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1.
  • 2018
  • In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 58:1
  • Research review (peer-reviewed)
  •  
2.
  • Bombarda, F., et al. (author)
  • Runaway electron beam control
  • 2019
  • In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 61:1
  • Journal article (peer-reviewed)
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3.
  • 2017
  • In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
  • Journal article (peer-reviewed)
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4.
  • 2018
  • In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 58:9
  • Journal article (peer-reviewed)
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5.
  • Meyer, H., et al. (author)
  • Overview of progress in European medium sized tokamaks towards an integrated plasma-edge/wall solution
  • 2017
  • In: Nuclear Fusion. - : Institute of Physics Publishing (IOPP). - 0029-5515 .- 1741-4326. ; 57:10
  • Journal article (peer-reviewed)abstract
    • Integrating the plasma core performance with an edge and scrape-off layer (SOL) that leads to tolerable heat and particle loads on the wall is a major challenge. The new European medium size tokamak task force (EU-MST) coordinates research on ASDEX Upgrade (AUG), MAST and TCV. This multi-machine approach within EU-MST, covering a wide parameter range, is instrumental to progress in the field, as ITER and DEMO core/pedestal and SOL parameters are not achievable simultaneously in present day devices. A two prong approach is adopted. On the one hand, scenarios with tolerable transient heat and particle loads, including active edge localised mode (ELM) control are developed. On the other hand, divertor solutions including advanced magnetic configurations are studied. Considerable progress has been made on both approaches, in particular in the fields of: ELM control with resonant magnetic perturbations (RMP), small ELM regimes, detachment onset and control, as well as filamentary scrape-off-layer transport. For example full ELM suppression has now been achieved on AUG at low collisionality with n = 2 RMP maintaining good confinement H-H(98,H-y2) approximate to 0.95. Advances have been made with respect to detachment onset and control. Studies in advanced divertor configurations (Snowflake, Super-X and X-point target divertor) shed new light on SOL physics. Cross field filamentary transport has been characterised in a wide parameter regime on AUG, MAST and TCV progressing the theoretical and experimental understanding crucial for predicting first wall loads in ITER and DEMO. Conditions in the SOL also play a crucial role for ELM stability and access to small ELM regimes.
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6.
  • Meyer, H., et al. (author)
  • Overview of progress in European medium sized tokamaks towards an integrated plasma-edge/wall solution
  • 2017
  • In: Nuclear Fusion. - : Institute of Physics Publishing (IOPP). - 0029-5515 .- 1741-4326. ; 57:10
  • Journal article (peer-reviewed)abstract
    • Integrating the plasma core performance with an edge and scrape-off layer (SOL) that leads to tolerable heat and particle loads on the wall is a major challenge. The new European medium size tokamak task force (EU-MST) coordinates research on ASDEX Upgrade (AUG), MAST and TCV. This multi-machine approach within EU-MST, covering a wide parameter range, is instrumental to progress in the field, as ITER and DEMO core/pedestal and SOL parameters are not achievable simultaneously in present day devices. A two prong approach is adopted. On the one hand, scenarios with tolerable transient heat and particle loads, including active edge localised mode (ELM) control are developed. On the other hand, divertor solutions including advanced magnetic configurations are studied. Considerable progress has been made on both approaches, in particular in the fields of: ELM control with resonant magnetic perturbations (RMP), small ELM regimes, detachment onset and control, as well as filamentary scrape-off-layer transport. For example full ELM suppression has now been achieved on AUG at low collisionality with n = 2 RMP maintaining good confinement H-H(98,H-y2) approximate to 0.95. Advances have been made with respect to detachment onset and control. Studies in advanced divertor configurations (Snowflake, Super-X and X-point target divertor) shed new light on SOL physics. Cross field filamentary transport has been characterised in a wide parameter regime on AUG, MAST and TCV progressing the theoretical and experimental understanding crucial for predicting first wall loads in ITER and DEMO. Conditions in the SOL also play a crucial role for ELM stability and access to small ELM regimes.
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7.
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8.
  • Goldstein, A., et al. (author)
  • Fermi Observations of the LIGO Event GW170104
  • 2017
  • In: Astrophysical Journal Letters. - : IOP PUBLISHING LTD. - 2041-8205 .- 2041-8213. ; 846:1
  • Journal article (peer-reviewed)abstract
    • We present the Fermi Gamma-ray Burst Monitor (GBM) and Large Area Telescope (LAT) observations of the LIGO binary black hole merger (BBH) event GW170104. No candidate electromagnetic counterpart was detected by either GBM or LAT. A detailed analysis of the GBM and LAT data over timescales from seconds to days covering the Laser Interferometer Gravitational-wave Observatory (LIGO) localization region is presented. The resulting flux upper bound from the GBM is (5.2-9.4). x. 10(-7) erg cm(-2) s(-1) in the 10-1000 keV range and from the LAT is (0.2-90). x. 10(-9) erg cm(-2) s(-1) in the 0.1-1 GeV range. We also describe the improvements to our automated pipelines and analysis techniques for searching for and characterizing the potential electromagnetic counterparts for future gravitational-wave events from Advanced LIGO/Virgo.
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9.
  • Martin, P., et al. (author)
  • Overview of the RFX-mod fusion science programme
  • 2013
  • In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 53:10, s. 104018-
  • Research review (peer-reviewed)abstract
    • This paper reports the highlights of the RFX-mod fusion science programme since the last 2010 IAEA Fusion Energy Conference. The RFX-mod fusion science programme focused on two main goals: exploring the fusion potential of the reversed field pinch (RFP) magnetic configuration and contributing to the solution of key science and technology problems in the roadmap to ITER. Active control of several plasma parameters has been a key tool in this endeavour. New upgrades on the system for active control of magnetohydrodynamic (MHD) stability are underway and will be presented in this paper. Unique among the existing fusion devices, RFX-mod has been operated both as an RFP and as a tokamak. The latter operation has allowed the exploration of edge safety factor q edge < 2 with active control of MHD stability and studies concerning basic energy and flow transport mechanisms. Strong interaction has continued with the stellarator community in particular on the physics of helical states and on three-dimensional codes.
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10.
  • Ballan, M., et al. (author)
  • Nuclear physics midterm plan at Legnaro National Laboratories (LNL)
  • 2023
  • In: European Physical Journal Plus. - 2190-5444. ; 138:8, s. 3-26
  • Journal article (peer-reviewed)abstract
    • The next years will see the completion of the radioactive ion beam facility SPES (Selective Production of Exotic Species) and the upgrade of the accelerators complex at Istituto Nazionale di Fisica Nucleare – Legnaro National Laboratories (LNL) opening up new possibilities in the fields of nuclear structure, nuclear dynamics, nuclear astrophysics, and applications. The nuclear physics community has organised a workshop to discuss the new physics opportunities that will be possible in the near future by employing state-of-the-art detection systems. A detailed discussion of the outcome from the workshop is presented in this report.
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11.
  • Martin, P., et al. (author)
  • Overview of the RFX fusion science program
  • 2011
  • In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 51:9, s. 094023-
  • Journal article (peer-reviewed)abstract
    • This paper summarizes the main achievements of the RFX fusion science program in the period between the 2008 and 2010 IAEA Fusion Energy Conferences. RFX-mod is the largest reversed field pinch in the world, equipped with a system of 192 coils for active control of MHD stability. The discovery and understanding of helical states with electron internal transport barriers and core electron temperature >1.5 keV significantly advances the perspectives of the configuration. Optimized experiments with plasma current up to 1.8 MA have been realized, confirming positive scaling. The first evidence of edge transport barriers is presented. Progress has been made also in the control of first-wall properties and of density profiles, with initial first-wall lithization experiments. Micro-turbulence mechanisms such as ion temperature gradient and micro-tearing are discussed in the framework of understanding gradient-driven transport in low magnetic chaos helical regimes. Both tearing mode and resistive wall mode active control have been optimized and experimental data have been used to benchmark numerical codes. The RFX programme also provides important results for the fusion community and in particular for tokamaks and stellarators on feedback control of MHD stability and on three-dimensional physics. On the latter topic, the result of the application of stellarator codes to describe three-dimensional reversed field pinch physics will be presented.
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12.
  • Zuin, M., et al. (author)
  • Overview of the RFX-mod fusion science activity
  • 2017
  • In: Nuclear Fusion. - : Institute of Physics Publishing (IOPP). - 0029-5515 .- 1741-4326. ; 57:10
  • Journal article (peer-reviewed)abstract
    • This paper reports the main recent results of the RFX-mod fusion science activity. The RFX-mod device is characterized by a unique flexibility in terms of accessible magnetic configurations. Axisymmetric and helically shaped reversed-field pinch equilibria have been studied, along with tokamak plasmas in a wide range of q(a) regimes (spanning from 4 down to 1.2 values). The full range of magnetic configurations in between the two, the so-called ultra-low q ones, has been explored, with the aim of studying specific physical issues common to all equilibria, such as, for example, the density limit phenomenon. The powerful RFX-mod feedback control system has been exploited for MHD control, which allowed us to extend the range of experimental parameters, as well as to induce specific magnetic perturbations for the study of 3D effects. In particular, transport, edge and isotope effects in 3D equilibria have been investigated, along with runaway mitigations through induced magnetic perturbations. The first transitions to an improved confinement scenario in circular and D-shaped tokamak plasmas have been obtained thanks to an active modification of the edge electric field through a polarized electrode. The experiments are supported by intense modeling with 3D MHD, gyrokinetic, guiding center and transport codes. Proposed modifications to the RFX-mod device, which will enable further contributions to the solution of key issues in the roadmap to ITER and DEMO, are also briefly presented.
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13.
  • Terranova, D., et al. (author)
  • A 3D approach to equilibrium, stability and transport studies in RFX-mod improved regimes
  • 2010
  • In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 52:12, s. 124023-
  • Journal article (peer-reviewed)abstract
    • The full three-dimensional (3D) approach is now becoming an important issue for all magnetic confinement configurations. It is a necessary condition for the stellarator but also the tokamak and the reversed field pinch (RFP) now cannot be completely described in an axisymmetric framework. For the RFP the observation of self-sustained helical configurations with improved plasma performances require a better description in order to assess a new view on this configuration. In this new framework plasma configuration studies for RFX-mod have been considered both with tools developed for the RFP as well as considering codes originally developed for the stellarator and adapted to the RFP. These helical states are reached through a transition to a very low/reversed shear configuration leading to internal electron transport barriers. These states are interrupted by MHD reconnection events and the large Te gradients at the barriers indicate that both current and pressure driven modes are to be considered. Furthermore the typically flat Te profiles in the helical core have raised the issue of the role of electrostatic and electromagnetic turbulence in these reduced chaos regions, so that a stability analysis in the correct 3D geometry is required to address an optimization of the plasma setup. In this viewtheVMECcode proved to be an effectiveway to obtain helical equilibria to be studied in terms of stability and transport with a suite of well tested codes. In this work, the equilibrium reconstruction technique as well as the experimental evidence of 3D effects and their first interpretation in terms of stability and transport are presented using both RFP and stellarator tools.
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14.
  • Lorenzini, R., et al. (author)
  • Self-organized helical equilibria as a new paradigm for ohmically heated fusion plasmas
  • 2009
  • In: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 5:8, s. 570-574
  • Journal article (peer-reviewed)abstract
    • In the quest for new energy sources, the research on controlled thermonuclear fusion has been boosted by the start of the construction phase of the International Thermonuclear Experimental Reactor (ITER). ITER is based on the tokamak magnetic configuration, which is the best performing one in terms of energy confinement. Alternative concepts are however actively researched, which in the long term could be considered for a second generation of reactors. Here, we show results concerning one of these configurations, the reversed-field pinch (RFP). By increasing the plasma current, a spontaneous transition to a helical equilibrium occurs, with a change of magnetic topology. Partially conserved magnetic flux surfaces emerge within residual magnetic chaos, resulting in the onset of a transport barrier. This is a structural change and sheds new light on the potential of the RFP as the basis for a low-magnetic-field ohmic fusion reactor.
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15.
  • Martin, P., et al. (author)
  • Overview of RFX-mod results
  • 2009
  • In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 49:10, s. 104019-
  • Journal article (peer-reviewed)abstract
    • With the exploration of the MA plasma current regime in up to 0.5 s long discharges, RFX-mod has opened new and very promising perspectives for the reversed field pinch (RFP) magnetic configuration, and has made significant progress in understanding and improving confinement and in controlling plasma stability. A big leap with respect to previous knowledge and expectations on RFP physics and performance has been made by RFX-mod since the last 2006 IAEA Fusion Energy Conference. A new self-organized helical equilibrium has been experimentally achieved ( the Single Helical Axis-SHAx-state), which is the preferred state at high current. Strong core electron transport barriers characterize this regime, with electron temperature gradients comparable to those achieved in tokamaks, and by a factor of 4 improvement in confinement time with respect to the standard RFP. RFX-mod is also providing leading edge results on real-time feedback control of MHD instabilities, of general interest for the fusion community.
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16.
  • Pfaller, M.A., et al. (author)
  • Twelve years of fluconazole in clinical practice : Global-trends in species distribution and fluconazole susceptibility of bloodstream isolates of Candida
  • 2004
  • In: Clinical Microbiology and Infection. - : Elsevier BV. - 1198-743X .- 1469-0691. ; 10:SUPPL. 1, s. 11-23
  • Journal article (peer-reviewed)abstract
    • We determined the species distribution and in-vitro susceptibility of 6082 bloodstream infection (BSI) isolates of Candida spp. collected from 250 medical centres in 32 nations over a 10-year period from 1992 through 2001. The species included 3401 C. albicans, 984 C. glabrata, 796 C. parapsilosis, 585 C. tropicalis, 153 C. krusei, 67 C. lusitaniae, 48 C. guilliermondii, 10 C. famata, 10 C. kefyr, six C. pelliculosa, five C. rugosa, four C. lipolytica, three C. dubliniensis, three C. inconspicua, two C. sake and one isolate each of C. lambica, C. norvegensis and C. zeylanoides. Minimum inhibitory concentration determinations were made using the National Committee for Clinical Laboratory Standards reference broth microdilution method. Variation in the rank order and frequency of the different species of Candida was observed over time and by geographic area. The proportion of BSI due to C. albicans and C. glabrata increased and C. parapsilosis decreased over time in Canada, the USA and Europe. C. glabrata was an infrequent cause of BSI in Latin America and the Asia-Pacific region. Very little variation in fluconazole susceptibility was observed among isolates of C. albicans, C. tropicalis and C. parapsilosis. These species accounted for 78% of all BSI and remained highly susceptible (91-100% susceptible) to fluconazole from 1992 to 2001 irrespective of geographic origin. The prevalence of fluconazole resistance among C. glabrata isolates was variable both over time and among the various countries and regions. Resistance to fluconazole among C. glabrata isolates was greatest in the USA and varied by US census region (range 0-23%). These observations are generally encouraging relative to the sustained usefulness of fluconazole as a systemically active antifungal agent for the treatment of candida BSI. © 2004 Copyright by the European Society of Clinical Microbiology and Infectious Diseases.
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17.
  • Puiatti, M. E., et al. (author)
  • Helical equilibria and magnetic structures in the reversed field pinch and analogies to the tokamak and stellarator
  • 2009
  • In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 51:12, s. 124031-
  • Journal article (peer-reviewed)abstract
    • The reversed field pinch configuration is characterized by the presence of magnetic structures both in the core and at the edge: in the core, at high plasma current the spontaneous development of a helical structure is accompanied by the appearance of internal electron transport barriers; at the edge strong pressure gradients, identifying an edge transport barrier, are observed too, related to the position of the field reversal surface. The aim of this paper is the experimental characterization of both the internal and edge transport barriers in relation to the magnetic topology, discussing possible analogies and differences with other confinement schemes.
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18.
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19.
  • Puiatti, M. E., et al. (author)
  • Internal and external electron transport barriers in the RFX-mod reversed field pinch
  • 2011
  • In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 51:7, s. 073038-
  • Journal article (peer-reviewed)abstract
    • An interesting result of magnetic chaos reduction in RFX-mod high current discharges is the development of strong electron transport barriers. An internal heat and particle transport barrier is formed when a bifurcation process changes the magnetic configuration into a helical equilibrium and chaos reduction follows, together with the formation of a null in the q shear. Strong temperature gradients develop, corresponding to a decreased thermal and particle transport. Turbulence analysis shows that the large electron temperature gradients are limited by the onset of micro-tearing modes, in addition to residual magnetic chaos. A new type of electron transport barrier with strong temperature gradients develops more externally (r/a = 0.8) accompanied by a 30% improvement of the global confinement time. The mechanism responsible for the formation of such a barrier is still unknown but it is likely associated with a local reduction of magnetic chaos. These external barriers develop primarily in situations of well-conditioned walls so that they might be regarded as attempts towards an L-H transition. Both types of barriers occur in high-current low-collisionality regimes. Analogies with tokamak and stellarators are discussed. 
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22.
  • Granadillo, JL, et al. (author)
  • Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD
  • 2020
  • In: Journal of medical genetics. - : BMJ. - 1468-6244 .- 0022-2593. ; 57:10, s. 717-724
  • Journal article (peer-reviewed)abstract
    • Rare variants in hundreds of genes have been implicated in developmental delay (DD), intellectual disability (ID) and neurobehavioural phenotypes. TNRC6B encodes a protein important for RNA silencing. Heterozygous truncating variants have been reported in three patients from large cohorts with autism, but no full phenotypic characterisation was described.MethodsClinical and molecular characterisation was performed on 17 patients with TNRC6B variants. Clinical data were obtained by retrospective chart review, parent interviews, direct patient interaction with providers and formal neuropsychological evaluation.ResultsClinical findings included DD/ID (17/17) (speech delay in 94% (16/17), fine motor delay in 82% (14/17) and gross motor delay in 71% (12/17) of subjects), autism or autistic traits (13/17), attention deficit and hyperactivity disorder (ADHD) (11/17), other behavioural problems (7/17) and musculoskeletal findings (12/17). Other congenital malformations or clinical findings were occasionally documented. The majority of patients exhibited some dysmorphic features but no recognisable gestalt was identified. 17 heterozygous TNRC6B variants were identified in 12 male and five female unrelated subjects by exome sequencing (14), a targeted panel (2) and a chromosomal microarray (1). The variants were nonsense (7), frameshift (5), splice site (2), intragenic deletions (2) and missense (1).ConclusionsVariants in TNRC6B cause a novel genetic disorder characterised by recurrent neurocognitive and behavioural phenotypes featuring DD/ID, autism, ADHD and other behavioural abnormalities. Our data highly suggest that haploinsufficiency is the most likely pathogenic mechanism. TNRC6B should be added to the growing list of genes of the RNA-induced silencing complex associated with ID/DD, autism and ADHD.
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24.
  • Leclercq, R, et al. (author)
  • EUCAST expert rules in antimicrobial susceptibility testing
  • 2013
  • In: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. - : Elsevier BV. - 1469-0691. ; 19:2, s. 141-160
  • Journal article (peer-reviewed)
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27.
  • Sartelli, Massimo, et al. (author)
  • Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
  • 2023
  • In: WORLD JOURNAL OF EMERGENCY SURGERY. - 1749-7922. ; 18:1
  • Research review (peer-reviewed)abstract
    • Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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28.
  • Uhlig, Jens, et al. (author)
  • Table-Top Ultrafast X-Ray Microcalorimeter Spectrometry for Molecular Structure
  • 2013
  • In: Physical Review Letters. - 1079-7114. ; 110:13
  • Journal article (peer-reviewed)abstract
    • This work presents an x-ray absorption measurement by use of ionizing radiation generated by a femtosecond pulsed laser source. The spectrometer was a microcalorimetric array whose pixels are capable of accurately measuring energies of individual radiation quanta. An isotropic continuum x-ray spectrum in the few-keV range was generated from a laser plasma source with a water-jet target. X rays were transmitted through a ferrocene powder sample to the detector, whose pixels have average photon energy resolution Delta E = 3.14 eV full-width-at-half-maximum at 5.9 keV. The bond distance of ferrocene was retrieved from this first hard-x-ray absorption fine-structure spectrum collected with an energy-dispersive detector. This technique will be broadly enabling for time-resolved observations of structural dynamics in photoactive systems. DOI: 10.1103/PhysRevLett.110.138302
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31.
  • Alfier, A., et al. (author)
  • Electron temperature profiles in RFX-mod
  • 2008
  • In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 50:3, s. 035013-
  • Journal article (peer-reviewed)abstract
    • Electron temperature profiles have been measured by the main Thomson scattering ( TS) diagnostic on the RFX-mod reversed field pinch experiment in Padova, Italy. The increased accuracy and spatial and temporal resolution permits one to measure in detail the improvements in T-e profiles, obtained with the active saddle coil system, which allows one to obtain core temperature 30% higher and scaling stronger with plasma current, steeper gradients in the core (+30%) and at the edge (+60%). 1D power balance calculations show that the active control of MHD modes largely reduces the values of electron heat diffusivity along the whole plasma radius, with similar to 50% reduction at the edge and similar to 30% in the core. The resulting electron energy confinement time is doubled. Further improvements occur during quasi-single helicity (QSH) states: the new TS allows one to study in detail the hot island that develops in the core. A characterization of the island electron thermal profile is presented, in terms of width, temperature increase, gradients and asymmetry; the effect on density profile is also discussed. A 2D transport code has been applied to calculate the heat diffusivity inside the magnetic island corresponding to the QSH state, also considering the correlation between temperature increase and pressure gradient with the chaos level around the island. Finally, electron energy confinement time during QSH states is compared with that in MH states.
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34.
  • Bautista, Rocí­o, et al. (author)
  • Toward a Pinus pinaster bacterial artificial chromosome library
  • 2007
  • In: Annals of Forest Science. - : Springer Science and Business Media LLC. - 1286-4560 .- 1297-966X. ; 64:8, s. 855-864
  • Journal article (peer-reviewed)abstract
    • Conifers are of great economic and ecological importance, but little is known concerning their genomic organization. This study is an attempt to obtain high-quality high-molecular-weight DNA from Pinus pinaster cotyledons and the construction of a pine BAC library. The preparation incorporates modifications like low centrifugation speeds, increase of EDTA concentration for plug maintenance, use of DNase inhibitors to reduce DNA degradation, use of polyvinylpyrrolidone and ascorbate to avoid secondary metabolites, and a brief electrophoresis of the plugs prior to their use. A total of 72 192 clones with an average insert size of 107 kb, which represents an equivalent of 11X pine haploid genomes, were obtained. The proportions of clones lacking inserts or containing chloroplast DNA are both approximately 1.6%. The library was screened with cDNA probes for seven genes, and two clones containing Fd-GOGAT sequences were found, one of them seemingly functional. Ongoing projects aimed at constructing a pinebacterial artificial chromosome library may benefit from the methods described here.
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35.
  • Brem, Jürgen, et al. (author)
  • Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors
  • 2022
  • In: Nature Chemistry. - : Springer Nature. - 1755-4330 .- 1755-4349. ; 14:1, s. 15-24
  • Journal article (peer-reviewed)abstract
    • Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.
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36.
  • Cañas, Rafael A, et al. (author)
  • Molecular and functional analyses support a role of Ornithine-{delta}-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination
  • 2008
  • In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 148:1, s. 77-88
  • Journal article (peer-reviewed)abstract
    • We report the molecular characterization and functional analysis of a gene (PsdeltaOAT) from Scots pine (Pinus sylvestris) encoding Orn-delta-aminotransferase (delta-OAT; EC 2.6.1.13), an enzyme of arginine metabolism. The deduced amino acid sequence contains a putative N-terminal signal peptide for mitochondrial targeting. The polypeptide is similar to other delta-OATs from plants, yeast, and mammals and encoded by a single-copy gene in pine. PsdeltaOAT encodes a functional delta-OAT as determined by expression of the recombinant protein in Escherichia coli and analysis of the active enzyme. The expression of PsdeltaOAT was undetectable in the embryo, but highly induced at early stages of germination and seedling development in all different organs. Transcript levels decreased in later developmental stages, although an increase was observed in lignified stems of 90-d-old plants. An increase of delta-OAT activity was observed in germinating embryos and seedlings and appears to mirror the observed alterations in PsdeltaOAT transcript levels. Similar expression patterns were also observed for genes encoding arginase and isocitrate dehydrogenase. Transcripts of PsdeltaOAT and the arginase gene were found widely distributed in different cell types of pine organs. Consistent with these results a metabolic pathway is proposed for the nitrogen flow from the megagametophyte to the developing seedling, which is also supported by the relative abundance of free amino acids in embryos and seedlings. Taken together, our data support that delta-OAT plays an important role in this process providing glutamate for glutamine biosynthesis during early pine growth.
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39.
  • Fernández-Pozo, Noé, et al. (author)
  • EuroPineDB : a high-coverage web database for maritime pine transcriptome
  • 2011
  • In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 12, s. 366-
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. DESCRIPTION: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. CONCLUSIONS: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.
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  • Isolation and Characterization of Polymorphic Microsatellite DNA Markers from an Amazonian White-sand Vegetation Specialist Bird, Xenopipo atronitens (Aves: Pipridae)
  • 2016
  • In: Wilson Journal of Ornithology. - : Wilson Ornithological Society. - 1559-4491 .- 1938-5447. ; 128:3, s. 668-672
  • Journal article (peer-reviewed)abstract
    • Thirteen novel polymorphic microsatellite loci were isolated and characterized from the Amazonian Black Manakin, Xenopipo atronitens. The loci were screened using 30 samples from Brazil. A total of 13 loci were variable with number of alleles per locus ranging from 2 to 17, whilst the observed and expected heterozygosities varied from 0.067-0.900 and 0.310-0.910, respectively. Five loci deviated significantly from the Hardy-Weinberg equilibrium, whereas one pair of loci deviated significantly from linkage disequilibrium. The set of markers will be a useful tool for future population genetic and kinship studies of X. atronitens, an Amazonian white-sand vegetation specialist.
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  • Kluytmans, J, et al. (author)
  • Obituary: Johan Willem Mouton
  • 2020
  • In: CLINICAL MICROBIOLOGY AND INFECTION. - : Elsevier BV. - 1198-743X. ; 26:1, s. 125-126
  • Journal article (other academic/artistic)
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  • Mouton, JW, et al. (author)
  • MIC-based dose adjustment: facts and fables
  • 2018
  • In: The Journal of antimicrobial chemotherapy. - : Oxford University Press (OUP). - 1460-2091 .- 0305-7453. ; 73:3, s. 564-568
  • Journal article (peer-reviewed)
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