Detection of Random Test Failures and their Impact on CI Testing Pipelines
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Bartlett, Roscoe [Sandia National Laboratories (SN↗
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Software Quality Assurance for the MOOSE-Based Open-Source Multiphysics Code Cardinal - An Expanded CI Testing Suite
Cardinal is a wrapping of the GPU-oriented spectral element Computational Fluid Dynamics (CFD) code NekRS and the Monte Carlo particle transport code OpenMC within the Multiphysics Object-Oriented Simulation Environment (MOOSE). Cardinal provides high-resolution thermal-hydraulics and/or radiation transport feedback to MOOSE multiphysics simulations. Multiphysics feedback is implemented in a geometry-agnostic manner which eliminates the need for rigid one-to-one mappings. A generic data transfer implementation also allows NekRS and OpenMC to couple to any MOOSE application, enabling a broad set of multiphysics capabilities. Cardinal simulations can also leverage combinations of MPI, OpenMP, and GPU resources. Cardinal continuous development and improvement efforts have led to the software being considered as a high-fidelity design and licensing tool for key areas of nuclear reactor relevant physics, including neutron transport, fluid flow, heat transfer, and mechanical processes. The fast development and expansion of the software from a pure R&D framework towards its application in the nuclear industry and regulation require a focus on developing, enhancing and, maintaining Cardinal’s software quality through strict adherence to a Software Quality Assurance (SQA) framework and SQA program. To facilitate compliance with SQA standards, the Cardinal SQA Program has been initiated during Fiscal Year 2023 (FY23). During the development of the Cardinal SQA Program, multiple gaps have been identified. These gaps are primarily related to model verification and code pedigree as they relate to the use of Cardinal as a safety analysis tool. These gaps have been captured in a report published in 2023. A second report highlighted the progress made during Fiscal Year 2024 (FY24) and described Argonne’s effort to document and integrate software verification within Cardinal’s software development process. This report documents a snapshot of the verification test cases currently available for Cardinal and NekRS in their assimilation into a Continuous Integration (CI) platform. Following the CI practice permits the integrating of source code changes frequently and ensuring that the integrated codebase clears the verification testing for the software. It should be noted that the SQA program itself, including the program plans, procedures, configuration management, and testing strategies, need to be developed in a future step of this task.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Progress Towards NQA-1 for Cardinal in FY25
Cardinal is a wrapping of the GPU-oriented spectral element Computational Fluid Dynamics (CFD) code NekRS and the Monte Carlo particle transport code OpenMC within the Multiphysics Object-Oriented Simulation Environment (MOOSE). Cardinal provides high-resolution thermal-hydraulics and/or radiation transport feedback to MOOSE multiphysics simulations. Multiphysics feedback is implemented in a geometry-agnostic manner which eliminates the need for rigid one-to-one mappings. A generic data transfer implementation also allows NekRS and OpenMC to couple to any MOOSE application, enabling a broad set of multiphysics capabilities. Cardinal simulations can also leverage combinations of MPI, OpenMP, and GPU resources. Cardinal continuous development and improvement efforts have led to the software being considered as a high-fidelity design and licensing tool for key areas of nuclear reactor relevant physics, including neutron transport, fluid flow, heat transfer, and mechanical processes. The fast development and expansion of the software from a pure R&D framework towards its application in the nuclear industry and regulation require a focus on developing, enhancing,and maintaining Cardinal’s software quality through strict adherence to a Software Quality Assurance (SQA) framework and SQA program. To facilitate compliance with SQA standards, the Cardinal SQA Program was initiated during Fiscal Year 2023 (FY23). During the development of the Cardinal SQA Program, multiple gaps have been identified. These gaps are primarily related to model verification and code pedigree as they relate to the use of Cardinal as an analysis tool. These gaps were captured in a report published in 2023. A second report highlighted the progress made during Fiscal Year 2024 (FY24) and described Argonne’s effort to document and integrate software verification within Cardinal’s software development process. This report documents the progress made towards NQA-1 for Cardinal in the Fiscal Year 2025 (FY25). All cases in the expanded Continuous Integration (CI) suite of NekRS are included in this report which test the solvers and modules available in NekRS exhaustively. The NekRS tests are integrated with the Cardinal CI suite and made available in publicly accessible Github documentation. Following the CI practice permits integrating of source code changes frequently and ensuring that the integrated codebase clears the verification testing for the software. Also in this report is a brief overview of the development of the Cardinal Software Quality Assurance Plan (SQAP) that was done in FY25, though it should be noted that the rest of the documentation for the SQA program needs to be developed in a future step of this task.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Thoroughly testing and integrating hundreds of Pull Requests per month: ROOT’s new Cost-efficient and Feature Rich GitHub-based CI
ROOT is an open source framework, freely available on GitHub, at the heart of data acquisition, processing and analysis of HE(N)P experiments, and beyond. It is developed collaboratively: contributions are not authored only by ROOT team members, but also by the user community at large: developers and scientists from universities, labs as well as the private sector. More than 1500 GitHub Pull Requests are merged on average per year. It is in this context that code integration acquires a primary role. The review of code contributions isn’t enough: not only they need to be thoroughly reviewed, they also need to be thoroughly tested through a powerful CI infrastructure on several different platforms to comply with the high code quality standards of the project. Since the end of 2023, ROOT moved its continuous integration system from Jenkins to GitHub Actions. In this contribution, we characterise the transition to the GitHub CI, focussing on our strategy, its implementation and the lessons learned, as well as the advantages the new system offers with respect to the previous one. Particular emphasis will be given to the evaluation of the cost-benefit ratio for Jenkins and GitHub Actions for the ROOT project. We also describe how we manage to run in less than one hour thousands of unit, integration, functional and end-to-end tests on different flavours of Windows, four versions of macOS, as well as about ten of the most used Linux distributions, taking advantage of the CERN computing infrastructure.
Piparo, Danilo [CERN]↗
dCache CI/CD migration to Kubernetes
For over two decades, the dCache project has provided open-source to satisfy ever-more demanding storage requirements. More than 80 sites worldwide rely on dCache to provide services for LHC experiments, Belle-II, Eu- XFEL, and others. This can be achieved only with a well-established process from a whiteboard, where ideas are created through development, packaging, and testing. The project’s build and test infrastructure is based on Jenkins CI and a set of virtual machines. This infrastructure is maintained by dCache developers. With the introduction of the DESY-central Gitlab server, the developers have started migrating from VM-based testing to container-based deployments in the onsite Kubernetes cluster. As a result, we have packaged dCache containers and Helm charts that can be used by other sites to reproduce our test and build steps quickly or to evaluate new releases on their pre-production systems and, eventually, become a standard model of dCache deployment at the sites. This paper describes the challenges we have faced, the techniques we used to solve them, and the issues that still need to be addressed.
Mkrtchyan, Tigran [DESY]↗
Combining Machine Learning and Comparative Effectiveness Methodology to Study Primary Care Pharmacotherapy Pathways for Veterans With Depression
Our objective is to demonstrate an innovative method combining machine learning with comparative effectiveness research techniques and to investigate a hitherto unstudied question about the effectiveness of common prescribing patterns. For Operation Enduring Freedom/Operation Iraqi Freedom veterans with major depressive disorder, we generate pharmacotherapy pathways (of antidepressants) using process mining and machine learning. We select the medication episodes that were started at subtherapeutic doses by the first assigned primary care physician and observe the paths that those medication episodes follow. Using 2-stage least squares, we test the effectiveness of starting at a low dose and staying low for longer versus ramping up fast while balancing observable and unobservable characteristics of patients and providers through instrumental variables. We leverage predetermined provider practice patterns as instruments. We collected outpatient pharmacy data for selective serotonin reuptake inhibitors and selective norepinephrine reuptake inhibitors, patient and provider characteristics (as control variables), and the instruments for our cohort. All data were extracted for the period between 2006 and 2020. There is a statistically significant positive effect (0.68, 95% CI 0.11–1.25) of “ramping up fast” on engagement in care. When we examine the effect of “ramping up slow”, we see an insignificant negative impact on engagement in care (−0.82, 95% CI −1.89 to 0.25). As expected, the probability of drop-out also seems to have a negative effect on engagement in care (−0.39, 95% CI −0.94 to 0.17). We further validate these results by testing with medication possession ratios calculated periodically as an alternative engagement in care metric. Our findings contradict the “Start low, go slow” adage, indicating that ramping up the dose of an antidepressant faster has a significantly positive effect on engagement in care for our population.
60 APPLIED LIFE SCIENCES↗
Software stewardship and advancement of a high-performance computing scientific application: QMCPACK
Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.
97 MATHEMATICS AND COMPUTING↗
Understanding the Competition between Alcohol Formation and Dimerization during Electrochemical Reduction of Aromatic Carbonyl Compounds
The electrochemical reductive dimerization of small aromatic carbonyl compounds derived from lignocellulosic biomass is a crucial C−C coupling reaction for upgrading small molecules to longchain hydrocarbons, particularly in the synthesis of drop-in sustainable aviation fuels. Although other electrochemical reduction reactions of these reactants (i.e., hydrogenation and hydrogenolysis) have undergone extensive mechanistic investigation, the understanding of dimerization remains relatively underdeveloped. Most importantly, there is a lack of understanding of the selectivity-determining step between dimerization and monomer reduction and critical factors that can affect this step. In this study, we provide a comprehensive mechanistic model to explain the competition between dimerization and monomer reduction of benzaldehyde under various conditions. Our model proposes that the selectivity between dimerization and monomer reduction depends on the competition between desorption of a ketyl radical from the electrode, necessary for dimerization, and further reduction of the ketyl radical to an alcohol on the electrode by proton-coupled electron transfer (PCET). Computationally comparing the adsorption/desorption energy and PCET activation barrier energy is challenging because conventional DFT calculations substantially underestimate the PCET kinetic barriers. In this study, we employed constrained DFTbased configuration interaction (CDFT-CI) to obtain a reliable comparison of these energies. Our mechanistic model was tested and supported by experimental results obtained with four electrodes (Cu, Pb, Bi, graphite), three pH conditions (acidic, neutral, basic), and three potentials. Our study offers a coherent mechanistic foundation that can explain how each of these conditions impacts the desorption and PCET processes and the selectivities for dimerization and alcohol production.
09 BIOMASS FUELS↗
Reducing stomatal density by expression of a synthetic epidermal patterning factor increases leaf intrinsic water use efficiency and reduces plant water use in a C4 crop
Abstract Enhancing crop water use efficiency (WUE) is a key target trait for climatic resilience and expanding cultivation on marginal lands. Engineering lower stomatal density to reduce stomatal conductance (gs) has improved WUE in multiple C3 crop species. However, reducing gs in C3 species often reduces photosynthetic carbon gain. A different response is expected in C4 plants because they possess specialized anatomy and biochemistry which concentrates CO2 at the site of fixation. This modifies the relationship of photosynthesis (AN) with intracellular CO2 concentration (ci), such that photosynthesis is CO2 saturated and reductions in gs are unlikely to limit AN. To test this hypothesis, genetic strategies were investigated to reduce stomatal density in the C4 crop sorghum. Constitutive expression of a synthetic epidermal patterning factor (EPF) transgenic allele in sorghum led to reduced stomatal densities, reduced gs, reduced plant water use, and avoidance of stress during a period of water deprivation. In addition, moderate reduction in stomatal density did not increase stomatal limitation to AN. However, these positive outcomes were associated with negative pleiotropic effects on reproductive development and photosynthetic capacity. Avoiding pleiotropy by targeting expression of the transgene to specific tissues could provide a pathway to improved agronomic outcomes.
59 BASIC BIOLOGICAL SCIENCES↗
pnnl-predictive-phenomics/csc052-gem
Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Bacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.
Torres, Victor E.↗
pnnl-predictive-phenomics/csc031-gem
Genome-Scale Metabolic Model of CarbStor Community member Microbacterium (csc031) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity
McNaughton, Andrew [@PNNL]↗
pnnl-predictive-phenomics/csc009-gem
Genome-Scale Metabolic Model of CarbStore Community member Curtobacterium (csc009) Continuous Validation with Memote These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity
Lin, Tesia↗
pnnl-predictive-phenomics/csc040-gem
Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Rhodococcus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.
McNaughton, Andrew [@PNNL]↗
pnnl-predictive-phenomics/csc043-gem
Genome-Scale Metabolic Model Continuous Validation with Memote for CarbStor Community Member Paenibacillus These repositories contain the continuous validation environment for an organism-specific genome-scale metabolic model (GEM) using Memote. Memote is a software tool that provides a suite of tests to ensure the quality and consistency of metabolic models. By integrating Memote into a continuous integration (CI) workflow, we can automatically validate updates to the GEM, ensuring that model modifications improve or maintain the model's integrity.
Zucker, Jeremy [Pacific Northwest National Laborat↗
Machine-learning-based estimates of global natural vegetated wetland methane emissions (2000–2025)
Wetlands are the largest natural source of atmospheric methane (CH 4 ), yet comprehensive global budgets are typically delayed by years, preventing a timely understanding of CH 4 sources, sinks, and trends. To reduce this delay, we present a model emulator-driven framework and accompanying workflow that enable timely, continuous emission updates using a machine-learning emulator to reconstruct spatially explicit monthly emission fields at 1° × 1° resolution. We apply this framework to a global dataset of natural vegetated wetland CH 4 emissions to extend the most recent Global Methane Budget (GMB; Saunois et al., 2025) record that covers the 2000–2020 emissions through 2025. In the test data (∼ 30 % of the total dataset), the emulator achieved a global R 2 of 0.65 ± 0.003 (mean ± 95 % CI, hereafter) and an RMSE of 5.49 ± 0.12×10 -3 Tg CH 4 yr −1 . The emulator is trained on 35 GMB model estimates, including 22 process-based models and 13 atmospheric inversions, paired with 10 ensemble realizations of 11 gridded climate predictor variables from atmospheric reanalyses. Our results show that the global mean predicted wetland CH 4 emissions for 2021–2025 (157.8 ± 2.4 Tg CH 4 yr −1 ) are not significantly higher (∼ 0.05 Tg CH 4 yr −1 ) than the 2000–2020 baseline. However, this stability masks a significant hemispheric redistribution of emissions. We detect an increase in Northern Hemisphere (NH) emissions in 2021–2025, with mid- and high-latitudes increasing by 0.76 ± 0.07 and 0.35 ± 0.03 Tg CH 4 yr −1 , respectively, while the tropics and Southern Hemisphere (SH) extratropics show offsetting negative trends (−0.95 ± 0.19 and -0.11 ± 0.02 Tg CH 4 yr −1 , respectively). The predicted emissions are able to capture the low emissions in 2023 in South America linked to El Niño-related drought, as reported by recent studies (Ciais et al., 2026; Quinn et al., 2025). Furthermore, we identify a distinct seasonal amplification of global emission trends that peaks in late boreal summer. This new modeled dataset and operational framework bridge the gap between the latest updated budgets and low-latency monitoring, providing a scalable capacity to frequently update global emission estimates and critical early warnings of regional wetland feedback loops. The data are publicly available at https://doi.org/10.5281/zenodo.18870108 (Li et al., 2026).
Li, Mengze [National University of Singapore (Sing↗
Developing an Energy-Conscious Traffic Signal Control System for Optimized Fuel Consumption in Connected Vehicle Environments
The project titled “Developing an Energy-Conscious Traffic Signal Control System for Optimized Fuel Consumption in Connected Vehicle Environments” addresses energy-related challenges associated with adaptive traffic control systems by integrating connected vehicles (CV) and connected infrastructure (CI). The system developed in this project, a CV-based adaptive traffic control system, aims to improve fuel consumption in mixed traffic environments by capitalizing on emerging CV and CI communication technologies, as well as leveraging recent advances in Artificial Intelligence (AI), optimization, and edge computing. The system was tested at the MLK Smart Corridor, an urban testbed managed by the University of Tennessee at Chattanooga (UTC) and the City of Chattanooga. The system was validated through extensive simulations, both Software-in-the-Loop (SILS) and Hardware-in-the-Loop (HILS), and was further implemented and tested in real-world conditions at several intersections along the corridor. The Fuel Consumption Performance Index (FC-PI) and the Ecological Performance Index (Eco-PI) were developed as the key components for evaluating the system’s impact on fuel consumption and emissions. These metrics provided a comprehensive means of understanding the impact of traffic signal control optimization in mixed traffic environments. The report presents an in-depth analysis of the Eco-PI, FC-PI, adaptive traffic control system integration, and the testing and field implementation of the system. The results demonstrate significant reductions in fuel consumption and emissions, showcasing the system’s capability to contribute to more sustainable urban traffic management. The report also documents the challenges encountered and recommendations for scaling and further improving the system.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Ion Exchange Processing of AN-107 Hanford Tank Waste through Crystalline Silicotitanate in a Staged 2- then 3-Column System
The Hanford Site stores an estimated 56 million gallons of mixed radioactive and chemically hazardous waste in large underground tanks. In support of the Direct Feed Low-Activity Waste (DFLAW) Program for expediting Hanford tank waste supernate treatment, laboratory-scale ion exchange processing using prototypic unit operations was conducted on AN-107 tank waste at the Pacific Northwest National Laboratory Radiochemical Processing Laboratory. This report describes the small-scale ion exchange testing with 13.7 L of diluted and filtered supernate from Tank 241-AN-107 (hereafter referred to as AN-107) at 16 °C (62 °F). One of the waste acceptance criteria (WAC) for the Waste Treatment Plant (WTP) Low-Activity Waste Facility is that the waste must contain less than 3.18×10 -5 Ci 137 Cs per mole of Na. For the AN-107 tank waste to meet this criterion, only 0.147% of the influent 137 Cs concentration may be delivered to the WTP; this requires a Cs decontamination factor of 678. Testing with AN-107 matched current Tank Side Cesium Removal (TSCR) facility prototypic operations where a lead-lag configuration was used until the lag column reached the WAC limit, then a polish column was brought online for continued processing in a lead-lag-polish column configuration. Feed was processed at 1.9 bed volumes (BVs) per hour; the flowrate, in terms of contact time with the crystalline silicotitanate (CST) bed, matched the expected flowrate at TSCR. The Cs-decontaminated product was retained for vitrification testing (to be reported separately). The lead column reached 40% Cs breakthrough after processing ~1700 BVs of feed; the 50% Cs breakthrough was extrapolated from the breakthrough data to occur at 1873 BVs. Testing compared to previous AP-101 and AP-107 testing at 16 °C showed ~300 BV increases in volume processed to reach the WAC limit for both lead and lag columns. The increase in capacity was determined to be due to the significantly lower K concentration in the AN-107 compared to the other tank waste matrices. A comparison in breakthrough curves for the three tests indicated slightly slower kinetic behavior in the AN-107, with variations in feed matrices (high organic complexants) likely responsible for the deviation. The Cs effluent from the lag column reached the WAC limit after processing 1097 BVs. Anticipating this breakthrough point, the polish column was preemptively installed around 900 BVs. Cs breakthrough from the lag column began at 500 BVs, reaching 3.06×10 0 µCi/mL, or 2.6 % Cs breakthrough, after processing all 1700 BVs of feed. Table S.1 and Figure S.1 summarize the observed column performance and relevant Cs loading characteristics.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Ion Exchange Processing of AW-105 Hanford Tank Waste through Crystalline Silicotitanate in a Staged 2- then 3-Column System
The Hanford Site stores an estimated 56 million gallons of mixed radioactive and chemically hazardous waste in large underground tanks. In support of the Direct Feed Low-Activity Waste (DFLAW) Program for expediting Hanford tank waste supernate treatment, laboratory-scale ion exchange processing using prototypic unit operations was conducted on AW-105 tank waste at the Pacific Northwest National Laboratory Radiochemical Processing Laboratory. This report describes the small-scale ion exchange testing with 9.2 L of diluted and filtered supernate from Tank 241-AW-105 (hereafter referred to as AW-105) at 16 °C (62 °F). One of the waste acceptance criteria (WAC) for the Waste Treatment Plant (WTP) Low-Activity Waste Facility is that the waste must contain less than 3.18×10 -5 Ci 137 Cs per mole of Na. For the AW-105 tank waste to meet this criterion, only 0.225% of the influent 137 Cs concentration may be delivered to the WTP; this requires a Cs decontamination factor of 445. Testing with AW-105 matched current Tank Side Cesium Removal (TSCR) facility prototypic operations where a lead-lag configuration was used until the lag column reached the WAC limit, then a polish column was brought online for continued processing in a lead-lag-polish column configuration. Feed was processed at 1.9 bed volumes (BVs) per hour; the flowrate, in terms of contact time with the crystalline silicotitanate (CST) bed, matched the expected flowrate at TSCR. The Cs-decontaminated product was retained for vitrification testing (to be reported separately). The lead column reached 83% Cs breakthrough after processing ~1500 BVs of feed; the 50% Cs breakthrough was interpolated from the breakthrough data and occurred at 1041 BVs. Despite the AW-105 having a significantly higher K concentration (0.55 M compared to 0.10 M), testing compared to previous AP-107 ion exchange column testing at 16 °C showed no difference in BVs processed to reach the WAC on the lead column and only an approximate ~20 BV decrease in volume processed to reach the WAC limit on the lag column. The negligible differences in capacity despite the 5x concentration differences in K was determined to be due to the significantly lower NO3 concentration in the AW-105 supernate compared to the AP-107 tank waste matrix. A comparison in breakthrough curves for the two tests also indicated slightly faster kinetic behavior in the AW-105, with the variations in feed matrices (lower NO3 concentration) likely responsible for the deviation. The Cs effluent from the lag column reached the WAC limit after processing 772 BVs. Anticipating this breakthrough point, the polish column was preemptively installed around 675 BVs. Cs breakthrough from the lag column began at 300 BVs, reaching 1.10×10 1 µCi/mL, or 14.13 % Cs breakthrough, after processing all 1500 BVs of feed. The polish column processed nominally 830 BVs and reached 2.10×10 -1 µCi/mL, or 0.27 % Cs breakthrough at the conclusion of the test. Table S.1 and Figure S.1 summarize the observed column performance and relevant Cs loading characteristics.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗