dataesr/scientific-paragraphs-categorization huggingface dataset:
Further in this analysis, the pressure balance has been analysed for orbit 3151 since it is a useful parameter to diagnose the interaction between the ionosphere and the solar wind (e. g. Zhang and Luhmann, 1992). The objective is to perform additional tests to evaluate if the magnetic field could penetrate down to the transition altitude in that orbit. Theoretically, the induced magnetic field penetrates down to an altitude where the magnetic pressure equals the plasma thermal pressure. Below, the thermal pressure is higher than the magnetic pressure, and the magnetic field intensity decreases to zero because of the magnetic diffusion effect. Since the available dataset does not give access to all necessary observables such as a magnetic field profile and temperatures, the pressure balance assumption has been used to find whether reasonable values can be estimated for these parameters.
Conclusion This study has shown an analysis of data acquired by the MARSIS instrument aboard Mars Express. These data, when interpreted carefully and successfully compared with modelling, indicate that an induced magnetic field can penetrate deep in the ionosphere of Mars, and strongly compresses the plasma. We list here the elements which are in favour of this conclusion: -The ionosphere in the presence of a magnetic field is compressed compared to the ionosphere in orbits where no magnetic field is measured (see Fig. 4 ). In particular in orbit 3151, the vertical electron density profile exhibits a clear compression identified in 14 ionograms, which is characterised by a general smaller scale height (Fig. 6 ), and a change in scale height from $ 40 to 45 down to $ 30 km (Fig. 9 ). This is also confirmed with the other 2 orbits within the magnetic field regimen (Tables in Annex).
Acknowledgements MR-N and LV want to thank  MetNet project  ( AYA2009-29967-C05-02 ,  AYA2011-29967-C05-02 ). BS-C and ML acknowledge support through  STFC  Grants  ST/K001000/1  and  ST/N000749/1. The authors acknowledge the Principal Investigators of the Mars Express MARSIS instrument, the  MARSIS team at the University of Iowa  and the  European Space Agency  for making the data available on the Planetary Science Archive (http://www. rssd. esa. int/PSA). Also, MR-N wishes to thank  M. Herraiz Sarachaga  for useful discussions.
Objectives: The aim of this analysis was to provide an estimate of drug utilization indicators (persistence, switch rate and drug consumption) on biologics and the corresponding costs (drugs, admissions and specialist care) incurred by the Italian National Health Service in the management of adult patients with rheumatoid arthritis (RA). Methods: We conducted an observational retrospective cohort analysis using the administrative databases of three local health units. We considered all patients aged ≥18 years with a diagnosis of RA and at least one biologic drug prescription between January 2010 and December 2012 (recruitment period). Persistence was defined as maintenance over the last 3 months of the follow-up period of the same biological therapy administered at the index date. A switch was defined as the presence of a biological therapy other than that administered at the index date during the last 3 months of the follow-up period.
Data sources This study was based on the administrative databases of Italian Local Health Authorities (LHAs), based in Lombardy, Lazio and Campania, which include ~1. 5 million health-assisted individuals. For each LHA, an administrative database is available that includes data (pharmaceutical expenditure, admissions, services, etc. ) that describe a "contact" (ie, predefined and classified in a univocal manner) between a patient and a facility of the social and health care system. Therefore, it is possible to trace each service provided to the patient who initiated a contact. Data were collected from the three administrative databases on demographic aspects, consumption and costs of the health care resources administered to the patients considered herein. More specifically, the patient register provided information on demographic characteristics (date of birth, gender, date of death, exemption code, etc.
The register for specialist ambulatory care includes all specialist services (laboratory tests, instrumental tests and visits) provided to patients and paid by the Italian NHS. For each of these services, the register reports the date it was provided, along with the code, description and unit cost. Finally, the medical exemption register contains all disease exemptions; this database was our source for identifying diagnoses and comorbidities in the sample (to be integrated with information from hospital admissions and drug consumption). Each patient was given a progressive number to anonymize the data extracted, which was in full compliance with the Personal Data Privacy Act (Law 196/03) and the resolution issued by the Italian Personal Data Privacy Authority on March 1, 2012, and published in the Official Gazette no.
Discussion and conclusion This analysis was based on information from the administrative databases of three Italian LHAs covering the 4-year period 2010-2013. Therefore, it was possible to create a large sample of RA patients who had been treated with a biological therapy. In addition to the mean costs of treatment, we assessed indicators of consumption of biological drugs, such    as persistence, switch rate and drug consumption. Attempts were also made to identify relationships between these consumption indicators and costs of treatment. The features of treatment (eg, persistence, switch rate and drug consumption) seem to directly influence its costs. In subjects not persisting with initial treatment, other health care costs (hospitalizations, specialist services, etc. ; €1,088) were approximately three times higher than for persistent patients (€375).
Consequently, the analysis on the three biologics (adalimumab, etanercept and infliximab) could be characterized by patient recruitment bias, since the three groups we compared could have been not perfectly homogeneous in terms of disease severity. Another limitation is that the reasons for switching and low persistence to treatment, as well as the reasons for drug dose escalation or reduction, are not recorded in the databases. In addition, unlike adalimumab and etanercept, infliximab is given as an intravenous infusion; this may not only influence patient selection but is also likely to have an impact on costs that these administrative databases may not include. One study, conducted from a different perspective, estimated that the cost of a single infusion (including materials and health care professionals) was €43.
Circular blast wave problems The computational domain for two 2D blast wave problems is an open disk with center in (0, 0) and radius R = 1. 5. In order to create the initial distribution of the particles, shown in Figure  9 , we first define the Delaunay triangulation of given sets of generators, then the particles are matched to the barycenters of the triangulation. A regular and radially symmetric and a unstructured set of 74651 generators are considered. As mentioned these generators are used as the initial vertex of the triangles of the associated and unique Delaunay triangulation (using the algorithm from PDE toolbox of MATLAB). We use this procedure in order to obtain a correct computation of the initial particle volumes V i required by the scheme  [22]. The SPH-MOOD-MLS scheme with cubic Taylor reconstruction and Rusanov flux is used for this example.
Acknowledgments This work has been partially supported by the  Ministerio de Economía y Competitividad  (grant # DPI2012-33622 ) of the  Spanish Government  and by the,  Consellería de Cultura ,  Educación e Ordenación Universitaria of the Xunta de Galicia  (grant # GRC2014/039  ) cofinanced with FEDER funds, and the  Universidade da Coruña.
Proteomics Proteins were revealed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) or NuPAGE (Tris-Glycine 4-12% acrylamide gradient; Life Technologies) using silver staining (Silver staining kit, # 24612; Pierce, Rockford, IL, USA). For mass spectrometry analysis, a first experiment permitted to sequence all the peptides in G3BP IP from WT mouse brain and in non-specific IgG IP. A second experiment reproduced the results after G3BP IP in WT and KO brain extracts, subjected or not to RNAse treatment. Proteins in silver-stained gel were cut out and ingel digested with endoproteinase trypsin. Peptides were extracted from the gel and analyzed by LC-MSMS and an Orbitrap XL under standard conditions. Proteins were identified after database search against the NCBI non-redundant database, using Mascot as search engine.
Mapping of high-throughput sequencing data to the mouse genome For each sample, we filtered out reads shorter than 21 nucleotides to avoid ambiguous mapping locations, as any random sequence shorter than 21 nt is highly likely to be found in the genome. We did a two-step mapping, first using as reference the mouse mm9 genome (NCBI Build 37 assembly, July 2007) using Bowtie v0. 12. 7  (Langmead et al. 2009 ) allowing up to two mismatches. Furthermore, to avoid missing any tags in mature transcripts, split reads that could correspond to exon junctions were obtained using the genome multitool (GEM) split mapper (build 592) from the GEM library (Marco-Sola et al. 2012) using the following filters for split reads: same strand, same chromosome, and a maximum of 100 000 bases apart, based on a intron length estimation in mm9.
Clusters annotation to Ensembl database Uniquely read-tags mapped to the same strand were clustered according to their overlapping genomic positions with Pyicos  (Althammer et al. 2011). Annotations of gene classes (biotypes) and location of genic structural regions were downloaded from Ensembl 62 database, NCBI37/mm9 assembly. Clusters were classified according to the overlap with the gene class  (protein-coding, rRNA, miRNA, etc. ). Clusters that do not fall in such regions were classified as intergenic. Protein coding-associated clusters were classified into exonic or intronic, and exonic ones into 5'-untranslated region (UTR), coding sequence (CDS), or 3'UTR. Because of the nature of gene structure annotation, a given cluster may fall in more than one category, e. g. miRNA and intronic.
Gene ontology annotations We assigned the gene ontology (GO) terms using expression analysis systematic explorer (EASE)  (Hosack et al. 2003) , to compute the overrepresented functional categories in 'Biological Process,' 'Cellular Component,' and 'Molecular Function' systems according to database for annotation, visualization and integrated discovery database. EASE scores (modified Fisher's exact test probabilities) were computed for our input gene lists compared to mouse genome and also compared to a data set regrouping all cap analysis gene expression transcripts identified in mouse brain (Fantom 4) correlated with RefGene annotations, to avoid a bias toward brain expressed genes in our CLIP experiment. Both analyses gave the same results.
Data were analyzed with the Roche LightCycler480 software. Absolute RNA concentrations were recovered from standard curves plotted for each pair of primer oligonucleotides used, and relative analysis were performed as described in the results. The oligonucleotides were designed with Geneious software (see Appendix S1), and concerning the real-time PCR experiments, they were chosen to produce amplicons of equivalent size and to use the same annealing temperature. Furthermore, the establishment of standard curves permitted to normalize the efficiency of each primer pair and thus rule out possible experimental PCR biases toward specific amplicons. Concerning IP, the result was expressed as an enrichment of the tested transcripts in specific G3BP IP relative to their quantitation in IgG non-specific IP (log10 scale histograms).
For an exhaustive and precise analysis of G3BP-complexassociated RNAs, we performed two independent replicate HITS-CLIP experiments using WT mouse brain (RNAs sequenced from band no. 2, Fig. 2a, lane c ). Reads were filtered then mapped to the genome, and uniquely mapped reads (59 800 in one experiment and 53 183 in the second experiment) were clustered according to genomic position. Furthermore, we used the GEM split mapper (build 592) from the GEM library (Marco-Sola et al. 2012) to detect any exon-exon junction on the remaining reads, in order not to discard tags that would fall into junctions in mature transcripts (see Materials and Methods). Data from the two alignment methods were combined and confronted to Ensembl 62 database to identify their precise location. 39 671 different clusters in one experiment and 19 631 in the second were identified, mapping respectively to 5800 and 4890 different protein-coding or non-coding genes (1 or more clusters per gene).
We also scanned the clusters for the presence of previously identified consensus sequences for G3BP1 (systematic evolution of ligands by exponential enrichment motif; Tourri ere et al. 2001) or G3BP2 (RNAcompete;  Ray et al. 2013) , and as for the previous sequences, these motifs were present but not highly enriched in the clusters from G3BP-complex HITS-CLIP over the background  (Figure S2c, (3) (4). GO terms were attributed to the G3BP-complex targets using EASE  (Hosack et al. 2003). Annotation enrichment was ascertained by attributing an EASE score for each GO classification, relative to the mouse genome and also more specifically to all the transcripts identified in mouse brain in Fantom 4 cap analysis gene expression database, to avoid potential enrichment bias toward brain functions because of the fact that HITS-CLIP was performed in brain.
Both analyses gave the same results and indicated that G3BPcomplex target genes are involved in synaptic transmission, in particular glutamate-mediated transmission (Fig. 2c ). We experimentally validated some of the identified targets using both real-time PCR and traditional PCR (Fig. 2d  and e ). Real-time PCR data were expressed as enrichment of the transcripts in specific IP over a non-specific IP performed with IgG. Thresholds of immunoprecipitation efficiency were determined by including positive and negative controls. As a positive control, we used the non-coding RNA growth arrestspecific 5 (Gas5), a well-known G3BP target  (Zekri et al. 2005 ) that was identified among the G3BP HITS-CLIP tags, and as a negative control Hprt1, a housekeeping gene not present in G3BP HITS-CLIP. Thus, several protein-coding transcripts involved in synaptic transmission like Kpna1, Trpm3 and some involved in plasticity through glutamate signaling like the metabotropic receptor mGluR1 or the a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit Gria2 transcripts were highly enriched in G3BP-complex.
We also considered the expression of these different transcripts regions in brain (Fig. 4b ). For two transcripts, Fgf14 and Btbd9, amplifications of the retained intronic sequences were comparable to amplification of the 3'UTR, suggesting that the premature transcripts are up-regulated over mature transcripts; whereas for RNA-binding protein, Fox-1 homolog (Rbfox1), Cadm2 and Ctnnd2 transcripts, the amplification of 3'UTR was higher than intron sequences, indicating expression of both mature and premature transcripts at comparable levels. Traditional (not quantitative) PCR further validated the presence of these intronic sequences in the brain and in the G3BP-complex (Fig. 4c ). Altogether, the G3BP-complex in the brain appears to be associated with premature transcripts containing at least two introns rather than excised introns or transcribed small transcripts from the same locus.
The fold enrichment in G3BP IP over non-specific IgG IP is given for each transcript section tested. Hypoxanthine phosphoribosyltransferase 1 (Hprt1) and growth arrest-specific 5 (Gas5) are used as negative and positive threshold controls of enrichment, respectively. X axis: regions targeted by PCR, using specific primers, with: e: exon; i: intron, e-i: exon-intron junction; numbers: exon or intron number of the transcript as established in NCBI database (See Figure  S4 ). (b) Input enrichments (total brain extract) of the same transcripts regions. (c) Examples of RT-PCR products (nonquantitative) from input total extract, non-specific IgG IP, G3BP IP and negative control of PCR without reverse transcription (G3BP IP RNA) run on an agarose gel. note also, the protein CtBP1 seems to be less abundant in the cerebellum after G3BP depletion ( Figure  S7b ).
Also, similar to SGs where transcripts are not degraded, the G3BP-complex could prevent these intron-retaining transcripts from degradation. While our study did not address the function and the localization of these unspliced transcripts in neurons, a large number of intronic sequences have been reported in some dendritically localized mRNAs of primary rat and mouse hippocampal neurons, among which we found G3BPcomplex targets  (Buckley et al. 2011; Khaladkar et al. 2013). One hypothesis is thus that a larger than expected fraction of incompletely spliced transcripts could reach the cytoplasm. As there is good evidence that transport of mRNPs and translational regulation in neuron might be intimately coupled, it would suggest a mechanism whereby G3BP-complex may play an important role in the regulation of stability/translation and/or transport of transcripts with retained introns.
Acknowledgments and conflict of interest disclosure This work was supported by a  Fondation pour la Recherche M edicale (FRM)  grant (Equipe FRM 2011no. DEQ20111223745). S. M. was supported by a graduate fellowship from the Minist ere D el egu e a la Recherche et aux Technologies and FRM. J. G. V. , N. B. and E. E. were supported by the  Spanish Ministry of Science  with grants  BIO2011-23920  and  CSD2009-00080. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare to have no conflict of interest. All experiments were conducted in compliance with the ARRIVE guidelines.
Anthropometric Measurements and Body Composition Weight and height were measured with an accuracy of 0. 1 kg and 0. 5 cm, respectively. Waist circumference was measured between the last ribs and the upper iliac wings with a flexible tape measure. Body composition was evaluated by dual energy X-ray absorptiometry (DXA; Hologic QDR-4500A, Bedford, MA, USA)  [15, 16]. The subjects laid on the DXA table in a supine position and remained still for the duration of the scanning procedure. Data was analyzed using the Hologic QDR Software for Windows (version 12. 6), which integrates whole-body measurement and standard body regions, such as trunk, arms and legs, delineated by specific anatomical landmarks. From this the fat mass percentage by DXA was calculated. Thereafter, the percentage of abdominal fat mass was determined manually by a trained experimenter, by delineating a rectangular box around the region of interest between vertebral bodies L1 and L4.
Maximal Incremental Exercise Test The initial power was set at 30 W during 3 min followed by a 15-watt increment every minute until exhaustion. The adolescents were strongly encouraged by the experimenters throughout the test to perform at maximal effort. Maximal criteria were: heart rate (HR) > 90% of the theoretical maximum heart rate (210 -0. 65 × age), respiratory exchange ratio (RER = V CO 2 /V O 2 ) > 1. 1 and/or V O 2 plateau. Cardiac electrical activity was monitored (Ultima Series TM ; MGC Diagnostics, Saint Paul, MN, USA), and the test was coupled with a measurement of gas exchanges breath by breath (BreezeSuite Software; MGC Diagnostics) that determined respiratory minute volume (V E), oxygen consumption (V O 2 ) and CO 2 production (V CO 2 ). Volumes and gases were calibrated before each test.
The data were collected at a frequency of 10 Hz, and averaged every 30 s. The results were expressed relative to the average resting value: the value 0 was thus arbitrarily taken for the start of the exercise. The variations in IR-BV and IR-SO 2 gave a continuous estimate of the regional changes in blood volume and the local balance between oxygen delivery to muscle and its extraction by muscle  [22]. Kinetics of IR-BV and IR-SO 2 at W 0 and W 12 were compared.
Central Vascular Adaptations The cardiac output (CO) was measured continuously by PF05 Lab1 TM ,(PhysioFlow, Bristol, PA, USA). The stroke volume (SV) was calculated from the measurement of variations in thoracic bioimpedance fluctuations  [23]. HR, SV, and CO were averaged over 30 s. In all, the parameters collected over the exercise at constant power were: IR-BV(t), IR-SO 2 (t), HR(t), SV(t), and CO(t).
Statistical Analysis Sample size estimation has been initially proposed to show an important effect size around 1, according to Cohen's recommendations  [24]. Also, with n = 13 subjects, an effect size equaling 1 can be highlighted for a two-sided type I error at 5% and a statistical power at 90%. Finally, 15 subjects have been included to take into account possible lost to follow-up. Statistical analysis was performed using Stata software, version 13 (StataCorp, College Station, TX, USA). The tests were two-sided, with a type I error set at α = 0. 05. Data were presented as the mean ± standard deviation or the median (interquartile range) according to statistical distribution (assumption of normality studied by Shapiro-Wilk test). For paired comparisons between W 0 or W 12 , usual statistical tests were performed: paired t-test or Wilcoxon test for quantitative variables and Stuart-Maxwell's test for categorical parameters.
Background: The occurrence of brain death in patients with hypoxic-ischaemic brain injury after resuscitation from cardiac arrest creates opportunities for organ donation. However, its prevalence is currently unknown. Methods: Systematic review. MEDLINE via PubMed, ISI Web of Science and the Cochrane Database of Systematic Reviews were searched for eligible studies (2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016). The prevalence of brain death in adult patients resuscitated from cardiac arrest and the rate of organ donation among brain dead patients were summarised using a random effect model with double-arcsine transformation. The quality of evidence (QOE) was evaluated according to the GRADE guidelines. Results: 26 studies [16 on conventional cardiopulmonary resuscitation (c-CPR), 10 on extracorporeal CPR (e-CPR)] included a total of 23,388 patients, 1830 of whom developed brain death at a mean time of 3.
Search strategy and study selection MEDLINE via PubMed was searched using the keywords "heart arrest" (MESH) OR "cardiac arrest" (MESH) AND "brain death". ISI Web of Science and the Cochrane Database of Systematic Reviews were searched using the search strings "cardiac arrest" AND "brain death". The search was iterated until April 30, 2016. The websites of relevant journals were searched to identify relevant studies in press. The reference lists of relevant studies were screened to identify other studies of interest.
Data extraction and analysis For each study included in the final analysis, the following data were extracted: patients' age and sex; location of cardiac arrest (IHCA or OHCA); witnessed status; cause of cardiac arrest; initial cardiac rhythm; CPR technique (c-CPR vs. e-CPR); cardiac arrest duration, defined as the interval between collapse to either return of spontaneous circulation (ROSC) or to the start of extracorporeal circulation; hospital mortality; mode of death; rate and timing of brain death; rate of organ donation. Whenever possible, the authors of the original studies where contacted to retrieve missing data. Data of the study populations were summarized using proportions and weighted means. The mean and standard deviations in individual studies were estimated from median and interquartile range, when needed, according to the method described by Wan et al.