dataesr/scientific-paragraphs-categorization huggingface dataset:
Radionuclide purity and half-life determination Radionuclide purity and half-life determination were realized according to the "Radiopharmaceutical preparations" monograph n°07/2016:0125 of the European Pharmacopeia 9. 7 by γ-ray spectrometry and radioactive decay measurement (Gamma ray spectrometry, gamma vision-32 V6. 07 software, Ortec, France). Purity was assessed by the detection of the 511 keV γ-ray (> 99. 9%) on the γ-spectrum (up to a total peak energy of 1022 keV) and half-life was calculated by decay measurement during a 2 minutes period.
The linear resistive MHD code CASTOR is used to simulate the frequency scan of an AEAD-like external antenna. For the limiter pulses, the high-f mode is determined to be an n = 0 GAE, while the low-f mode is likely an n = 2 TAE. During the transition from limiter to X-point configuration, CASTOR indicates that n = 1 and 2 EAEs are excited in the edge gap. These results extend previous experimental studies in JET and Alcator C-Mod; validate the computational work performed by Dvornova et al 2020 Phys. Plasmas 27 012507; and provide guidance for the optimization of PA coupling in upcoming JET energetic particle experiments, for which the AEAD will aim to identify the contribution of alpha particles to AE drive during the DT campaign.
Recent computational efforts This study is also motivated by recent computational work which accurately modeled PA coupling and explained some of the experimental observations of the previous section. In the study by Dvornova et al  [40] , the effects of PA separation and magnetic configuration on the efficiency of the JET AE antenna were thoroughly investigated using the linear, resistive MHD code CASTOR  [42, 43]  and nonlinear, reduced MHD code JOREK  [44]. In both codes, an external antenna was modeled in the vacuum region between the plasma and wall. An n = 1 antenna perturbation was simulated, and its frequency was scanned to diagnose the response of the plasma (specifically JPN 42870). Here, we briefly summarize the main results of their study: In limiter configuration, two resonant modes (n = 1 TAEs) were excited and identified with distinct "low" and "high" frequencies within the simulated frequency scan, ∆f ≈ 100 -150 kHz.
2% -1. 2%. For a PA separation d ≈ 15 cm, the low-f mode is more stable than the high-f mode, i. e. |γ high | < |γ low |, which agrees with the findings of  [40] ; however, for d ≈ 10 cm, it is the opposite: |γ low | < |γ high |. Thus, the damping rate appears to increase with PA separation for the low-f mode; this agrees with the experimental results from C-Mod, but not the simulations from  [40]. This variation in γ low could be explained, in part, by the slightly different edge conditions for the plasmas with two PA separations: q 95 ≈ 3. 3 and 3. 45 for d ≈ 10 cm and 15 cm, respectively. In  [34] , the damping rate was found to increase with q 95 for data in the same stable AE database described above, consistent with enhanced continuum damping. As will be discussed in the next section, this could more strongly affect the low-f mode due to its localization in the outer plasma region, whereas the high-f mode has a more global structure.
Computational analysis of plasma-antenna separation A suite of MHD codes is used to analyze the JET plasmas of the previous section and the next. First, the magnetic geometry from EFIT ¶  [45]  is converted into the appropriate format, via HELENA  [46] , to compute the Alfvén continuum with CSCAS  [47]  with no sound wave coupling included. Here, an even, eighth-order polynomial is fit to the electron density profile, and n i = n e is assumed for the ion density. For example, the fitted density and safety factor profiles for JPN 96585 at t = 10 s are plotted in Fig. 4a  as a function of the square root of the normalized poloidal flux, s = √ ψ N , not to be confused with the magnetic shear discussed in the next section. Next, the linear resistive MHD code CASTOR  [42, 43]  is run with the external antenna module enabled.
Experimental study of limiter versus X-point configuration Utilizing the same database from  [34] , we provide a breakdown of AE antenna operation and resonance detection in Table  1  for both limiter and X-point magnetic configurations. Because most JET experiments require diverted plasmas, the AE antenna was operated far less often in limiter compared to X-point configuration: 12% compared to 88% of the time. Naturally, the fraction of resonances detected in limiter plasmas (18%) is also less than that for X-point plasmas (82%). However, the probability of resonance detection is greater in limiter (62%) compared to X-point configuration (38%). This is consistent with the simulation results of  [40]  which indicated reduced PA coupling in X-point, as discussed in Section 2. 2. We also note that PA separation is a conflating factor since it is typically greater for X-point compared to limiter plasmas (see Fig.
7b ), although the improvement in resonance detection is marginal (see Fig. 1a ). Filled/open symbols are toroidal mode number estimates including/excluding n = 0. Vertical (dotted) lines separate magnetic configurations: outer limiter, inner limiter, and X-point. In JPN 96600, the high-f mode is tracked consistently throughout the outer limiter phase and somewhat during the inner limiter phase, but tracking is more difficult during X-point. The magnetics data provide an explanation: As seen in Fig. 8 , the sharp peaks in the signal amplitude, corresponding to AE resonances, are easily identifiable in the outer limiter phase, but become less distinguishable during the inner limiter phase as the plasma become more like X-point. In X-point, the high-f resonances are no longer high-amplitude, sharp peaks, but low-amplitude, broad "bumps.
5 s. Safety factor and density profiles are shown in Fig. 10a. The strong shear at the plasma edge introduces some complications in the modeling. For instance, CSCAS could only be simulated within s ∈ [0, 0. 9], as seen in the continua in Fig. 10b. As with the n = 1 TAE gap in Fig. 9b , the n = 2 TAE gap is closed, and instead a more highly damped mode is found in the edge of the EAE gap, here with strongest coupling between poloidal harmonics m = 4, 6 near s ≈ 0. 8. The frequency scan in CASTOR finds a resonant peak at ω 0 R 0 /v A = 0. 570 (f 0 ≈ 252 kHz). This is higher than the experimentally measured resonant frequency f 0 ≈ 215 kHz, but only by ∼17% which is allowable within uncertainties of the density and safety factor profiles. Furthermore, better agreement would likely be attained with improved modeling of the edge plasma and scrape-off layer, which then requires a more computationally intensive code like JOREK.
Summary In this work, we reported on a dedicated study of plasma-antenna (PA) coupling between JET plasmas and the Alfvén Eigenmode Active Diagnostic, or AE antenna. The resonant excitation of stable AEs -and measurements of their frequencies f 0 , damping rates γ, and toroidal mode numbers n -were monitored while scanning the PA separation and varying the magnetic configuration (limiter versus X-point). These experiments were motivated by similar studies carried out previously in Alcator C-Mod and in JET with the old AE antenna system, as well as by recent computational efforts by Dvornova et al  [40]  to interpret past data. In the first part of the study, we assessed the impact of PA separation on AE antenna coupling, stable AE excitation, and AE stability itself. From a database of almost 5000 AE resonances, it was found that two quantities decreased as PA separation increased: the probability of resonance detection (see Fig.
The resonant frequencies (and estimated toroidal mode numbers) of both the low-f and high-f AEs did not vary with PA separation, and neither did the damping rate of the high-f mode, consistent with  [40]. However, the damping rate of the low-f mode was found to increase with PA separation, in disagreement with  [40]  but agreeing with C-Mod results  [35]. A closer inspection of these plasmas indicated that slightly differing edge conditions could explain this trend, at least in part; specifically, a lower q 95 for the plasma with lower PA separation could lead to less continuum damping of the more edge-localized low-f mode. However, a quantitative assessment of the damping rate would require kinetic modeling, which is beyond the scope of this paper and left for future work. One of the limiter plasmas was modeled with the linear, resistive MHD code CASTOR with the external antenna module enabled.
In the second part of the study, we investigated the effect of the magnetic configuration on the efficiency of the AE antenna and AE stability. A database analysis revealed that resonance detection is ∼50% more likely in limiter compared to X-point configuration (see Table  1 ). Furthermore, the damping rate was observed to increase strongly with edge magnetic shear for resonances detected in X-point configuration (see Fig. 6a ). A closer look at the distribution of damping rates (see Fig. 6b ) found that observations of low normalized damping rates, -γ/ω 0 < 0. 4%, were more likely in X-point than in limiter configuration, agreeing with previous C-Mod results  [35]. Once again, these data come from a wide variety of JET plasmas, yet the general trends observed -especially the enhancement in AE stability with edge shear -are then seen more clearly in our dedicated study.
Acknowledgments The authors thank  H. J. C. Oliver  and  E. Rachlew  for fruitful discussions, as well as the reviewers for improving this paper. This work was supported by  US DOE  through  DE-FG02-99ER54563 ,  DE-AC05-00OR22725 , and  DE-AC02-05CH11231 , as well as the Brazilian agency  FAPESP  Project  2011/50773-0. This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training program 2014-2018 and  2019-2020  under grant agreement No  633053. The views and opinions expressed herein do not necessarily reflect those of the  European Commission.
Statistical analysis The numerical data are presented as the arithmetic mean and standard deviation. The significance of differences among the treatments was statistically evaluated by ttests and one-way ANOVA with Tukey's pairwise comparison as post hoc test for multiple comparisons (p<0. 05). Homogeneity of variance was calculated by Levene's test. Pearson's correlation test was performed to measure the strength of associations. All calculations were performed with SPSS. 24 software.
Promotion of in vitro seed germination by yeasts An experiment was conducted to evaluate the effects of the 69 yeast strains on the germination process. Nicotiana tabacum was the species chosen due to its homogeneity in the germination and phenotype of the seedlings. For this purpose, seeds were inoculated with yeasts on filter paper in a water-agar plate for 15 days (Fig. 3A ). The percentage of germination and germination time were not affected by inoculation with yeasts (data not shown). However, it was observed that some yeast strains significantly promoted the vigour of the tobacco plantlets relative to the control after 15 days of inoculation (Table  2 ): up to 5. 7-fold greater dry weight with M. guilliermondii Mg-62 and twice the number of roots with several strains. In addition, five of these strains increased the root length, although only seedlings inoculated with P.
Maternal outcomes All analyses in this secondary analysis followed the intention-to-treat principle: all randomly allocated women were analysed according to the group they were allocated to, irrespective of the treatment they received, if any. The analyses required data collected at post-randomisation visits therefore women without post-randomisation visit data were excluded. For bile acid concentrations, subgroups were defined based on accepted thresholds from the literature related to perinatal risk. 2  For itch, subgroups were defined based on median itch at baseline in the trial participants. 6 The effect of baseline bile acid concentration (<40 lmol/l versus ≥40 lmol/l, <100 lmol/l versus ≥100 lmol/l) and baseline itch score (<60 mm versus ≥60 mm) on two maternal outcomes were analysed: (1) serum bile acid concentration post-randomisation and (2) itch score post-randomisation.
Results Between 23rd December 2015 and 7th August 2018, 2737 women were screened for trial inclusion, of whom 1418 were found to be eligible. 605 women were recruited to the trial, including 37 women with a twin pregnancy, across 33 maternity units. 17 of the 33 maternity units used a threshold of 14 lmol/l as the upper limit of normal for serum bile acid concentration, whereas the remaining units used thresholds between 10 and 13 lmol/l, according to local laboratory reference ranges. 305 women were randomly allocated to UDCA and 300 women were randomly allocated to placebo. Follow-up to maternal and infant discharge continued until December 2018. 6 f the 605 women recruited, 76 women with no postrandomisation visit data were excluded from the secondary analysis. The majority of these women (73/76, 96%) delivered within 2 weeks of randomisation.
Two women withdrew from the trial: one withdrew consent for further data collection and no post-randomisation data was collected, and one withdrew consent to use data. Both were also excluded. Maternal baseline characteristics and maternal outcomes for the 527 women included in the secondary analysis (256 allocated to placebo, 271 allocated to UDCA) are shown in Table  S1. Perinatal outcomes for the 558 infants born to these women are shown in Table  S2. A flow diagram describing the participants included in each individual analysis is shown in Figure  S1.
Acknowledgements LCC is funded by the  National Institute for Health Research (NIHR) Professorship ,  RP-2014-05-019. Paul T Seed is partly funded by  King's Health Partners Institute of Women and Children's Health, Tommy 's (Registered charity no. 1060508 ) and by  ARC South London (NIHR). The views expressed in this publication are those of the authors and not necessarily those of KHP, Tommy's, the  NHS , the  NIHR  or the Department of Health. We thank the independent  Trial Steering Committee (David Williams ,  Judith Hibbert ,  Julia Sanders ,  Deborah Stocken ,  Julian Walters ,  Win Tin ) and the independent Data Monitoring Committee ( John Norrie ,  William McGuire ,  Jenny Myers ).
Although recent studies approaching the coding potential of metagenome-assembled genomes (MAGs) have provided useful insights into symbiosis factors that govern sponge-prokaryote interactions  [7, 8] , examination of cultivated sponge associated bacteria and their genomes is still much required to address the abovementioned knowledge gaps, especially in regards with the laboratory validation of the observed genomic traits. In the present study, we describe the general genomic features and provide brief functional information of 14 bacterial strains isolated from the marine sponge Spongia sp. in the northeast Atlantic. This study releases new data for the further exploration of complex sponge-microbe interactions and promotes comparative genomics studies of symbiotic microorganisms by adding up novel genome resources to public databases, including original genomes of three novel bacterial lineages unclassifiable at the genus level, the first genome sequence for the genus Lentilitoribacter and further genome assemblies of thus-far poorlystudied genera such as Agarivorans, Sphingorhabdus and Tropicibacter.
Data description 2. 1. Sampling, Isolation, and Genome sequencing In April 2015, Spongia sp. specimens (4 biological replicates) were collected by SCUBA diving at 20 m open water stations in Algarve, Faro (Portugal). In the lab, microbial cell suspensions (MCSs) were prepared from sponge samples through grinding and homogenization in artificial seawater as described previously  [9]. MCSs were then serially diluted (10 -3 to 10 -8 ) and 100 µL of each dilution were spread plated in triplicates on 1/10R2A  [10]  and VXA  [11]  media. Plates were incubated at 18°C for up to 8 weeks. Bacterial growth was monitored weekly and colony forming units (CFUs) were counted. Colonies were selected randomly considering morphologically different ones as well, and pure cultures obtained by streaking colonies on the same isolation media.
In total, 252 colonies (160 from 1/10-R2A and 92 from VXA, Table  S1 ) were selected. Genomic DNA was extracted from cell pellets derived from freshly grown cultures using the Wizard® Genomic DNA Purification Kit (Promega, Madison, USA) according to the manufacturer's instructions. Genomic DNA samples of all isolates were then subjected to 16S rRNA gene amplification by PCR followed by Sanger sequencing according to established procedures  [12]. Taxonomic assignment of bacterial isolates to the genus level was performed using the classifier tool of the ribosomal database project (RDP, release 11,  [13]. Identification of closest matches to all sequence queries were also obtained using the BLAST algorithm (February 2018, Table  S1 ). Alphaproteobacteria and Gammaproteobacteria strains were frequently isolated from R2A and VXA, respectively (Figure  1 ).
Based on the taxonomic assignments obtained with RDP (Table  S2 ), 14 strains originating from both media were chosen for genome analysiswhich in most cases would likely correspond to novel genus/species from sponges (Table  S1&S2 ). These were classified into 11 formally described and 3 potentially novel genera from Actinobacteria (3 genera), Bacteroidetes (1 putatively new genus and family), and Proteobacteria (10 genera from Alpha -6 strains, with two putatively new genera-and from Gamma -4 strains -classes) phyla (Table  1 ). Afterwards, Illumina MiSeq sequencing was carried out at MR DNA (CA, United States). Paired-end libraries (2×301bp) were accomplished and de novo assembly was performed with the NGen DNA assembly software by DNAStar, Inc. as described previously  [14]. Additionally, CheckM v.
1. 0. 18 was used to assess the completeness and contamination of the generated genomes  [15]. Genome annotations were conducted using RAST  [16] , also using COG database via WebMGA  [17]. Furthermore, the genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH version 5. 0. 1  [18]. Default parameters were used for all software. The number in brackets indicate the number of isolates obtained for each genus.
Basic Genome Features The genomic feature information of all strains is outlined in Table  1. All genomes possessed > 99% completeness (except three genomes) and <1% contamination, suggesting high data reliability for further comparative genomic studies, for example. Three genera including Arthrobacter sp. Alg241-R88, Dietzia sp. Alg238-R159, Micrococcus sp. Alg238-R198 isolated on 1/10R2A were sequenced from phylum Actinobacteria. The size of the genomes ranged from 2. 59 to 4. 37 Mbp with GC content ranging from 64. 8 to 72. 8 %. Gene annotation using RAST identified 4040, 3629, and 2375 protein-coding sequences (CDs) for strains Alg241-R88, Alg238-R159, and Alg238-R198, respectively. From COG annotations, the genes for glycosyltransferase, acetyltransferases, ABC-type multidrug transport system were assigned for these three strains (Table  S3 ).
Genome sequence accession number The assembled genome sequences are available in the European Nucleotide Archive -European Molecular Biology Laboratory-EBI under the project number PRJEB28331 and can be accessed using the accession numbers given in Table  1. (http://www. ebi. ac. uk/ena/data/view/ <ACCESSION NUMBER>). Also, 16S rRNA gene sequences of the bacterial isolates (OTUs) were deposited at NCBI GenBank under the accession numbers MH818465 to MH818518 (Table  S2 ).
Acknowledgments The authors would like to thank  Jorge M. S. Gonçalves ' research team at  CCMAR-UAlg  for sampling the sponges from the sea. We thank  Telma Franco  for her help during sample processing and  Marta Valente  for Sanger-sequencing of 16S rRNA genes. EK would like sincerely to thank  Alireza Asvadi  for his encouragement to write up the study. This work was performed when EK was PhD student supported by a full scholarship from the  Erasmus Mundus Programme / SALAM EMA2 lot7/SALA1206422. Material and resources for the lab experiments were funded by  FCT-Fundação para a Ciência e a Tecnologia (Portugal)  through the project grant  PTDC/BIA-MIC/3865/2012 , conceded to RC. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Image acquisition and 3D modelling Fourteen patients with intracranial aneurysm of different shapes, sizes, and locations were chosen for the study. The data acquisition protocol of this retrospective study was approved by the University Hospitals of Tours, Toulouse, France, institutional review board. Pre-treatment anatomical models were generated from 3D Rotational Angiography (3DRA) images using an INNOVA 3131 IQ TM (General Electric Healthcare, Milwaukee, USA, ). Vascular anatomy was extracted from 3DRA images with voxel size of using threshold-based segmentation  (Moyano et al. , 2017)  Threshold values were chosen by an expert in neurovascular angiography to best fit the patient's anatomy depending on contrast density and image quality. When selecting the threshold value, both the treated vessel and aneurysm, were considered as the priority to achieve a high quality reconstruction of the local vascular anatomy  (Larrabide et al.
Simulations The open source Finite Volume software OpenFOAM was used for CFD simulations. A steady state solver capable of modelling heterogeneous PM was implemented and used in all the experiments  (Jasak et al. , 2007; Dazeo et al. , 2018b). Morales et al. showed that local differences between Newtonian and non Newtonian fluids in coiled intracranial aneurysm are not sufficient to alter the main flow characteristics  (Morales et al. , 2013). With this in mind, and because velocities in aneurysms treated with coils are smaller than velocities in aneurysms treated with FDs, blood behaviour can be safely assumed as Newtonian in the former. Viscosity was considered as and density to approximate physiological range of human blood. Each patient's inlet flow rate (q) was set using the following equation proposed by  Reneman et al.
The tectonic evolution of the European Eastern Alps within the Alpine orogeny is still under debate. Open questions include: the link between surface, crustal and mantle structures; the nature of the Moho gap between the two plates; the relationship between the Alps, the adjacent foreland basin and the Bohemian Massif lithospheric blocks. We collected one year of continuous data recorded by ~250 broadband seismic stations -55 of which installed within the EASI AlpArray complementary experiment-in the Eastern Alpine region. Exploiting surface wave group velocity from seismic ambient noise, we obtained an high-resolution 3D S-wave crustal model of the area. The Rayleigh-wave group-velocity from 3 s to 35 s are inverted to obtain 2-D group velocity maps with a resolution of ~15 km. From these maps, we determine a set of 1D velocity models via a Neighborhood Algorithm, resulting in a new 3D model of S-wave velocity with associated uncertainties.