dataesr/scientific-paragraphs-categorization huggingface dataset:
Sequences without complete reading frames and non-immunoglobulin sequences were removed and only reads with significant similarity to reference IgHV and J genes from the IMGT database were retained using BLAST  70. IgH gene usages and sequence annotation was performed in IMGT V-QUEST, where repertoire differences were performed by custom scripts in python, and statistics were performed in R using Wilcoxon tests for significance (non-parametric test of differences between distributions). Software and algorithms for repertoire analysis. The following software and algorithms were used: QUASR  68  (http://sourceforge. net/projects/quasr/), BLAST  70  (https://blast. ncbi. nlm. nih. gov/Blast. cgi), IMGT V-QUEST  69  (http://www. imgt. org/HighV-QUEST/), Immune_receptor_NETWORK-GENERATION  71  (https:// github.
Acknowledgements We are grateful to  Robert Brink  for providing the SW HEL mice. We thank  Devina Devikar ,  Alexander Hatton ,  Alessandra De Riva ,  James Lee  and  Tim Wilson  for technical help. We gratefully acknowledge  Valerie Morrison , all  National Institute for Health Research (NIHR) Cambridge BioResource volunteers , the  NIHR Cambridge BioResource centre  and staff and  NHS Blood and Transplant. This research was supported by the  Cambridge NIHR BRC Cell Phenotyping Hub. In particular, we wish to thank  Anna Petrunkina Harrison ,  Chris Bowman ,  Natalia Savinykh  and  Esther Perez  for their advice and support in flow cytometry. This work was funded by the  Wellcome Trust  (Programme Grant Number  083650/Z/07/Z  and  Wellcome Trust   Investigator Award   200871/Z/16/Z  to KGCS and  Sir Henry Wellcome Fellowship   WT106068AIA  to RBG) and supported by the  NIHR Cambridge Biomedical Research Centre.
ME was funded by the  Wellcome Trust  (Programme Grant Number  083650/Z/07/Z ), by a  Junior Team Leader starting grant  from the  Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LabEx LERMIT)  supported by a grant from  ANR  ( ANR-10-LABX-33 ) under the  programme "Investissements d'Avenir"  ( ANR-11-IDEX-0003-01 ) and by an  ANR @RAction starting grant  ( ANR-14-ACHN-0008 ). KGCS is an  NIHR Senior Clinical Investigator  and a Distinguished Innovator of the  Lupus Research Institute.
Data availability A reporting summary for this article is available as a Supplementary Information file. The source data underlying Figs. 1 to 6 and Supplementary Figs. 1 2 3 4 5 6 are available as a Source Data file. EGA accession numbers for sequencing data are provided in Supplementary Table  4  (https://www. ebi. ac. uk/ega/). All other relevant data are available from the authors upon reasonable requests.
These initiatives should prepare and support individuals, teams and organizations in making organizational change centred around the patient. mHealth, such as apps running on consumer smart devices, is becoming increasingly popular and has the potential to profoundly affect health care and health outcomes  [58]. Several apps exist for AR and asthma  [59] [60] [61] [62] [63]. A review of the Apps in the field of allergic diseases has recently been completed (Matricardi et al. in preparation). One of the reviews-MASK (Mobile Airways Sentinel NetworK), the Phase 3 ARIA initiative  [37, 64] is based on the freely-available MASK app (the Allergy Diary, Android and iOS platforms) for AR and asthma. Importantly, MASK is available in 17 languages and deployed in 23 countries  [64]. Data from 26,000 users reporting over 200,000 days of treatment are available.
However, there has been only one direct testing of individual guideline recommendations in real-life studies in an effort to achieve optimization  [94]. Next-generation ARIA-GRADE guidelines should consider testing the recommendations based on the GRADE approach with real-world evidence (RWE) using data obtained by mHealth tools such as MASK in order to confirm the efficiency or to refine current GRADE-based recommendations. The first results of MASK confirm the feasibility of the project  [19]. Adherence to treatment is very low as < 5% of users record symptoms and medications for a period of 2 weeks. This indicates that it is important to further test whether on-demand is equally or even more efficient than regular-continuous treatment and that guidelines should consider both regular and ondemand treatment  [19, 95].
Adaptation to FASII Inhibitors Is Not due to FASII Mutations Mutations in FASII initiation genes may confer antibiotic resistance  (Gloux et al. , 2017; Morvan et al. , 2016 Morvan et al. , , 2017;; Parsons et al. , 2011). We monitored mutations in FASII antibiotic-adapted USA300 or Newman strains by DNaseq using FASII inhibitors triclosan or AFN-1252 (Table  S1 ). DNaseq of USA300 grown in BHI and SerFA, and Newman grown in BHI, were used as references. Adaptation was confirmed by exogenous fatty acid profiles of antibiotic-grown samples in 12-14-h cultures (data not shown). Eight of nine genome sequences displayed parental FASII genes (the exception was mutated in SAUSA300_1476 encoding FASII initiation gene accB). One isolate displayed S. aureus strain USA300 was cultured in BHI, FA (a 3-fatty acid cocktail of C14:0, C16:0, and C18:1cis, 0.
Fluorescence microscopy Bacteria were grown in BHI, FA, Ser-FA to OD 600 = 0. 5-1, or FA-Tric and SerFA-Tric for 6 hours. Cells (OD 600 equivalent of 10-20) were centrifuged and washed once in phosphate buffered saline. Syto9 TM (0. 5 ml sample of a 5 mM solution in DMSO; Thermo Fischer Scientific) and propidium iodide (3 ml of 1. 5 mM solution in water; Sigma, France) were added to 30 ml samples for respectively viable and permeabilized cell visualization. Cells were observed 10 min post-staining by fluorescent microscopy using a Zeiss AxioObserver Z1 inverted fluorescence microscope equipped with a Zeiss AxioCam MRm digital camera and Zeiss fluorescence filters. Images were processed with the Zeiss ZEN software package using a 38 HE Green Fluorescent Protein filter (excitation wavelength 450/ 490 nm; beam splitter, 495 nm; emission, 500/550 nm) and 45 Texas Red filter (excitation: 540/580 nm; beam splitter, 585 nm; emission, 595-668 nm).
DNA extractions were performed using the QIAGEN ''DNeasy â Blood & Tissue Kit,'' following manufacturer's protocol, except that cell pellets were first resuspended in 0. 1 mg lysostaphin/ml Tris 10 mM (AMBI, USA) and incubated 30 minutes at 37 C. Genomic DNA sequencing by Illumina HiSeq next generation sequencing was outsourced (GATC-Biotech, Konstanz, Germany). Coverage was estimated to be at least 70-fold for USA300 SerFA-Tric samples, and at least 400-fold for all other samples. The 2 3 150 paired-end reads were analyzed using ''Variation Analysis'' method provided by Patricbrc. org. Bowtie2 (Patricbrc. org) was used to align sequences and SAMtools to identify SNPs  (Wattam et al. , 2017). SNPs that differed in non-antibiotic-treated USA300 and Newman strains from those in the reference sequence (GenBank Nucleotide accession codes NC_007793.
5% SDS-PAGE gels run at 150 V for 2 h. Gels were then electro-transferred to PVDF membranes (0. 2 mm; BioRad; 75mA) for 3 h on a semi-dry transfer unit (Hoefer TE 70). Western blotting and exposure used an ECL kit (Perkin-Elmer) as per supplier's instructions. Rabbit anti-S. aureus ACP antibodies  (Morvan et al. , 2016)  were used at 1:1,300 dilution. Proteomic analyses of USA300 responses to anti-FASII Four independent overnight BHI precultures of USA300 spa::Tn strain were used to inoculate BHI, FA, SerFA, FA-Tric, or SerFA-Tric media at OD600 = 0. 1. Culture extracts were prepared as described for western blotting, and after verification of protein concentration and quality, 10 mg of each protein sample was short-run on SDS-PAGE. Further sample treatment by LC-MS/MS, and bioinformatics and statistical analyses of data are as described  (Perez-Pascual et al.
, 2017). The reference genome GenBank Nucleotide accession code NC_007793. 1 was used for protein annotation. The complete list of proteins expressed in the five growth conditions is available on the Mendeley database (https://doi. org/10. 17632/9292c75797. 2; https://data. mendeley. com/datasets/9292c75797/ draft?a=bb34343b-6314-4421-89bd-b25e2bbdb0df).
3 kV. Heater temperature of the probe was set at 200 C. Sheath gas, auxiliary gas and sweep gas flow rates were set at 20, 8 and 0 (arbitrary unit) respectively. Capillary temperature was set at 325 C and S-lens RF level at 60%. Analysis was performed in negative mode to obtain structural information on phosphatidylglycerol fatty chains. The mass spectrometer is equipped with two analyzers: a double linear ion trap (LTQ Velos Pro) for fragmentation at low resolution and an orbital trap (Orbitrapª) for high resolution detection. Detection was performed in full MS Scan with 100,000 resolution and data dependent MS 2 and MS 3 with collision induced dissociation (CID; collision energy set at 35). Chromatographic retention time was used for polar head identification by comparing to commercial standards.
QUANTIFICATION AND STATISTICAL ANALYSIS Means and standard errors of replicate growth curves and proportions of fatty acids were determined (Excel, Microsoft, USA). For phospholipid determinations, the average of two experiments with the range of duplicates is presented. Data from animal experiments using USA300 only were statistically analyzed by the non-paired non-parametric Mann-Whitney test with GraphPad Prism 5. 0 (GraphPad Software, San Diego, California). The same test was used in USA300:fakB2 competition studies to compare results in non-treated and antibiotic-treated animals. In the competition study, the paired and non-parametric Wilcoxon test was used to determine p values in separate organs.
ACKNOWLEDGMENTS Nebraska Transposon Mutant Library strains were generously provided by  BEI Resources, NIAID, NIH, USA. We are grateful to  B. Michel  and  P. Bouloc  ( I2BC, France ),  P. Casedesus  ( Univ. Sevilla, Spain ), and  P. Trieu-Cuot  ( Institut Pasteur, France ) for stimulating discussion of this work;  A. Picart  ( I. Cochin ) and  M. Benard  (animal facility,  I. Cochin ) for expert assistance in animal studies;  M. Gohar  ( Micalis ) for advice in fluorescence microscopy studies; and  E. Boreze  ´e-Durant,  R. Boudjemaa ,  R. Briandet ,  J. Deschamps ,  P. Gaudu , and  D. Lechardeur  ( Micalis ) for frequent discussion. This work was supported by funding from the  French  granting agencies: the regional  DIM-Malinf , the Agence.
DATA AVAILABILITY Genome sequence data have been deposited in the European Nucleotide Archive and can be accessed at https://www. ebi. ac. uk/ena/data/view/PRJEB24433. The complete list of proteins from the proteomic study is available on the Mendeley database (https://data. mendeley. com/datasets//9292c75797/2; https://data. mendeley. com/datasets/9292c75797/draft?a=bb34343b-6314-4421-89bd-b25e2bbdb0df). The authors declare that all other data supporting the findings of this study are available within the article and its Supplementary Information files, or from the corresponding author upon request.
, 2015; Gilaberte-Búrdalo et al. , 2017). The present work aims at producing snow reliability investigations of a wide range of ski resorts in France (Alps and Pyrenees), Spain and Andorra under past and future conditions using state-of-the-art snowpack modelling. We accounted for snow grooming and snowmaking using a detailed snowpack model  (Spandre et al. , 2016b)  and used adjusted and downscaled climate projections from the EURO-CORDEX dataset  (Verfaillie et al. , 2017 (Verfaillie et al. , , 2018) )  to compute snow reliability elevations with distinct levels of snow reliability requirements. The mean elevation of residential population in a ski resort  (Breiling and Charamza, 1999)  and the mean elevation of ski lifts  (Falk and Vanat, 2016)  were compared to the snow reliability line.
Definition of relevant elevations of ski resorts All data on the geographical location and technical data on ski resorts were extracted from the "BD Stations" database  (François et al. , 2014; Spandre et al. , 2015). Ski lift installation and operation in France are supervised by the STRMTG ("Services Techniques de Remontées Mécaniques et Transports Guidés"). The STRMTG is a public service in charge of the safety control of French ski lifts providing authorizations for ski lift operations. The STRMTG manages a database (CAIRN: CAtalogue Informatisé des Remontées Mécaniques Nationales) dedicated to ski lifts which includes technical characteristics of each ski lift such as the ski lift power. The ski lift power is an indicator of the size of a ski lift, defined as the product of the elevation difference between the bottom and the top of a ski lift (in kilometres) and its capacity, i.
e. the flow of persons per hour (persons h -1 ), expressed in persons km h -1. Ski lift infrastructures in France have a total ski lift power of 977 000 persons km h -1 , 94 % of which are included in the present study (Appendix B). These data are complemented with geographical information from the database BD TOPO (25 m of resolution) developed by the French Geographical Institute (IGN, "Institut Géographique National"). The following elevations were used to be compared with the snow reliability line. -The mean ski lift elevation of a ski resort is defined as the average of top and bottom elevations of each ski lift weighted by its ski lift power, referred to as the mean elevation of the ski resort  (François et al. , 2014; Falk and Vanat, 2016). -The village elevation of a ski resort is defined as the mean elevation of tourism housing infrastructure, where tourists stay during their ski holidays.
Based on the OpenStreetMap (OSM) project (http: //www. openstreetmap. org/, last access: 12 April 2019), we estimated the main features for the Spanish and Andorran ski resorts (village elevation, ski lift mean elevation and ski lift power). However, ski lift capacity is not included in OSM, and building height data are incomplete, which hampers our ability to proceed using the method developed for the French ski resorts. To circumvent this issue, we extracted all ski slopes from OSM for all ski resorts in France, Spain and Andorra, and computed linear regressions between information extracted from OSM and independent estimates for French ski resorts, which were then used to compute the indicators for ski resorts in Spain and Andorra (Fig. 1 ). -The linear model of the ski lift power versus the OSM surface area (Fig.
Climate forcing data The meteorological system SAFRAN  (Durand et al. , 1993)  provides meteorological data (temperature, precipitations, etc. ) for mountain areas of an approximate 1000 km 2 surface referred to as a "massif", covering the French Alps and Pyrenees, including the Spanish and Andorran Pyrenees (Fig. 2 ). Within each massif, the meteorological conditions are considered to be homogeneous and to depend only on the elevation (by steps of 300 m) with a time resolution of 1 h. SAFRAN forcing data are available for the 1958-2015 period  (Durand et al. , 2009a; Durand et al. , 2012; Maris et al. , 2009). Computations of snow conditions over the reference period using SAFRAN forcing data are further referred to as "SAFRAN" and can be considered as the reference observational dataset.
This study uses the EURO-CORDEX dataset  (Jacob et al. , 2014; Kotlarski et al. , 2014)  for climate projections consisting of six regional climate models (RCMs) forced by five different global climate models (GCMs) from the CMIP5 ensemble  (Taylor et al. , 2012)  over Europe, for the historical, RCP2. 6, RCP4. 5 and RCP8. 5 scenarios  (Moss et al. , 2010). All EURO-CORDEX data were adjusted using the ADA-MONT method  (Verfaillie et al. , 2017)  using the SAFRAN data as the reference observation dataset  (Verfaillie et al. , 2018). Historical runs generally cover the period 1950-2005 and climate projections (RCPs) cover the period 2006-2100 (Table  1 ). Continuous hourly resolution meteorological time series derived from RCM output by the ADAMONT statistical adjustment method are then used as input of the SURFEX/ISBA-Crocus snowpack model  (Verfaillie et al.
Past climate conditions Figure  3  shows that a significant spatial variability of the snow reliability line can be observed for the reference period  (1986) (1987) (1988) (1989) (1990) (1991) (1992) (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005). The median elevation of the 70 % groomed snow reliability ranges between 1750 m a. s. l. in the northern Alps, 2000 m a. s. l. in the French Pyrenees, 2250 m a. s. l. in the southern Alps, and up to 2300 m a. s. l. in the Spanish and Andorran Pyrenees (HIST, Fig. 3 ). Although a deviation can be observed, the spatial variability is consistent between climate model computations over the reference period (HIST) and the reference dataset (SAFRAN). The 90 % snow reliability using snowmaking is significantly lower than the 70 % groomed snow reliability line (Fig.
Past climate conditions Figures  3  and 4  and Table  2  show a deviation between the SAFRAN reference dataset and results derived from climate models (HIST) for the reference period. We therefore focus our analysis on the comparison of snow conditions computed by climate models for the reference and future periods. Based on climate models, ski lift infrastructures were reliable during the reference period  (1986) (1987) (1988) (1989) (1990) (1991) (1992) (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005) , with either natural snow conditions (50 % in categories 1, 2 and 3 altogether; Table  2 , HIST) or with snowmaking (49 % in categories 4 and 5 altogether). Natural snow conditions in larger ski resorts were more reliable than in the smaller ones with 44 resorts representing 50 % of the ski lift power being reliable using natural snow only and 129 ski resorts also representing 49 % of the ski lift power being only reliable with snowmaking (Table  2 ).
, 2015). This situation is likely to be more frequent under future climate conditions, resulting in increasingly optimistic results compared to the reference period. Additionally, all results computed based on the observational reference dataset and climate models exhibit differences in the reference period (Figs. 3  and 4  and Table 2 ). Discrepancies may be due to potential biases of the multivariate distribution of the meteorological variables produced by the adjustment and downscaling method  (Verfaillie et al. , 2017). This could result in potential nonlinear effects due to multiple dependencies, especially on temperature, relative humidity, precipitation and wind speed. Beyond the modelling of snow conditions, the main limitations pertain to the snow reliability line approach. Singlepoint representations are considered on a flat field, i.
Acknowledgements. This study was funded by  Région Rhône-Alpes  (PhD grant of  Pierre Spandre ), and benefited from funding from the  French Ministry for Ecology (MTES)  to the ADA- MONT  project through GICC and  ONERC , from the  Interreg  project  POCTEFA/Clim ' Py  ( OPCC2 ), from the  IDEX Univ. Grenoble Alpes Cross Disciplinary Project  " Trajectories ", and from the  Conseil Départemental de l'Isère -Isère Tourisme. The  CGET -Comité de Massif Alpes  funded the creation of the BD Stations database. CNRM/CEN and Irstea are part of  LabEX OSUG@2020  ( ANR10 LABX56 ). Deborah Verfaillie 's work has been funded by the  European  project  EUCP  ( H2020-SC5-2016-776613 ). We acknowledge useful comments and suggestions from  O. Cenk Demiroglu ,  Robert Steiger , one anonymous reviewer and the editor  Jürg Schweizer.
(2014). These pseudopotentials are designed to reproduce accurately the all-electrons results obtained for the individual atomic species. This provides a warranty that the use of the pseudopotential does not cause any important spurious effect. For the two atomic species considered here, hydrogen and oxygen, this consists in a cutoff radius of respectively 0. 7a 0 and 1. 2a 0 , where a 0 = 2 /(m e e 2 ) is the Bohr radius, and an oxygen pseudopotential with the 1s state treated as a core state. To reach densities above 7 g cm -3 , we use the ATOM-PAW  (Holzwarth et al. 2001 ) package to generate pseudopotentials with cutoff radius of r paw = 0. 4 a 0 and r paw = 0. 6 a 0 for, respectively, the hydrogen and oxygen atomic species. We further find that the oxygen 1s state needs to be included as a valence state to reach the highest density treated, 50 g cm -3.
We therefore show the 1σ limits for each secondary Hugoniot that arise from these uncertainties in the initial state. Figure  9  shows a comparison between the predictions of our analytical fit with two EOS measurements in experiments using laser-induced shock in statically compressed water. We find a better agreement with the latest dataset of  Kimura et al. (2015)  compared to the ones of  Lee et al. (2006). We show these for completeness as the scatter in the experimental data cannot further constrain the validity of the analytical fit. Lee et al. (2006) ; (b) points obtained by  Knudson et al. (2012). The inset in each panel shows the initial pressures and densities measured. Overall, we find that our present analytical fit provides a satisfactory description of both the static and dynamical experimental results available to date for dense water.
Acknowledgements. Part of this work was supported by the  SNR  grant  PLAN-ETLAB 12-BS04-0015  and the  Programme National de Planetologie (PNP)  of  CNRS-INSU  co-funded by  CNES. Funding and support from  Paris Sciences et Lettres (PSL)  university through the project origins and conditions for the emergence of life is also acknowledged. This work was performed using HPC resources from  GENCI-TGCC  (Grant  2017-A0030406113 ).
We present a multi-frequency study of PKS J1222+0413 (4C +04. 42), currently the highest redshift γ-ray emitting narrow-line Seyfert 1 (γ-NLS1). We assemble a broad spectral energy distribution (SED) including previously unpublished datasets: X-ray data obtained with the NuSTAR and Neil Gehrels Swift observatories; near-infrared, optical and UV spectroscopy obtained with VLT X-shooter; and multiband radio data from the Effelsberg telescope. These new observations are supplemented by archival data from the literature. We apply physical models to the broadband SED, parameterising the accretion flow and jet emission to investigate the disc-jet connection. PKS J1222+0413 has a much greater black hole mass than most other NLS1s, M BH ≈ 2 × 10 8 M , similar to those found in flat spectrum radio quasars (FSRQs).
The source PKS J1222+0413 PKS J1222+0413 (RA: 12 22 22. 548, Dec: +04 13 15. 75) was identified as a γ-ray NLS1 candidate by  Yao et al. (2015)  and, at redshift z = 0. 9662, is currently the most distant example of this class known. From its SDSS spectrum, they determined its mass to be M BH = 1. 8-2. 0 × 10 8 M. Its simultaneous and quasi-simultaneous SED was studied by  Giommi et al. (2012) , although at the time it was not known to be a NLS1. Like 1H 0323+342, which was studied in great detail by  Kynoch et al. (2018) , the accretion disc of PKS J1222+0413 is a prominent feature in its spectral energy distribution, unlike other γ-NLS1s which are more jetdominated. PKS J1222+0413 is therefore another ideal object in which to examine the disc-jet connection. We present new data from NuSTAR, VLT X-shooter and Effelsberg.
The VLT X-shooter data allows us to investigate the NLS1 nature of the source and measure the AGN continuum emission from the accretion disc. The 0. 3-10 keV X-ray band has been shown to contain contributions from both the accretion flow and jet (e. g. Kynoch et al. 2018 , Larsson et al. 2018 ) whereas the higher-energy X-rays, sampled by NuSTAR and Swift BAT, are jet-dominated. Throughout this paper, we assume a ΛCDM cosmology with H 0 = 70 km s -1 Mpc -1 , Ω m = 0. 3 and Ω Λ = 0. 7. Therefore the redshift z = 0. 9662 implies a luminosity distance of 6332. 3 Mpc and a flux-to-luminosity conversion factor of 4. 80 × 10 57 cm 2. Length scales are often quoted in gravitational radii, R g = GM BH /c 2 = 2. 95×10 11 m = 1. 14×10 -2 light days for our derived mass.