dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements : We would like to thank  Vasily Belokurov  for helpful discussions. MYW acknowledges support of the McWilliams Postdoctoral Fellowship. T. d. B. acknowledges support from the  European Research Council  ( ERC StG-335936 ). This paper has gone through internal review by the  DES collaboration. This research has made use of  NASA's Astrophysics Data System Bibliographic Services. Funding for the DES Projects has been provided by the  U. S. Department of Energy , the  U. S. National Science Foundation , the  Ministry of Science and Education of Spain , the  Science and Technology Facilities Council of the United Kingdom , the  Higher Education Funding Council for England , the  National Center for Supercomputing Applications  at the  University of Illinois at Urbana-Champaign , the  Kavli Institute of Cosmological Physics at the University of Chicago , the  Center for Cosmology and Astro-Particle Physics at the Ohio State University , the  Mitchell Institute for Fundamental Physics and Astronomy at Texas A&M University ,  Financiadora de Estudos e Projetos, Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro ,  Conselho Nacional de Desenvolvimento Científico e Tecnológico  and the  Ministério da Ciência, Tecnologia e Inovação , the  Deutsche Forschungsgemeinschaft  and the  Collaborating Institutions in the Dark Energy Survey.
METHODS Children aged 6 to 14 years attending primary and secondary schools in the district of Rome were enrolled. They received a family medical history questionnaire at school that was filled-up by their parents at home. Participation was almost 100%. Fourteen children with incomplete questionnaire data on dietary habits were excluded from the analysis. Written consent was given by parents directly to school secretaries and kept on records. The Study Protocol was approved locally by the Council of each School and regionally by the Regional Institute for Research and Experimentation for Education, today called IRRE (Istituto Regionale Ricerca e Sperimentazione per l'Educazione, Rome, Italy), the last one acting as an Ethical Committee. Lifestyle: eating habits, physical activity and sedentary activities.
Conclusions. Our data show that cardiovascular risk factors in children are not adequately evaluated. In addition, total cholesterol blood levels are not frequently considered. However, among children adherent to the Mediterranean diet, there is a greater awareness of the levels of total blood cholesterol that are known more frequently among children and parents (Table  1 ) and of healthy lifestyle condensed in more hours spent in outdoor sport activities that are in turn related directly to KidMed score as shown multivariately. Most probably, parents influence their children with their educational behavior and awareness of the problem. We noted that the adherence to the Mediterranean diet as indexed by the KidMed score was associated with larger sports' practice, with a lower BMI and with a tendency to have lower total cholesterol blood levels also measured more often.
Methods Patients. A prospective clinical pilot study was performed to evaluate in vivo the effect of spironolactone, an oral MRA, in patients with exudative signs of nAMD. This study was approved by the local ethics committee (#184/14 ethical committee approval, Canton de Vaud), and performed following the regulations of the mentioned committees. It adhered to the Declaration of Helsinki for human research. Informed consent was obtained from all human participants. This study has been retrospectively registered on 16 November, 2018 under the registration number NCT03744767. Only patients with refractory stable intraretinal or subretinal fluid present for ≥6 months in a row on monthly SD-OCT despite monthly intravitreal of the same anti-VEGF treatment (ranibizumab or aflibercept) were included.
All quantitative follow-up parameters were statistically analyzed and compared with the baseline parameters using paired Wilcoxon signed-rank tests. For data analysis, Microsoft Excel 2010 and JMP software for Windows (version 8. 0. 1, SAS Institute Inc. , Cary, NC) were used. A two-tailed probability of 0. 05 or less was considered statistically significant. The required study sample size was estimated before study initiation. According to the available literature on CSCR, and assuming that the treatment would be less effective in eyes with nAMD, our goal was to examine whether spironolactone could produce a minimum decrease of 15% in all measured retinal thicknesses. Therefore, to achieve a 90% power for detecting this degree of change, we estimated that 21 eyes would be required. Microsphere elaboration.
The area of CNV-related fluorescence on each horizontal section was measured using the ImageJ software. The summation of the entire fluorescent area on z-stack images from the top to the bottom of the CNV was used as an index for the CNV volume. Mice were perfused with 200 µl FITC-dextran (FD2000S, 5 mg/ml, molecular weight 2,000,000, Sigma-Aldrich) before enucleation. After RPE-choroidal flatmounting, the FITC-dextran perfused CNV was examined and analyzed as previously described. Immunofluorescence of RPE-choroid flat-mounts. Three days after laser induction (peak of macrophage infiltration), RPE-choroid flat-mounts were also prepared for immunofluorescence. A polyclonal rabbit anti-IBA1 antibody (019-19741, 1:400, Wako, Neuss, Germany) was applied overnight at -4 °C. After washing with 0.
1% Triton X100/PBS, the flat-mounts were incubated with Alex-aFluo® 594 goat anti-rabbit IgG (A-11012, 1:200, ThermoFisherScientific, Saint Aubin, France), the nuclei were counterstained with DAPI. Images of IBA1 positive macrophage/microglia were observed and captured with a confocal microscope. The IBA1 positive area was measured using the ImageJ software. The average fluorescent area per burn per eye was calculated. Immunohistochemistry. Enucleated eyes were fixed in 4% PFA for 2 h, dehydrated and embedded in paraffin. Eight-µm-thick sections were deparaffinized in xylene, hydrated in a graded alcohol series, and washed in PBS-Tween (PBST). After antigen retrieval by heating in citrate buffer and inactivation of endogenous peroxidase by 3% H2O2, sections were incubated with 3% normal horse serum to reduce the non-specific signal.
As no significant difference was shown between controls (no experiment effect), the pooling was considered interpretable. Analyses were performed in SAS® 9. 4 for Windows, SAS Institute Inc. , Cary, NC. For data related to QPCR and western blot, comparison between two groups was performed using Mann-Whitney U-test. Comparison between multiple groups was analyzed using non-parametric Kruskal-Wallis followed by Dunns test (GraphPad Prism 5 for Windows, GraphPad Software Inc. , San Diego, CA, USA). p-values of 0. 05 or less were considered significant. RNA-sequencing and data analysis. Male 8-week-old Lewis rats were injected intravitreously with aldosterone (20 nM final concentration in the vitreous) and sacrificed after 24 h. Control rats received vehicle injection. The whole retinas (comprising neuroretina and RPE-choroid complex) were isolated for RNAsequencing.
Total RNA was extracted using the RNeasyMini Kit (Qiagen) including DNase I treatment. RNA integrity was checked on the Agilent 2100 Bioanalyzer. At least three independent biological replicate samples were sequenced and used for downstream analysis. RNA-sequencing was performed on Illumina HiSeq2000 platform. The average number of reads per sample was 27 M. Reads from each sample were processed as follows. First, reads were trimmed using an in-house Perl script with a minimum phred quality of 20 per vase and a minimum read length of 30 bp. On average, 24% of reads per sample were discarded. The resulting reads were later aligned to the Rattus Norvegicus genome assembly 3. 4 (from Ensembl) using Tophat version 2. 0. 10. At least 12 million reads were aligned to the genome for each sample. We next quantified gene expression to obtain read count and FPKM values.
The non-adjusted read counts for each gene were used for statistical calculation of global differential expression using DESeq2. Differentially expressed genes were selected at an adjusted p-values of ≤ 0. 05 and fold changes >1. 5. Differential expression between aldosterone-and vehicle-injected rats was also analyzed using the GOlandscape, a threshold-free gene ontology tool (The GOlanscape R-package and a detailed description of the tool are available at the website https://github. com/andreaprunotto/GOlandscape). This software computes a stepwise GO-analysis all over the range of DE significance, assigning a p-value for each GO term at each step. Then it selects the most significant annotated categories in the range, displaying them in combination with the most represented annotated genes within these terms.
Acknowledgements We thank INSERM, the  Agence Nationale de la Recherche  ( ANR  Mineraloret  ANR-11-BSV1-0022 , and  ROCK-SUR-MeR   ANR-15-CE18-0032 ), the  Fondation pour la Recherche Médicale  (FRM Visual System 2013,  DVS20131228894 ) and the  Swiss National Science Foundation  (grant # 156260  to C. R. ) for financial support. This research was also supported by grants from  MAT2013-43127-R  and  MAT2017-83858-C2-1 MINECO/AEI/FEDER ,  UE. We thank  Christophe Klein  from  Center d'Histologie, d'Imagerieet de Cytométrie , and  Georges Zadigue from Center d'Explorations Fonctionnelles of Center de Recherche des Cordeliers  for their technical support. We thank  Maëva Dupuis-Deniaud ,  MDSTAT Consulting Lyon, France  for her assistance in the statistical analysis.
In the following, the use of m only for the determination of the tilt angle is assessed. The slope m computed with equation (  14 ) is shown in figure  4  for a scan of the tilt angle q turb and three values of elongation ℓ max /ℓ min. The red symbols are results of synthetic turbulence for the same elongation as in figures 1 and 2. The agreement between the analytical expression and the synthetic data confirms the dependence of m on the turbulence parameters given in equation  (14). For all three cases and small θ turb , m increases as the structure's major axis misaligns with respect to the x-axis, whereas for finite elongation and θ turb close to 90°, m decreases as the structure's minor axis aligns with the x-axis. As a result of these behaviours, m has a maximum whose position depends on the elongation.
Discharge #34631 without NBI has low u ⊥ and is used to investigate the effect of the temporal decorrelation of the turbulence on the measurements (see section 3) at the end of this section. The plasma density profiles for both discharges are shown in figure  7(a). ρ pol is the normalized poloidal flux radius, which is 0 at the magnetic axis and 1 at the last closed flux surface. The measurements depicted with symbols are obtained from Thomson scattering  [51]  and lithium beam diagnostics  [52]. The solid lines depict the fits which are used for ray tracing calculations with the TORBEAM code  [53].
Measurements on the TJ-II stellarator In this section the tilt angle measurement method is applied on TJ-II, a heliac type stellarator with major and minor radii of 1. 5 and 0. 2 m. One series of reproducible discharges is investigated (#43459-91). The scenario is a low density (line averaged density 5. 5×10 19 m -3 ) L-mode discharge in the standard magnetic configuration with 1 T on-axis. An ECRH power of 0. 5 MW is applied. Similar discharges have been recently investigated using the gyrokinetic code EUTERPE  [58]. It was found that turbulence is dominated by trapped electron modes locally destabilized by electron temperature gradient with a normalized scale length of 30. The density profile is shown in figure  11(a). It has been obtained by Bayesian inference of Thomson scattering, interferometry and reflectometry data  [59].
Tilt angle measurement The time delay of the cross-correlation function is investigated for the measurements at r = 0. 72. Experimental data are analysed in a similar way as for AUG in section 4. 2. Measurements of the tilt angle of the turbulent structures in the confined region of TJ-II are obtained for the first time. The measurement positions obtained with TRUBA are shown on the perpendicular cross-section of TJ-II in figure  12(a). Closed flux surfaces are depicted by solid grey lines, the magnetic axis is indicated with an 'x', and a section of the vessel is shown. Figure  12(b)  shows in detail the measurement positions of reference (squares) and hopping (circles) channels. The eight sets of points correspond to different angles of incidence of the probing beam. Measurements are differently aligned; the blue measurement points define a negative (clockwise) angle Θ ray with respect to the radial direction, while the red ones define a positive one (counter-clockwise).
Radial profile of tilt angle The radial profile of the tilt angle has been investigated by two-point correlation measurements. A fine scan of the probing frequency of both channels in the range 33-39 GHz has been performed. The frequency difference between the channels is fixed at 500MHz, thus the cross-correlation function is obtained for only one Δr value per probed radial position. Four angles of incidence, two with Θ ray <0 and two with Θ ray >0, have been used. This configuration provides measurements at k ⊥ =3. 5 or 5. 5 cm -1 , which do not change appreciably within the radial scan. The time delay t max profiles for different angles of incidence (blue data with Θ ray <0 and red with Θ ray >0) are shown in figure  13(b ). Note that the data sets have an opposite sign due to the opposite sign of Θ ray leading to a different alignment of measurement positions with the turbulent structures.
Plant Materials Fifteen rice cultivars (Oryza sativa ssp. indica) from the International Rice Research Institute (IRRI, Los Baños, Philippines) were used in our study. Ten out of the 15 cultivars were selected to maximize the genetic variation using the SNP information available from a published study  (Zhao et al. , 2011). The five additional cultivars were selected based on their drought tolerance phenotype, and their information is available in IRGCIS database: http://www. irgcis. irri. org:81/grc/SearchData. htm (Table  S3 ).
Sequence data trimming and clustering After demultiplexing, sequences were filtered to remove reads containing homopolymers longer than 6 nucleotides, undetermined nucleotides, anomalous length and differences (one or more) in the primer. Quality trimming and filtering of amplicons, OTU identification, and taxonomic assignments were carried out with a combination of amplicon data analysis tools and in-house Python scripts as described in Lê  Van et al. , 2017. In more detail, the sequences which passed all the filters were clustered using DNAClust  (Ghodsi, Liu & Pop, 2011). Operational Taxonomic Units (OTUs) were generated out of a minimum of two 100% identical sequences that appeared independently in the different replicates. After these steps, filtering of chimeric sequences was performed using the 'chimeric.
uchime' tool within  Mothur (v1. 31. 0, Schloss et al. , 2009). The trimming and clustering pipeline used was the same as used in previous studies (e. g. , Ben  Maamar et al. , 2015; Lê   Van et al. , 2017). The affiliation statistics to identify OTUs were run using the PHYMYCO-DB database  (Mahé et al. , 2012). A contingency table was produced to perform all the diversity and statistical analyses. Even though the difference in the number of sequences among samples was below 10%, the dataset was rarefied to the same number of sequences using the module VEGAN  (Oksanen et al. , 2015)  in R (R Core Team, 2014) before statistical analysis. All sequences were uploaded in the European Nucleotide Archive with the accession number PRJEB22764.
Statistical analysis All the statistical analyses were performed using R (R core team, 2013). From the contingency matrix, OTU richness (number of species), abundance (number of individual OTUs), evenness and diversity index (Shannon H index) estimators were calculated using the VEGAN  (Oksanen et al. , 2015)  and BIODIVERSITYR  (Kindt & Coe, 2005)  packages. Statistical differences in these measures were analyzed using ANOVA, with the treatments (control and drought) as factors using the CAR package  (Fox & Weisberg, 2011). To test for a field position effect on the microbial community results, a Mantel Test and correlogram analysis were performed using the VEGAN package. Each root sample was assigned a field position value (based on two coordinates) and the geographical Euclidean distances were calculated.
Root-fungal microbiota in rice As the samples were selected from a large field experiment, we performed a Mantel Test to check for the presence of field position effects. This analysis showed that there was no strong effect of field position on the fungal community composition for both treatments (Fig. S1 ). We analyzed a total of 444,757 fungal sequences of 560 bp forming 902 different OTUs (Fig. 1 ). The sequencing depth was sufficient to describe the root fungal microbiota (Fig. S2 ). The 18S rRNA marker has been shown to provide adequate species-level resolution for the identification of many fungal groups, with the exception of the Ascomycota  (Vandenkoornhuyse et al. , 2002). Despite the use of the fungal 18S rRNA gene database PHYMYCO-DB  (Mahé et al. , 2012)  and its better resolution compared to more generalists databases to identify fungal sequences, most of the OTUs did not match to curated sequences of known close relatives (i.
ACKNOWLEDGEMENTS We thank support staff of  IRRI  for their help with sample collection and processing and the  Human and Environmental Genomics platform  (https://geh. univ-rennes1. fr/) and  S. Michon-Coudouel  for technical support in the library preparation and sequencing, and  J. G. Maciá-Vicente  for providing R scripts for some of the statistical analyses and his support with some of the phylogenetic analyses.
The pixel size was determined at 10. 38 μm under the following conditions: 90 kV, 111 mA. About 1331 cuts were generated. The reconstructed images were processed with XAct (RX solution) software. 2. 1. 3. Image processing method 2. 1. 3. 1. Description of the method. The objective of our work is to carry out a qualitative and quantitative evaluation of the porous microstructure of HAP bio-ceramic using SEM and μCT images. An accurate method is proposed to characterize pores and separate them at the same time. The method makes it possible to easily calculate many quantitative measurements, in particular those that provide information on the connection and the size distribution of the pores. To realize those tasks, an adaptive method based on the morphological operation algorithm is proposed.
Clinical and radiological assessments The clinical and radiological follow-ups were carried out at 45 days, 3 months, 6 months, 1 year, then every 2 years until the final follow-up. The patients' general condition was evaluated using the Charlson score and the American Society of Anesthesiologists (ASA) score  [18] [19] [20]. The clinical outcomes were determined using the Postel Merle d'Aubigné (PMA) score and the Harris Hip Score (HHS)  [21, 22]. The duration of the surgical procedure was recorded. The radiological analysis was done with OSIRIX® software 5 to look for periprosthetic osteolysis, to determine the change in cup inclination between the immediate postoperative period and last follow-up, and to calculate the ARA score  [23]  and Brooker score  [24]. All of the complications, such as dislocation, infection, loosening, and periprosthetic fractures were recorded.
The difference between total and effective stress analyses is more pronounced for layer 1. The triggered nonlinearity is comparatively small, taking into account that the maximum deformation is less than 0. 1%, and only minor differences in stress-strain curves result from pore-pressure effects. Figure  12 : Comparison of stress-strain curves (left) at GL-3. 5 m (top panels) and GL-11. 5 m (bottom panel) and comparison of time histories (right) of surface-acceleration (top panel), velocity (middle panel), and displacement (bottom panel) between effective (dashed lines) and total (solid lines) stress analyses in the P-SV model. The same comparison as for the P-SV model is presented in Figure  13  for the SH model. The stress-strain data are obtained from the top two layers at a point located in the left section of the basin at x = 690 m, where the highest strain is computed.
Conclusions and Perspectives The 1D-3C spectral element modelling in  Oral et al. (2017)  has been extended to 2D for modelling the nonlinear soil response with pore-pressure effects in multi-dimensional media. The MPII model of  Iwan (1967)  and liquefaction front model of  Iai et al. (1990)  are implemented to SEM2DPACK software, and verification of the implementation of new features is performed. The code is suitable for studying the effects of various physical processes, such as attenuation and nonlinear material behaviour including pore-pressure effects on the ground motion. The extended numerical model has been applied to a two-dimensional sedimentary basin model to study the effect of soil nonlinearity on wave propagation in complex media. The 2D basin model consists of six soft layers situated within a basin surrounded by bedrock.
Acknowledgements The authors would like to thank  Harsha S. Bhat ,  Jean-Paul Ampuero  and  Marion Thomas  for their collaboration and helpful comments in using SEM2DPACK for multi-dimensional modelling of seismic wave propagation in nonlinear media, to  Elise Delavaud  for her assistance in the preparation of this work, and to  Martijn van den Ende  for his final touch to enrich the readability of the manuscript. We furthermore acknowledge the comments of the Editor  René-Edouard Plessix  and two anonymous reviewers, which definitely improved the quality of the manuscript.
A second centrifugation at 1500× g for 20 min at 24 °C was carried out to obtain the platelet-poor plasma (PPP). The PRP was standardised to 500,000 platelets µL -1 using a Shimadzu UV-1800 spectrophotometer (Kyoto, Japan), prior to analysis on a Chronolog-490 two channel platelet aggregometer (Chronolog, Havertown, PA, USA), coupled to the specialised AGGRO/LINK software package. Prior to testing, lipid samples and standard PAF were dissolved in a solution of BSA-saline (2. 5 mg BSA/mL saline), while aliquots of stock solutions of active thrombin were diluted in appropriate amounts of physiological saline to obtain solutions of active thrombin with a final concentration in the aggregometer cuvette, ranging from 0. 01 mU/mL NIH (National Institute of Health). The final concentration of PAF in the cuvette ranges from 1-5 × 10 -8 M.
A second centrifugation at 1500× g for 20 min at 24 • C was carried out to obtain the platelet-poor plasma (PPP). The PRP was standardised to 500,000 platelets µL -1 using a Shimadzu UV-1800 spectrophotometer (Kyoto, Japan), prior to analysis on a Chronolog-490 two channel platelet aggregometer (Chronolog, Havertown, PA, USA), coupled to the specialised AGGRO/LINK software package. Prior to testing, lipid samples and standard PAF were dissolved in a solution of BSA-saline (2. 5 mg BSA/mL saline), while aliquots of stock solutions of active thrombin were diluted in appropriate amounts of physiological saline to obtain solutions of active thrombin with a final concentration in the aggregometer cuvette, ranging from 0. 01 mU/mL NIH (National Institute of Health). The final concentration of PAF in the cuvette ranges from 1-5 × 10 -8 M.
Statistical Analysis All biological experimental analyses, extractions, and GC-MS analyses for each lipid sample were sample were completed in triplicate. The obtained results were expressed as a mean value ± standard deviation (SD). One-way analysis of variance (ANOVA) and the Tukey's honest significant difference (HSD) multiple comparison post-hoc test was used to determine the significant statistical differences between the analyses (SPSS Inc. , Chicago, IL, USA).