| 1. |
- Murari, A., et al.
(author)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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In: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 2. |
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| 6. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 7. |
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| 8. |
- Litaudon, X., et al.
(author)
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EUROfusion-theory and advanced simulation coordination (E-TASC): programme and the role of high performance computing
- 2022
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In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 64:3
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Journal article (peer-reviewed)abstract
- This paper is a written summary of an overview oral presentation given at the 1st Spanish Fusion High Performance Computer (HPC) Workshop that took place on the 27 November 2020 as an online event. Given that over the next few years ITER24 will move to its operation phase and the European-DEMO design will be significantly advanced, the EUROfusion consortium has initiated a coordination effort in theory and advanced simulation to address some of the challenges of the fusion research in Horizon EUROPE (2021-2027), i.e. the next EU Framework Programme for Research and Technological Development. This initiative has been called E-TASC, which stands for EUROfusion-Theory and Advanced Simulation Coordination. The general and guiding principles of E-TASC are summarized in this paper. In addition, an overview of the scientific results obtained in the pilot phase (2019-2020) of E-TASC are provided while highlighting the importance of the required progress in computational methods and HPC techniques. In the initial phase, five pilot theory and simulation tasks were initiated: towards a validated predictive capability of the low to high transition and pedestal physics; runaway electrons in tokamak disruptions in the presence of massive material injection; fast code for the calculation of neoclassical toroidal viscosity in stellarators and tokamaks; development of a neutral gas kinetics modular code; European edge and boundary code for reactor-relevant devices. In this paper, we report on recent progress made by each of these projects.
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| 9. |
- Ham, C. J., et al.
(author)
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Towards understanding reactor relevant tokamak pedestals
- 2021
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In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 61:9
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Journal article (peer-reviewed)abstract
- The physics of the tokamak pedestal is still not fully understood, for example there is no fully predictive model for the pedestal height and width. However, the pedestal is key in determining the fusion power for a given scenario. If we can improve our understanding of reactor relevant pedestals we will improve our confidence in designing potential fusion power plants. Work has been carried out as part of a collaboration on reactor relevant pedestal physics. We report some of the results in detail here and review some of the wider work which will be reported in full elsewhere. First, we attempt to use a gyrokinetic-based calculation to eliminate the pedestal top density as a model input for Europed/EPED pedestal predictions. We assume power balance at the top of the pedestal, that is, the heat flux crossing the separatrix must be equal to the heat source at the top of the pedestal and investigate the consequences of this assumption. Unfortunately, the transport assumptions of the EPED model mean that this method does not discriminate between different pairs of density and temperature profiles for a given pressure profile. Second, we investigate the effects of non flux surface density on the bootstrap current. Third, type I ELMs will not be tolerable for a reactor relevant regime due to the damage that they are expected to cause to plasma facing components. In recent years various methods of running tokamak plasmas without large ELMs have been developed. These include small and no ELM regimes, the use of resonant magnetic perturbations and the use of vertical kicks. We discuss the quiescent H-mode here. Finally we give a summary and directions for future work.
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| 10. |
- Hatch, D. R., et al.
(author)
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Microtearing modes as the source of magnetic fluctuations in the JET pedestal
- 2021
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 61:3
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Journal article (peer-reviewed)abstract
- We report on a detailed study of magnetic fluctuations in the JET pedestal, employing basic theoretical considerations, gyrokinetic simulations, and experimental fluctuation data to establish the physical basis for their origin, role, and distinctive characteristics. We demonstrate quantitative agreement between gyrokinetic simulations of microtearing modes (MTMs) and two magnetic frequency bands with corresponding toroidal mode numbers n = 4 and 8. Such disparate fluctuation scales, with substantial gaps between toroidal mode numbers, are commonly observed in pedestal fluctuations. Here we provide a clear explanation, namely the alignment of the relevant rational surfaces (and not others) with the peak in the omega(*) profile, which is localized in the steep gradient region of the pedestal. We demonstrate that a global treatment is required to capture this effect. Nonlinear simulations suggest that the MTM fluctuations produce experimentally-relevant transport levels and saturate by relaxing the background electron temperature gradient, slightly downshifting the fluctuation frequencies from the linear predictions. Scans in collisionality are compared with a simple MTM dispersion relation. At the experimental points considered, MTM growth rates can either increase or decrease with collision frequency depending on the parameters thus defying any simple characterization of collisionality dependence.
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| 11. |
- Heimisdottir, L.H., et al.
(author)
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Metabolomics Insights in Early Childhood Caries
- 2021
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In: Journal of Dental Research. - : Sage Publications. - 0022-0345 .- 1544-0591. ; 100:6, s. 615-622
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Journal article (peer-reviewed)abstract
- Dental caries is characterized by a dysbiotic shift at the biofilm–tooth surface interface, yet comprehensive biochemical characterizations of the biofilm are scant. We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study’s analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North Carolina and were enrolled in a community-based cross-sectional study of early childhood oral health. Clinical examinations were conducted by calibrated examiners in community locations using International Caries Detection and Classification System (ICDAS) criteria. Supragingival plaque collected from the facial/buccal surfaces of all primary teeth in the upper-left quadrant was analyzed using ultra-performance liquid chromatography–tandem mass spectrometry. Associations between individual metabolites and 18 clinical traits (based on different ECC definitions and sets of tooth surfaces) were quantified using Brownian distance correlations (dCor) and linear regression modeling of log2-transformed values, applying a false discovery rate multiple testing correction. A tree-based pipeline optimization tool (TPOT)–machine learning process was used to identify the best-fitting ECC classification metabolite model. There were 503 named metabolites identified, including microbial, host, and exogenous biochemicals. Most significant ECC-metabolite associations were positive (i.e., upregulations/enrichments). The localized ECC case definition (ICDAS ≥1 caries experience within the surfaces from which plaque was collected) had the strongest correlation with the metabolome (dCor P = 8 × 10−3). Sixteen metabolites were significantly associated with ECC after multiple testing correction, including fucose (P = 3.0 × 10−6) and N-acetylneuraminate (p = 6.8 × 10−6) with higher ECC prevalence, as well as catechin (P = 4.7 × 10−6) and epicatechin (P = 2.9 × 10−6) with lower. Catechin, epicatechin, imidazole propionate, fucose, 9,10-DiHOME, and N-acetylneuraminate were among the top 15 metabolites in terms of ECC classification importance in the automated TPOT model. These supragingival biofilm metabolite findings provide novel insights in ECC biology and can serve as the basis for the development of measures of disease activity or risk assessment.
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| 12. |
- Chapman-Oplopoiou, B., et al.
(author)
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The role of ETG modes in JET-ILW pedestals with varying levels of power and fuelling
- 2022
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:8
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Journal article (peer-reviewed)abstract
- We present the results of GENE gyrokinetic calculations based on a series of JET-ITER-like-wall (ILW) type I ELMy H-mode discharges operating with similar experimental inputs but at different levels of power and gas fuelling. We show that turbulence due to electron-temperature-gradient (ETGs) modes produces a significant amount of heat flux in four JET-ILW discharges, and, when combined with neoclassical simulations, is able to reproduce the experimental heat flux for the two low gas pulses. The simulations plausibly reproduce the high-gas heat fluxes as well, although power balance analysis is complicated by short ELM cycles. By independently varying the normalised temperature gradients (omega(T)(e)) and normalised density gradients (omega(ne )) around their experimental values, we demonstrate that it is the ratio of these two quantities eta(e) = omega(Te)/omega(ne) that determines the location of the peak in the ETG growth rate and heat flux spectra. The heat flux increases rapidly as eta(e) increases above the experimental point, suggesting that ETGs limit the temperature gradient in these pulses. When quantities are normalised using the minor radius, only increases in omega(Te) produce appreciable increases in the ETG growth rates, as well as the largest increases in turbulent heat flux which follow scalings similar to that of critical balance theory. However, when the heat flux is normalised to the electron gyro-Bohm heat flux using the temperature gradient scale length L-Te, it follows a linear trend in correspondence with previous work by different authors.
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| 13. |
- Field, A. R., et al.
(author)
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Comparing pedestal structure in JET-ILW H-mode plasmas with a model for stiff ETG turbulent heat transport
- 2023
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In: Philosophical Transactions. Series A. - : The Royal Society. - 1364-503X .- 1471-2962. ; 381:2242
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Journal article (peer-reviewed)abstract
- A predictive model for the electron temperature profile of the H-mode pedestal is described, and its results are compared with the pedestal structure of JET-ILW plasmas. The model is based on a scaling for the gyro-Bohm normalized, turbulent electron heat flux qe/qe,gB resulting from electron temperature gradient (ETG) turbulence, derived from results of nonlinear gyrokinetic (GK) calculations for the steep gradient region. By using the local temperature gradient scale length L-Te in the normalization, the dependence of q(e)/q(e,g)B on the normalized gradients R/L-Te and R/(Lne) can be represented by a unified scaling with the parameter eta(e) = L-ne/L-Te, to which the linear stability of ETG turbulence is sensitive when the density gradient is sufficiently steep. For a prescribed density profile, the value of R/L-Te determined from this scaling, required to maintain a constant electron heat flux qe across the pedestal, is used to calculate the temperature profile. Reasonable agreement with measurements is found for different cases, the model providing an explanation of the relative widths and shifts of the T-e and n(e) profiles, as well as highlighting the importance of the separatrix boundary conditions. Other cases showing disagreement indicate conditions where other branches of turbulence might dominate.This article is part of a discussion meeting issue "H-mode transition and pedestal studies in fusion plasmas'.
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| 14. |
- Field, A. R., et al.
(author)
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The dependence of exhaust power components on edge gradients in JET-C and JET-ILW H-mode plasmas
- 2020
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In: Plasma Physics and Controlled Fusion. - : IOP PUBLISHING LTD. - 0741-3335 .- 1361-6587. ; 62:5
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Journal article (peer-reviewed)abstract
- Exhaust power components due to ELMs, radiation and heat transport across the edge transport barrier (ETB) between ELMs are quantifed for H-mode plasmas in JET-C and JET-ILW for comparison with simulations of pedestal heat transport. In low-current, JET-ILW pulses with a low rate of gas fuelling, the pedestal heat transport is found not to be stiff, i.e. the effective, mean heat diffusivity ac n eff does not increase with the electron temperature gradient adTe dRnped across the pedestal and the parameter he = Lne LTe increases with the conducted loss power across the pedestal, with the latter saturating at mean values.h.. 2 e ped. This increase in pedestal temperature gradient is partly due to a relative reduction of the ion neo-classical heat transport (which is more significant at low plasma current) with decreasing collisionality at higher power. In JET-ILW pulses, significantly more power is required at a high gas puffing rate to achieve a similar pedestal pressure and normalised confinement to that in otherwise similar JET-C pulses without gas-puffing. The increased heat transport across the JET-ILW pedestals is caused by changes to the pedestal structure induced by the gas puffing, which is required to mitigate contamination by W impurities sputtered from the target plates. In high-power JET-ILW pulses, the radiated power is dominated by that from W, which exhibits a highly asymmetric poloidal distribution due to toroidal rotation. During the ELMy H-mode phase, the W is concentrated in the outer `mantle' region (0.7. r. 0.96 N) inside the pedestal top by a favourable alignment of profile gradients, where it can be effectively flushed by ELMs. Transport analysis reveals that the strong mantle radiation cools the outer region of the plasma, causing more of the heat to be lost through the electron channel. However, direct cooling by W radiation from the ETB region is shown to be insignificant compared to the power conducted through the pedestal.
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| 15. |
- Frassinetti, Lorenzo, et al.
(author)
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Role of the separatrix density in the pedestal performance in deuterium low triangularity JET-ILW plasmas and comparison with JET-C
- 2021
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In: Nuclear Fusion. - : IOP Publishing Ltd. - 0029-5515 .- 1741-4326. ; 61:12
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Journal article (peer-reviewed)abstract
- A reduction of the pedestal pressure with increasing separatrix density over pedestal density (n (e) (sep)/n (e) (ped)) has been observed in JET. The physics behind this correlation is investigated. The correlation is due to two distinct mechanisms. The increase of n (e) (sep)/n (e) (ped) till approximate to 0.4 shifts the pedestal pressure radially outwards, decreasing the peeling-balloning stability and reducing the pressure height. The effect of the position saturates above n (e) (sep)/n (e) (ped) approximate to 0.4. For higher values, the reduction of the pedestal pressure is ascribed to increased turbulent transport and, likely, to resistive MHD effects. The increase of n (e) (sep)/n (e) (ped) above approximate to 0.4 reduces backward difference n (e) /n (e), increasing eta (e) and the pedestal turbulent transport. This reduces the pressure gradient and the pedestal temperature, producing an increase in the pedestal resistivity. The work suggests that the increase in resistivity might destabilize resistive balloning modes, further reducing the pedestal stability.
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| 16. |
- Smith, Annabel L., et al.
(author)
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Global gene flow releases invasive plants from environmental constraints on genetic diversity
- 2020
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:8, s. 4218-4227
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Journal article (peer-reviewed)abstract
- When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata. Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area.
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| 17. |
- Villellas, Jesus, et al.
(author)
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Phenotypic plasticity masks range-wide genetic differentiation for vegetative but not reproductive traits in a short-lived plant
- 2021
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In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 24:11, s. 2378-2393
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Journal article (peer-reviewed)abstract
- Genetic differentiation and phenotypic plasticity jointly shape intraspecific trait variation, but their roles differ among traits. In short-lived plants, reproductive traits may be more genetically determined due to their impact on fitness, whereas vegetative traits may show higher plasticity to buffer short-term perturbations. Combining a multi-treatment greenhouse experiment with observational field data throughout the range of a widespread short-lived herb, Plantago lanceolata, we (1) disentangled genetic and plastic responses of functional traits to a set of environmental drivers and (2) assessed how genetic differentiation and plasticity shape observational trait–environment relationships. Reproductive traits showed distinct genetic differentiation that largely determined observational patterns, but only when correcting traits for differences in biomass. Vegetative traits showed higher plasticity and opposite genetic and plastic responses, masking the genetic component underlying field-observed trait variation. Our study suggests that genetic differentiation may be inferred from observational data only for the traits most closely related to fitness.
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| 18. |
- Wijewardene, A, et al.
(author)
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Change in Practice of Radioactive Iodine Administration in Differentiated Thyroid Cancer: A Single-Centre Experience
- 2021
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In: European thyroid journal. - : Bioscientifica. - 2235-0640 .- 2235-0802. ; 10:5, s. 408-415
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Journal article (peer-reviewed)abstract
- <b><i>Objective:</i></b> Our study aimed to analyse temporal trends in radioactive iodine (RAI) treatment for thyroid cancer over the past decade; to analyse key factors associated with clinical decisions in RAI dosing; and to confirm lower activities of RAI for low-risk patients were not associated with an increased risk of recurrence. <b><i>Methods:</i></b> Retrospective analysis of 1,323 patients who received RAI at a quaternary centre in Australia between 2008 and 2018 was performed. Prospectively collected data included age, gender, histology, and American Joint Committee on Cancer stage (7th ed). American Thyroid Association risk was calculated retrospectively. <b><i>Results:</i></b> The median activities of RAI administered to low-risk patients decreased from 3.85 GBq (104 mCi) in 2008–2016 to 2.0 GBq (54 mCi) in 2017–2018. The principal driver of this change was an increased use of 1 GBq (27 mCi) from 1.3% of prescriptions in 2008–2011 to 18.5% in 2017–2018. In patients assigned as low risk per ATA stratification, lower activities of 1 GBq or 2 GBq (27 mCi or 54 mCi) were not associated with an increased risk of recurrence. In patients assigned to intermediate- or high-risk categories who received RAI as adjuvant therapy, there was no difference in risk of recurrence between 4 GBq (108 mCi) and 6 GBq (162 mCi). <b><i>Conclusions:</i></b> Our data demonstrate an evolution of RAI activities consistent with translation of ATA guidelines into clinical practice. Use of lower RAI activities was not associated with an increase in recurrence in low-risk thyroid cancer patients. Our data also suggest lower RAI activities may be as efficacious for adjuvant therapy in intermediate- and high-risk patients.
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