| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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| 3. |
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| 4. |
- Bombarda, F., et al.
(författare)
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Runaway electron beam control
- 2019
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Ingår i: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 61:1
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Tidskriftsartikel (refereegranskat)
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| 5. |
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| 6. |
- Brezinsek, S., et al.
(författare)
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Beryllium migration in JET ITER-like wall plasmas
- 2015
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 55:6
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Tidskriftsartikel (refereegranskat)abstract
- JET is used as a test bed for ITER, to investigate beryllium migration which connects the lifetime of first-wall components under erosion with tokamak safety, in relation to long-term fuel retention. The (i) limiter and the (ii) divertor configurations have been studied in JET-ILW (JET with a Be first wall and W divertor), and compared with those for the former JET-C (JET with carbon-based plasma-facing components (PFCs)). (i) For the limiter configuration, the Be gross erosion at the contact point was determined in situ by spectroscopy as between 4% (E-in = 35 eV) and more than 100%, caused by Be self-sputtering (E-in = 200 eV). Chemically assisted physical sputtering via BeD release has been identified to contribute to the effective Be sputtering yield, i.e. at E-in = 75 eV, erosion was enhanced by about 1/3 with respect to the bare physical sputtering case. An effective gross yield of 10% is on average representative for limiter plasma conditions, whereas a factor of 2 difference between the gross erosion and net erosion, determined by post-mortem analysis, was found. The primary impurity source in the limiter configuration in JET-ILW is only 25% higher (in weight) than that for the JET-C case. The main fraction of eroded Be stays within the main chamber. (ii) For the divertor configuration, neutral Be and BeD from physically and chemically assisted physical sputtering by charge exchange neutrals and residual ion flux at the recessed wall enter the plasma, ionize and are transported by scrape-off layer flows towards the inner divertor where significant net deposition takes place. The amount of Be eroded at the first wall (21 g) and the Be amount deposited in the inner divertor (28 g) are in fair agreement, though the balancing is as yet incomplete due to the limited analysis of PFCs. The primary impurity source in the JET-ILW is a factor of 5.3 less in comparison with that for JET-C, resulting in lower divertor material deposition, by more than one order of magnitude. Within the divertor, Be performs far fewer re-erosion and transport steps than C due to an energetic threshold for Be sputtering, and inhibits as a result of this the transport to the divertor floor and the pump duct entrance. The target plates in the JET-ILW inner divertor represent at the strike line a permanent net erosion zone, in contrast to the net deposition zone in JET-C with thick carbon deposits on the CFC (carbon-fibre composite) plates. The Be migration identified is consistent with the observed low long-term fuel retention and dust production with the JET-ILW.
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| 7. |
- Brezinsek, S., et al.
(författare)
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Erosion, screening, and migration of tungsten in the JET divertor
- 2019
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Ingår i: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 59:9
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Tidskriftsartikel (refereegranskat)abstract
- The erosion of tungsten (W), induced by the bombardment of plasma and impurity particles, determines the lifetime of plasma-facing components as well as impacting on plasma performance by the influx of W into the confined region. The screening of W by the divertor and the transport of W in the plasma determines largely the W content in the plasma core, but the W source strength itself has a vital impact on this process. The JET tokamak experiment provides access to a large set of W erosion-determining parameters and permits a detailed description of the W source in the divertor closest to the ITER one: (i) effective sputtering yields and fluxes as function of impact energy of intrinsic (Be, C) and extrinsic (Ne, N) impurities as well as hydrogenic isotopes (H, D) are determined and predictions for the tritium (T) isotope are made. This includes the quantification of intra- and inter-edge localised mode (ELM) contributions to the total W source in H-mode plasmas which vary owing to the complex flux compositions and energy distributions in the corresponding phases. The sputtering threshold behaviour and the spectroscopic composition analysis provides an insight in the dominating species and plasma phases causing W erosion. (ii) The interplay between the net and gross W erosion source is discussed considering (prompt) re-deposition, thus, the immediate return of W ions back to the surface due to their large Larmor radius, and surface roughness, thus, the difference between smooth bulk-W and rough W-coating components used in the JET divertor. Both effects impact on the balance equation of local W erosion and deposition. (iii) Post-mortem analysis reveals the net erosion/deposition pattern and the W migration paths over long periods of plasma operation identifying the net W transport to remote areas. This W transport is related to the divertor plasma regime, e.g. attached operation with high impact energies of impinging particles or detached operation, as well as to the applied magnetic configuration in the divertor, e.g. close divertor with good geometrical screening of W or open divertor configuration with poor screening. JET equipped with the ITER-like wall (ILW) provided unique access to the net W erosion rate within a series of 151 subsequent H-mode discharges (magnetic field: B-t = 2.0 T, plasma current: I-p = 2.0 MA, auxiliary power P-aux = 12 MW) in one magnetic configuration accumulating 900 s of plasma with particle fluences in the range of 5-6 x 10(26) D(+ )m(-2) in the semi-detached inner and attached outer divertor leg. The comparison of W spectroscopy in the intra-ELM and inter-ELM phases with post-mortem analysis of W marker tiles provides a set of gross and net W erosion values at the outer target plate. ERO code simulations are applied to both divertor leg conditions and reproduce the erosion/deposition pattern as well as confirm the high experimentally observed prompt W re-deposition factors of more than 95% in the intra- and inter-ELM phase of the unseeded deuterium H-mode plasma. Conclusions to the expected divertor conditions in ITER as well as to the JET operation in the DT plasma mixture are drawn on basis of this unique benchmark experiment.
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| 8. |
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| 9. |
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| 10. |
- Garnier, Nicolas, et al.
(författare)
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Genetic newborn screening and digital technologies : A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:11
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Tidskriftsartikel (refereegranskat)abstract
- Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research project, which resulted of a joint effort between the European Union Commission and the European Federation of Pharmaceutical Industries and Associations. It focuses on genetic newborn screening and artificial intelligence-based tools which will be applied to a large European population of about 25.000 infants. The neonatal screening strategy will be based on targeted sequencing, while whole genome sequencing will be offered to all enrolled infants who may show early symptoms but have resulted negative at the targeted sequencing-based newborn screening. We will leverage artificial intelligence-based algorithms to identify patients using Electronic Health Records (EHR) and to build a repository "symptom checkers" for patients and healthcare providers. S4C will design an equitable, ethical, and sustainable framework for genetic newborn screening and new digital tools, corroborated by a large workout where legal, ethical, and social complexities will be addressed with the intent of making the framework highly and flexibly translatable into the diverse European health systems.
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| 11. |
- Haugg, Amelie, et al.
(författare)
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Can we predict real-time fMRI neurofeedback learning success from pretraining brain activity?
- 2020
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 41:14, s. 3839-3854
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Tidskriftsartikel (refereegranskat)abstract
- Neurofeedback training has been shown to influence behavior in healthy participants as well as to alleviate clinical symptoms in neurological, psychosomatic, and psychiatric patient populations. However, many real-time fMRI neurofeedback studies report large inter-individual differences in learning success. The factors that cause this vast variability between participants remain unknown and their identification could enhance treatment success. Thus, here we employed a meta-analytic approach including data from 24 different neurofeedback studies with a total of 401 participants, including 140 patients, to determine whether levels of activity in target brain regions during pretraining functional localizer or no-feedback runs (i.e., self-regulation in the absence of neurofeedback) could predict neurofeedback learning success. We observed a slightly positive correlation between pretraining activity levels during a functional localizer run and neurofeedback learning success, but we were not able to identify common brain-based success predictors across our diverse cohort of studies. Therefore, advances need to be made in finding robust models and measures of general neurofeedback learning, and in increasing the current study database to allow for investigating further factors that might influence neurofeedback learning.
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| 12. |
- Haugg, Amelie, et al.
(författare)
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Predictors of real-time fMRI neurofeedback performance and improvement - A machine learning mega-analysis.
- 2021
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Ingår i: NeuroImage. - : Elsevier. - 1053-8119 .- 1095-9572. ; 237
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Tidskriftsartikel (refereegranskat)abstract
- Real-time fMRI neurofeedback is an increasingly popular neuroimaging technique that allows an individual to gain control over his/her own brain signals, which can lead to improvements in behavior in healthy participants as well as to improvements of clinical symptoms in patient populations. However, a considerably large ratio of participants undergoing neurofeedback training do not learn to control their own brain signals and, consequently, do not benefit from neurofeedback interventions, which limits clinical efficacy of neurofeedback interventions. As neurofeedback success varies between studies and participants, it is important to identify factors that might influence neurofeedback success. Here, for the first time, we employed a big data machine learning approach to investigate the influence of 20 different design-specific (e.g. activity vs. connectivity feedback), region of interest-specific (e.g. cortical vs. subcortical) and subject-specific factors (e.g. age) on neurofeedback performance and improvement in 608 participants from 28 independent experiments. With a classification accuracy of 60% (considerably different from chance level), we identified two factors that significantly influenced neurofeedback performance: Both the inclusion of a pre-training no-feedback run before neurofeedback training and neurofeedback training of patients as compared to healthy participants were associated with better neurofeedback performance. The positive effect of pre-training no-feedback runs on neurofeedback performance might be due to the familiarization of participants with the neurofeedback setup and the mental imagery task before neurofeedback training runs. Better performance of patients as compared to healthy participants might be driven by higher motivation of patients, higher ranges for the regulation of dysfunctional brain signals, or a more extensive piloting of clinical experimental paradigms. Due to the large heterogeneity of our dataset, these findings likely generalize across neurofeedback studies, thus providing guidance for designing more efficient neurofeedback studies specifically for improving clinical neurofeedback-based interventions. To facilitate the development of data-driven recommendations for specific design details and subpopulations the field would benefit from stronger engagement in open science research practices and data sharing.
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| 13. |
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| 14. |
- Joffrin, E., et al.
(författare)
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Overview of the JET preparation for deuterium-tritium operation with the ITER like-wall
- 2019
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:11
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Forskningsöversikt (refereegranskat)abstract
- For the past several years, the JET scientific programme (Pamela et al 2007 Fusion Eng. Des. 82 590) has been engaged in a multi-campaign effort, including experiments in D, H and T, leading up to 2020 and the first experiments with 50%/50% D-T mixtures since 1997 and the first ever D-T plasmas with the ITER mix of plasma-facing component materials. For this purpose, a concerted physics and technology programme was launched with a view to prepare the D-T campaign (DTE2). This paper addresses the key elements developed by the JET programme directly contributing to the D-T preparation. This intense preparation includes the review of the physics basis for the D-T operational scenarios, including the fusion power predictions through first principle and integrated modelling, and the impact of isotopes in the operation and physics of D-T plasmas (thermal and particle transport, high confinement mode (H-mode) access, Be and W erosion, fuel recovery, etc). This effort also requires improving several aspects of plasma operation for DTE2, such as real time control schemes, heat load control, disruption avoidance and a mitigation system (including the installation of a new shattered pellet injector), novel ion cyclotron resonance heating schemes (such as the three-ions scheme), new diagnostics (neutron camera and spectrometer, active Alfven eigenmode antennas, neutral gauges, radiation hard imaging systems...) and the calibration of the JET neutron diagnostics at 14 MeV for accurate fusion power measurement. The active preparation of JET for the 2020 D-T campaign provides an incomparable source of information and a basis for the future D-T operation of ITER, and it is also foreseen that a large number of key physics issues will be addressed in support of burning plasmas.
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| 15. |
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| 16. |
- Kirschner, A., et al.
(författare)
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Modelling of tungsten erosion and deposition in the divertor of JET-ILW in comparison to experimental findings
- 2019
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Ingår i: Nuclear Materials and Energy. - : Elsevier. - 2352-1791. ; 18, s. 239-244
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Tidskriftsartikel (refereegranskat)abstract
- The erosion, transport and deposition of tungsten in the outer divertor of JET-ILW has been studied for an H-Mode discharge with low frequency ELMs. For this specific case with an inter-ELM electron temperature at the strike point of about 20 eV, tungsten sputtering between ELMs is almost exclusively due to beryllium impurity and self-sputtering. However, during ELMs tungsten sputtering due to deuterium becomes important and even dominates. The amount of simulated local deposition of tungsten relative to the amount of sputtered tungsten in between ELMs is very high and reaches values of 99% for an electron density of 5E13 cm(-3) at the strike point and electron temperatures between 10 and 30 eV. Smaller deposition values are simulated with reduced electron density. The direction of the B-field significantly influences the local deposition and leads to a reduction if the E x B drift directs towards the scrape-off-layer. Also, the thermal force can reduce the tungsten deposition, however, an ion temperature gradient of about 0.1 eV/mm or larger is needed for a significant effect. The tungsten deposition simulated during ELMs reaches values of about 98% assuming ELM parameters according to free-streaming model. The measured WI emission profiles in between and within ELMs have been reproduced by the simulation. The contribution to the overall net tungsten erosion during ELMs is about 5 times larger than the one in between ELMs for the studied case. However, this is due to the rather low electron temperature in between ELMs, which leads to deuterium impact energies below the sputtering threshold for tungsten.
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| 17. |
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| 18. |
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| 19. |
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| 20. |
- Litjens, Geert, et al.
(författare)
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Evaluation of prostate segmentation algorithms for MRI : The PROMISE12 challenge
- 2014
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Ingår i: Medical Image Analysis. - : Elsevier BV. - 1361-8415 .- 1361-8423. ; 18:2, s. 359-373
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Tidskriftsartikel (refereegranskat)abstract
- Prostate MRI image segmentation has been an area of intense research due to the increased use of MRI as a modality for the clinical workup of prostate cancer. Segmentation is useful for various tasks, e.g. to accurately localize prostate boundaries for radiotherapy or to initialize multi-modal registration algorithms. In the past, it has been difficult for research groups to evaluate prostate segmentation algorithms on multi-center, multi-vendor and multi-protocol data. Especially because we are dealing with MR images, image appearance, resolution and the presence of artifacts are affected by differences in scanners and/or protocols, which in turn can have a large influence on algorithm accuracy. The Prostate MR Image Segmentation (PROMISE12) challenge was setup to allow a fair and meaningful comparison of segmentation methods on the basis of performance and robustness. In this work we will discuss the initial results of the online PROMISE12 challenge, and the results obtained in the live challenge workshop hosted by the MICCAI2012 conference. In the challenge, 100 prostate MR cases from 4 different centers were included, with differences in scanner manufacturer, field strength and protocol. A total of 11 teams from academic research groups and industry participated. Algorithms showed a wide variety in methods and implementation, including active appearance models, atlas registration and level sets. Evaluation was performed using boundary and volume based metrics which were combined into a single score relating the metrics to human expert performance. The winners of the challenge where the algorithms by teams Imorphics and ScrAutoProstate, with scores of 85.72 and 84.29 overall. Both algorithms where significantly better than all other algorithms in the challenge (p < 0.05) and had an efficient implementation with a run time of 8 min and 3 s per case respectively. Overall, active appearance model based approaches seemed to outperform other approaches like multi-atlas registration, both on accuracy and computation time. Although average algorithm performance was good to excellent and the Imorphics algorithm outperformed the second observer on average, we showed that algorithm combination might lead to further improvement, indicating that optimal performance for prostate segmentation is not yet obtained. All results are available online at http://promise12.grand-challenge.org/. (C) 2013 Elsevier B.V. All rights reserved.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
-
Overview of the JET results
- 2015
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 55:10
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Tidskriftsartikel (refereegranskat)
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| 25. |
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| 26. |
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| 27. |
- Rubel, Marek, et al.
(författare)
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Fuel inventory and deposition in castellated structures in JET-ILW
- 2017
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Ingår i: Nuclear Fusion. - : Institute of Physics Publishing. - 0029-5515 .- 1741-4326. ; 57:6
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Tidskriftsartikel (refereegranskat)abstract
- Since 2011 the JET tokamak has been operated with a metal ITER-like wall (JET-ILW) including castellated beryllium limiters and lamellae-type bulk tungsten tiles in the divertor. This has allowed for a large scale test of castellated plasma-facing components (PFC). Procedures for sectioning the limiters into single blocks of castellation have been developed. This facilitated morphology studies of morphology of surfaces inside the grooves for limiters after experimental campaigns 2011-2012 and 2013-2014. The deposition in the 0.4-0.5 mm wide grooves of the castellation is 'shallow'. It reaches 1-2 mm into the 12 mm deep gap. Deuterium concentrations are small (mostly below 1 × 1018 cm-2). The estimated total amount of deuterium in all the castellated limiters does not exceed the inventory of the plasma-facing surfaces (PFS) of the limiters. There are only traces of Ni, Cr and Fe deposited in the castellation gaps. The same applies to the carbon content. Also low deposition of D, Be and C has been measured on the sides of the bulk tungsten lamellae pieces. Modelling clearly reflects: (a) a sharp decrease in the measured deposition profiles and(b) an increase in deposition with the gap width. Both experimental and modelling data give a strong indication and information to ITER that narrow gaps in the castellated PFC are essential. X-ray diffraction on PFS has clearly shown two distinct composition patterns: Be with an admixture of Be-W intermetallic compounds (e.g. Be22W) in the deposition zone, whilst only pure Be has been detected in the erosion zone. The lack of compound formation in the erosion zone indicates that no distinct changes in the thermo-mechanical properties of the Be PFC might be expected.
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| 28. |
- Schijven, Dick, et al.
(författare)
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Large-scale analysis of structural brain asymmetries in schizophrenia via the ENIGMA consortium
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 120:14
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Tidskriftsartikel (refereegranskat)abstract
- Left-right asymmetry is an important organizing feature of the healthy brain that may be altered in schizophrenia, but most studies have used relatively small samples and heterogeneous approaches, resulting in equivocal findings. We carried out the largest case-control study of structural brain asymmetries in schizophrenia, with MRI data from 5,080 affected individuals and 6,015 controls across 46 datasets, using a single image analysis protocol. Asymmetry indexes were calculated for global and regional cortical thickness, surface area, and subcortical volume measures. Differences of asymmetry were calculated between affected individuals and controls per dataset, and effect sizes were meta-analyzed across datasets. Small average case-control differences were observed for thickness asymmetries of the rostral anterior cingulate and the middle temporal gyrus, both driven by thinner left-hemispheric cortices in schizophrenia. Analyses of these asymmetries with respect to the use of antipsychotic medication and other clinical variables did not show any significant associations. Assessment of age- and sex-specific effects revealed a stronger average leftward asymmetry of pallidum volume between older cases and controls. Case-control differences in a multivariate context were assessed in a subset of the data (N = 2,029), which revealed that 7% of the variance across all structural asymmetries was explained by case-control status. Subtle case-control differences of brain macrostructural asymmetry may reflect differences at the molecular, cytoarchitectonic, or circuit levels that have functional relevance for the disorder. Reduced left middle temporal cortical thickness is consistent with altered left-hemisphere language network organization in schizophrenia.
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| 29. |
- Sergienko, G., et al.
(författare)
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Quartz micro-balance results of pulse-resolved erosion/deposition in the JET-ILW divertor
- 2017
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Ingår i: Nuclear Materials and Energy. - : ELSEVIER. - 2352-1791. ; 12, s. 478-482
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Tidskriftsartikel (refereegranskat)abstract
- A set of quartz crystal microbalances (QMB) was used at JET with full carbon wall to monitor mass erosion/ deposition rates in the remote areas of the divertor. After introduction of the ITER-like wall (ILW) in JET with beryllium main wall and tungsten divertor, strong reduction of the material deposition and accompanied fuel retention was observed. Therefore the existing QMB electronics have been modified to improve the accuracy of frequency measurements by a factor of ten down to 0.1 Hz which corresponds to 1.4 ng cm(-2). The averaged deposition rates of 1.2-3 ng cm(-2) s(-1) and erosion rates of 5.6-8.1 ng cm(-2) s(-1) were observed in the inner divertor of JET-ILW with the inner strike point positions close to the bottom edge of vertical tile 3 and at the horizontal tile 4 respectively. The erosion with averaged rates of approximate to 2.1 ng cm(-2) s(-1) and approximate to 120 ng cm(-2) s(-1) were observed in the outer divertor for the outer strike point positions at tile 5 and tile 6 respectively. (C) 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.
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| 30. |
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| 31. |
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| 32. |
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- 2018
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 58:9
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Tidskriftsartikel (refereegranskat)
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| 33. |
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- 2018
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 58:1
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Forskningsöversikt (refereegranskat)
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