling was performed by building an analog ‘library’, in which corresponding model forecasts and observed values during the training period were stored. In the testing period, unseen model forecasts referenced the closest historical forecast from the analog library and applied the corresponding observational value for each point. This analysis indicates that downscaled products can capture localized features more accurately than the original coarse resolution forecasts, reducing forecast error across the western United States. Moreover, downscaling individual ensemble members—rather than downscaling the ensemble mean—further reduces forecasting error for their multi-model ensemble mean products. The greatest error reductions in the downscaled product, measured by root mean squared error (RMSE), were observed at low to mid-elevations (500–2000 meters), with 50%–70% improvement relative to the original forecasts. In the higher elevations (2000 meters and above), changes in RMSE relative to the original forecast were limited to 10%–30% improvements. The improvement is more substantial for forecast systems with 10 ensemble members compared to that with 4 members, but this relationship does not hold for the system with 24 ensemble members. These findings show that analog statistical downscaling can effectively address the spatial limitations of seasonal precipitation forecasts with minimal computational cost, providing a valuable framework for enhancing coarse resolution forecasting products while providing insights into the timing of ensemble mean calculations during the downscaling process.

Vernon, B. (ORCID:0009000891670689)↗

Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users

Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. Here, we describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.

60 APPLIED LIFE SCIENCES↗

Biosensors for the detection of chorismate and cis,cis -muconic acid in Corynebacterium glutamicum

Abstract Corynebacterium glutamicum ATCC 13032 is a promising microbial chassis for industrial production of valuable compounds, including aromatic amino acids derived from the shikimate pathway. In this work, we developed two whole-cell, transcription factor based fluorescent biosensors to track cis,cis-muconic acid (ccMA) and chorismate in C. glutamicum. Chorismate is a key intermediate in the shikimate pathway from which value-added chemicals can be produced, and a shunt from the shikimate pathway can divert carbon to ccMA, a high value chemical. We transferred a ccMA-inducible transcription factor, CatM, from Acinetobacter baylyi ADP1 into C. glutamicum and screened a promoter library to isolate variants with high sensitivity and dynamic range to ccMA by providing benzoate, which is converted to ccMA intracellularly. The biosensor also detected exogenously supplied ccMA, suggesting the presence of a putative ccMA transporter in C. glutamicum, though the external ccMA concentration threshold to elicit a response was 100-fold higher than the concentration of benzoate required to do so through intracellular ccMA production. We then developed a chorismate biosensor, in which a chorismate inducible promoter regulated by natively expressed QsuR was optimized to exhibit a dose-dependent response to exogenously supplemented quinate (a chorismate precursor). A chorismate–pyruvate lyase encoding gene, ubiC, was introduced into C. glutamicum to lower the intracellular chorismate pool, which resulted in loss of dose dependence to quinate. Further, a knockout strain that blocked the conversion of quinate to chorismate also resulted in absence of dose dependence to quinate, validating that the chorismate biosensor is specific to intracellular chorismate pool. The ccMA and chorismate biosensors were dually inserted into C. glutamicum to simultaneously detect intracellularly produced chorismate and ccMA. Biosensors, such as those developed in this study, can be applied in C. glutamicum for multiplex sensing to expedite pathway design and optimization through metabolic engineering in this promising chassis organism. One-Sentence Summary High-throughput screening of promoter libraries in Corynebacterium glutamicum to establish transcription factor based biosensors for key metabolic intermediates in shikimate and β-ketoadipate pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Patient-Reported Outcomes in Pediatric Cancer Registration Trials: A US Food and Drug Administration Perspective

Pediatric patient-reported outcome (PRO) data can help inform the US Food and Drug Administration’s (FDA’s) benefit-risk assessment of cancer therapeutics by quantifying symptom and functional outcomes from the patient’s perspective. This study assessed use of PROs in commercial pediatric oncology trials submitted to the FDA for regulatory review. FDA databases were searched to identify pediatric oncology product applications approved between 1997 and 2020. Sponsor-submitted documents were reviewed to determine whether PRO data were collected, which instruments were used, and the quality of collected data (ie, sample size, completion rates, and use of fit-for-purpose instruments). The role of PROs in each trial (endpoint hierarchy) was also recorded in addition to whether any PRO endpoints were included in product labeling. We reviewed 17 pediatric oncology applications, 4 of which included PRO data: denosumab, tisagenlecleucel, larotrectinib, and selumetinib. In these 4 instances, PROs served as exploratory endpoints and were not incorporated in product labeling. Trials that collected PRO data were phase II or phase I/II single-arm studies with sample sizes of 28 to 88 patients. Symptomatic adverse events (AEs) were characterized using clinician-reported Common Terminology Criteria for Adverse Events (CTCAE) without additional patient self-report. PROs were infrequently used in pediatric cancer registration trials. When PROs were used, PRO data were limited by lack of a clear research objective and corresponding prospective statistical analysis plan. Contemporary PRO symptom libraries, such as the National Cancer Institute’s Pediatric PRO-CTCAE, may provide an opportunity to better evaluate the occurrence and impact of symptomatic AEs, from the patient’s perspective, in pediatric oncology trials.

Oncology↗

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗

Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites

Abstract Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗