dataesr/scientific-paragraphs-categorization huggingface dataset:
An external three-D-cell tethered battery pack allows up to 200 h of recording. The Acousonde operates autonomously, and has its own battery, memory, and programmed mission. Data processing is undertaken after the sensor is recovered. Initially developed to be attached to marine mammals  (Cazau et al. 2017) , it has also been used on ocean gliders  (Nott 2015). Details of the sampling method used in this study are given in section 3. The platform we used in this study is the Slocum glider, developed by Teledyne Webb Research. It is driven by buoyancy changes, controlled by 500 cm 3 of oil pumped into or out of a swim bladder, inducing a vertical motion in the water column, from the surface down to 1000-m depth. Fixed wings convert the vertical velocity into forward velocity, internal battery displacements enable pitch and roll management, and a moving rudder enables direction changes.
These cover 138 days of data, 37 of which are within the confidence area of one of the buoys and can be used to derive a relationship between sound pressure and surface wind speed (Table  1 ). Multiple factors can induce differences between our measurements in the different experiments: the two buoys have different measurement sampling frequencies; shipping activity, and therefore its generated noise, is different at the two sites; and our PAM sensors have different sensitivities per experiment, because of the varying mounting position on the glider, and the difficulty of using Acousonde to produce absolute sound level measurements  (Wiggins 2013). For these reasons, we decided to process each experiment separately. We merged the two Lion datasets, Asicsmed and MistralsT02_01 (referred to as Lion dataset), as both deployments used the same setup in the same area without any maintenance operations in between.
Acoustic data sampling and preprocessing procedures We designed the data acquisition protocol to evenly distribute the 200 h of recording time over the 3-month glider mission. The shortest sample allowed by the PAM sensor, 1 min, is sufficient for analysis of wind-generated noise  (Nystuen and Ma 2002). The PAM sensor recorded 1 min every 10 min, to allow a mission duration of 80 days. The sampling rate was set at 50 kHz, constrained by the PAM sensor's onboard memory capacity. This sampling method produces 27 GB of data every month. We adapted the WOTAN technique  (Vagle et al. 1990 ). We processed each 1-min sample individually, extracting the sound level on third octave frequency bands [third octave level (TOL)], according to the standards [American National Standards Institute (ANSI) S1.
11-2004] and using the software PAMGuide  (Merchant et al. 2015 ) on 1-s-long non overlapping Hanning windows. To focus on the wind contribution to the underwater ambient noise, any other sound sources have to be detected and removed from the dataset. The noise generated by the glider's oil pump is a loud broadband signal, lasting for several minutes. Slocum gliders generally activate their pump only during the apogee (surfacing) and perigee (bottom inflexion) phases of a dive. As we programmed only 1000-m-deep dives, we removed data acquired during apogee (depth , 20 m) and perigee (depth. 950 m) to focus on the quiet gliding phase of each dive (Fig. 5 ). The Lion dataset contains 4021 remaining 1-min samples, the equivalent of 40 days (Table  1 ). To eliminate transient sounds (e. g. , clicks, whistles, and glider's motors), we assumed that wind speed is constant over a 1-min sample and kept only the minimum TOL values.
g. , nearby ship) will be filtered out, and the time and length scales are the usual glider profiling scales (;2 h, 2 km for a 1000-m vertical profile). The number of observations is unevenly distributed over the wind speed range (Table  3 ). Therefore, to give an equal weight to each wind speed during the regressions between p fc and U 10 , we calculated the median sound pressure in each 2 m s 21 wind speed bin. During our experiment, we observed several high wind speed events of 6-48 h of wind speed above 15 m s 21 , with the glider in the confidence area around the buoy. Our dataset covers a broader wind range (2-21. 5 m s 21 ) than previous studies, allowing us to investigate the relationship between p fc and U 10 for wind speed regimes above 15 m s 21. To assess the validity of the historical single linear model [(1)] for our observations, we fitted a linear model, of parameters b single and s single (Table  4 ), to the wind speed range below 15 m s 21 , simulating the wind speed range of the previous studies.
Its coefficient of determination R 2 5 0:86 indicates a good fit for the 2-15 m s 21 range. We extrapolated this to the high wind speed range and tested it against the data available in the Lion dataset, revealing a tendency of the single linear model to overestimate wind speed in the higher wind speed range (15-21. 5 m s 21 ) (Fig. 8 ). To improve the agreement at high wind speed we investigated the hypothesis of two distinct sound production regimes, related to the physical processes of wind-generated underwater noise (bubbles, spray, and splash). Whitecaps can be observed on sea surface images at wind speeds as low as 3. 7 m s 21  (Callaghan et al. 2008) , with this threshold varying with air and sea temperature  (Monahan and O'Muircheartaigh 1986). Previous studies using ambient noise show a low wind speed detection threshold at 1.
The low wind speed model is very close to the single linear model, despite being fitted on a dataset of narrower wind speed range. The two-regime linear model allows a good description of the observations for the complete measured wind speed range (Fig. 8 ). As an alternative to the two-regime linear model, we investigated the possibility of fitting a power-law (p 5 a 1 U b ) relation. We obtained good results with the quadratic modelp 5 459:6 U 2 -but with a tendency to overestimate low wind speeds. We elected to use a two-regime model instead, as the fit was better and can be explained by a change in physical processes at elevated wind speeds. The physical processes explaining the regime change appear in a continuous and smooth way, around a wind speed limit that is believed to depend on multiple.
Further experiments are necessary to determine whether this critical wind speed exists. The positions of the meteorological buoys relative to the coast and the direction of the main winds limits the fetch to 100 km at the Lion buoy, and 50 km at the Azur buoy. This does not allow a fully developed sea at wind speed higher than 10 and 7 m s 21 at the sites Lion and Azur, respectively. Future experiments in the open ocean (e. g. , Southern Ocean) will provide more data at high wind speed and with unlimited fetch, which will allow studying the impact of sea state on the wind noise and assessing the validity of our model at high wind speed. The use of sound pressure level at 3 kHz in this study was driven by the instrument self noise at ;2 kHz and the possible contamination by traffic noise at lower frequencies on one side, and the limitations observed for the high frequencies at high wind speeds on the other side.
2017). Heat and freshwater transport can be monitored from the air-sea interface to the water column, linking heat content changes in the ocean to meteorological events  (Grist et al. 2016). Wind noise is caused by complex physical processes, such as wave breaking and bubble inclusion  (Wenz 1962) , driven by weather, sea surface conditions, and history. As a first approximation, we estimate the instantaneous surface wind speed from measurement of wind noise. We believe that further experiments (e. g. , glider campaigns together with surface processes monitoring) could improve the wind speed estimation, by TABLE 5. Parameters of the wind speed derivation two-regime linear models for the Lion, MooseT00_23, and MooseT00_25 datasets.
Conclusions Surface wind speed can be measured remotely, derived from underwater acoustic measurements. The proposed two-regime linear model yields improved results in high wind speed conditions, extending the wind speed range to 2-21. 5 m s 21. The PAM sensor can be mounted on an ocean glider, diving from the surface to 1000 m deep, thus allowing the surface wind speed measurements to be combined with the oceanographic profiles (e. g. , temperature, salinity). These PAM glider observations provide high-resolution, frequent, and localized in situ data for forcing numerical models and improving the understanding of the air-seaclimate system.
Acknowledgments. Support was provided by the  French CNRS/NOISE project , the '' Chantier Méditerranée '' MISTRALS program  ( HyMeX component ), the  ANR   ASICSMED  project ( ANR 12-BS06-0003 ), and the MOOSE long-term observatory ( SOERE/AllEnvi-SNO/ INSU ). The authors acknowledge the staff of the  French National Pool of Gliders  ( DT-INSU/CNRS-CETSM/ Ifremer ) for the sustained glider deployments carried out in the framework of MOOSE, and the other deployments during the 2012-2013 DEWEX experiment. Support was also provided by the  EU  projects  FP7 GROOM (Grant Agreement 284321 ) and the  COST Action ES0904 ''EGO'' (Everyone's Gliding Observatories ). The authors acknowledge  Météo-France  for supplying the meteorological buoy wind speed data, and  Météo-France  and the  HyMeX program  for supplying the model data, sponsored by Grants  MISTRALS/HyMeX  and the  ANR-11-BS56-0005   IODA-MED  project.
Design and subjects Details on the selection of patients and data collection have been published previously. 14 In short, this was a cross-sectional, observational study using the baseline visits of the U-BIOPRED cohort from 16 clinical centers in 11 countries across Europe. 421 Adult patients (≥18 years) with severe asthma were included according to the IMI consensus statement. 15 This comprised a confirmed diagnosis of asthma and either uncontrolled disease despite treatment with high dose inhalation medication (≥1000µg Fluticasone eq. ) and a second controller, or the need of systemic oral corticosteroids (OCS) or omalizumab to achieve asthma control, regardless of smoking history. The U-BIOPRED study was registered at ClinicalTrials. gov (identifier: NCT01976767) and was approved by all Medical Ethics Boards.
Data collection All data and samples were collected according to predefined standard operating procedures (SOPs). 14 nical data, such as age, gender, body mass index (BMI), age of onset of the disease, oral corticosteroid usage and smoking history were collected by history taking. Control of the disease was assessed with the Asthma Control Questionnaire (ACQ7)  16  and quality of life with the Asthma Quality of Life questionnaire (AQLQ). 17 Lung function was measured pre-and post-bronchodilator according to standardized procedures. 18 Atopy was defined as the presence of sensitisation to one or more common aero-allergens, identified either by a positive skin prick test (wheal diameter ≥3 mm) to an allergen extract or positive testing by analysis of allergen-specific IgE in serum (≥0. 35 kU/L).
Sequencing libraries were created using the Nextera XT DNA library preparation kit, and sequencing was performed using the MiSeq reagent kit v2 (Illumina). De novo assembly of the 4,028,320-bp paired-end sequences (3. 59 million reads) was generated using CLC Genomics Workbench v7. 5. 2. (CLC bio, Aarhus, Denmark), which resulted in 119 scaffolds, providing a coverage of 167ϫ and GϩC content of 46. 2%. Gene prediction was performed using three automated annotation pipelines, Rapid Annotations using Subsystems Technology (RAST) v2. 0 (3), the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (4), and the Joint Genome Institute-Integrated Microbial Genomes and Microbiomes (JGI-IMG/M) pipeline  (5). Species identity was determined by calculating the average nucleotide identity (ANI) and alignment fraction (AF) using the Microbial Species Identifier (MiSI) calculator employed in the IMG/M system (6) against previously sequenced genomes in the IMG/M database.
paralicheniformis. Conversely, the closest non-B. paralicheniformis species, Bacillus licheniformis ATCC 14580 T , exhibits 94. 69% ANI, 0. 88 AF, and 10. 96% dDDH. Two putative CRISPR modules, one prophage, and three genomic islands were discovered in the genome. The F47 genome contains several gene clusters with homology to known lipopeptide biosynthetic operons, including fengycin (fenABCDE) (1), surfactin (srfADCB)  (14) , and lichenysin (lchAA and lchAB)  (15). The operons for the antibiotics bacitracin (scaffolds 11, 43, and 103) and kanosamine (kabABC)  (16)  were detected in the genome. Two siderophore gene clusters were also predicted in the genome, including bacillibactin and a putative anthrachelin  (17). Lastly, a gene cluster of a putative circular bacteriocin was identified. Accession number(s).
ACKNOWLEDGMENTS We gratefully acknowledge the help of Georgina Mcintyre from the  Applied Genomic Core, University of Alberta , for assisting in library preparation and wholegenome sequencing. This work was performed under the auspices of the  Natural Sciences and Engineering Research Council of Canada  to J. C. V. J. Z. A. was funded by  Alberta Innovates-Health Solutions. This work, including the efforts of A. R. R. R. , was funded by the  Vanier Canada Graduate Scholarship, Alberta Innovates-Technology Futures , and the  President's Doctoral Prize of Distinction. M. S. D. was funded by  Agence Universitaire de la Francophonie ,  France. M. S. D. , M. D. , F. N. , and S. K. -G. were supported by the  National Fund for Scientific Research of Algeria.
Initialization for the one-dimensional coupled physical-biogeochemical model The initial profiles of temperature (T ), salinity (S), DIN and DIP were constructed by interpolating mean field data from the WOA13 climatology database  (Locarnini et al. , 2013; Zweng et al. , 2013)  at the exact location of the WMA (19 • 13. 00 S, 164 • 29. 40 W). Initial dissolved organic matter concentrations, BAC and autotroph abundances were obtained from the vertical profiles measured in the WMA: due to the homogeneity of the surface layer caused by winter mixing, the 0-70 m mean value was applied on the 0-70 m layer of the initial vertical profiles. Below 70 m, initial concentrations were the same as data. Since the model includes variable stoichiometry for organisms, initial intracellular contents of non-diazotroph organisms were set to 50 %, 25 % and 75 % of their respective intracellular quota ranges in C, N and P.
1 nmolN L -1 d -1 at 100 m. Regarding the model results of the simulation with diazotrophy, N 2 fix simWMA rates are consistent with data with a similar trend of higher rates (around 16. 0 nmolN L -1 d -1 ) from the surface to 40 m depth, and decreasing values from 40 to 70 m depth (down to 1. 0 nmolN L -1 d -1 at 70 m). At the WGY, very low N 2 fix obsWGY was measured compared to N 2 fix obsWMA , with a maximum rate of 2. 0 nmolN L -1 d -1 observed at the surface. In the simulation without diazotrophy, N 2 fix simWGY is nil (see Fig. 3c ).
Discussion The WTSP has been recently qualified as a hotspot of N 2 fixation  (Bonnet et al. , 2017). It is hypothesized that, while flowing westward following the South Equatorial Current (SEC), the N-depleted, P-enriched waters from areas of denitrification located in the eastern Pacific meet in the western Pacific waters with sufficient iron to allow N 2 fixation to occur  (Moutin et al. , 2008; Bonnet et al. , 2017). In situ data showed an ecosystem significantly more productive in the WMA where N 2 fixation rates were higher than in the WGY, where very low N 2 fixation rates were measured. These contrasted areas raised the question of whether the diazotrophy could be responsible for these differences observed between the WMA and WGY, which led us to run two simulations that only differed by taking into account (i.
Acknowledgements. This is a contribution of the  OUTPACE (Oligotrophy from Ultra-oligoTrophy PACific Experiment ) project (https://outpace. mio. univ-amu. fr/,last access: 8 October 2018) funded by the  French research national agency  ( ANR-14-CE01-0007-01 ), the  LEFE-CyBER program  ( CNRS-INSU) , the  GOPS program (IRD) , the  CNES , and the  European FEDER Fund  under project  1166-39417. The OUTPACE cruise (https://doi. org/10. 17600/15000900) was managed by the  MIO (OSU Institut Pytheas, AMU)  from  Marseilles (France). The authors thank the crew of the  R/V L'Atalante  for outstanding shipboard operation. Gilles Rougier  and  Marc Picheral  are warmly thanked for their efficient help in CTD rosette management and data processing, as is  Catherine Schmechtig  for the LEFE CYBER database management.
Individuals Created in 1989, the French Hospital Database on HIV (FHDH, ANRS CO4) is a large prospective cohort of HIV-infected individuals receiving care in one of 70 French participating hospitals, collecting standardized clinical, therapeutic and biological variables at each outpatient visit or hospital admission and/or at least every 6 months  [13]. The only enrolment criteria are documented HIV-1 or HIV-2 infection, follow-up in a FHDH participating centre, and written informed consent. Data submitted by the participating centres to the data coordinating and analysis centre are anonymized, then encrypted. The FHDH was approved by the French data protection agency (Commission Nationale de l'Informatique et des Libertes) on 27 November 1991 (Journal Officiel, 17 January 1992). For the present study, we selected antiretroviral-naive heterosexual HIV-1-infected individuals from the FHDH, aged at least 16 years, who started a first combined antiretroviral therapy (cART) between 1 January 2006 and 31 December 2011, at least one year prior to the database update (31 December 2012).
Statistical analysis The Chi2 and Kruskal-Wallis tests were used to compare the demographic, immunovirological and clinical characteristics of the individuals at cART initiation, across the three regions of origin, in men and in women. The number of severe events, person-years at risk, and incidence rates (IRs) of severe events (per 1000 person-years of follow-up) were calculated. Person-years of follow-up were calculated from the date of cART initiation to the date of death for known deceased individuals, last follow-up visit for individuals with no follow-up visit during the 6-month period before 31 December 2012 (last database update) or 31 December 2012 for the remainder of the cohort. Crude and adjusted IRs were estimated according to geographic origin, in men and in women. Poisson regression models were used to identify differences in morbidity/mortality according to geographic origin, in men and in women.
Incidence rates (IRs) and rate ratios (RRs) were adjusted for the following characteristics at cART initiation: age, region of care (Paris area, other regions of metropolitan France plus the Reunion Island and French West Indies), CD4 cell count, pVL, AIDS status, hepatitis B and/or C infection and smoking status for each category of events/deaths, plus the body mass index for cardiovascular diseases. All analyses were done with SAS v9. 4 software (SAS Institute, Inc, Cary, NC). A p value <0. 05 was considered to denote statistical significance.
First, no data on treatment adherence are available in the FHDH database. However, we recently showed that in women and in non homosexual men followed in France, SSA and NFW migrants had no difference in time to viral undetectability than their native French counterparts  [9]. Moreover, we used an intent-to-continue-treatment approach, meaning that cART interruption, which might have differed among the groups, was not taken into account in the models. However, it is noteworthy that the median number of visits per year and the median time between visits did not differ according to geographic origin or sex (data not shown). Because FHDH is implemented in infectious diseases and internal medicine departments, non-AIDS non-infectious events leading to hospitalization in other departments may have been under-reported, leading to an underestimation of non-AIDS events.
Mitochondrial genome (mtDNA) assemblies for 14 strains support previously published sequences  28  , although a small number of high quality novel sequence variants in AKR/J, BALB/cJ, C3H/HeJ, and LP/J conflicted with GenBank entries (Supplementary Table  4 ). Novel mtDNA haplotypes were identified in PWK/PhJ and NZO/HlLtJ. Notably, NZO/HlLtJ contains 55 SNPs (33 shared with the wild-derived strains) and appears distinct compared to the other classical inbred strains (Supplementary Figure  1 ). Previous variation catalogues have indicated high concordance (>97%) between NZO/HlLtJ and another inbred laboratory strain NZB/BlNJ  19. We assessed the base accuracy of the strain chromosomes relative to two versions of the C57BL/6J reference genome (MGSCv3 4 and GRCm38 5 ) by first realigning all of the paired-end sequencing reads from each strain back to the respective assembled genome and identifying SNPs and indels.
g. itch receptors  34  and γ-protocadherins  35  ) (Figure  1b , Supplementary Figure  5 ). The wild-derived strain, SPRET/EiJ contained the largest number of genes (1,442) and protein coding sequence base pairs (1. 2Mbp) within hSNP dense regions (Figure  1c ). All of the wild-derived strains contained gene and CDS base pair counts larger than any classical inbred strain (≥503 and ≥0. 36Mbp, respectively; Supplementary Table  9 ). Notably, the regions identified in C57BL/6J and C57BL/6NJ (117 and 141, respectively; 145 combined) intersect known GRCm38 assembly issues including gaps, unplaced scaffolds or centromeric regions (104/145, 71. 7%). The remaining candidate regions include large protein families (15/145, 10. 3%) and repeat elements (17/145, 11. 7%) (Supplementary Data 2). We examined protein classes present in the hSNP regions by identifying 1,109 PantherDB matches, assigned to 26 protein classes, from a combined set of all genes in hSNP dense regions (Supplementary Data 3).
In mouse, phenotypic differences, particularly diet and behaviour, have been linked to distinct OR repertoires  53, 54  , although very little is known about OR diversity between inbred laboratory strains. To this end, we have characterised the CAST/EiJ OR repertoire using our de novo assembly and identified 1,249 OR genes (Supplementary Data 5). Relative to the reference strain (C57BL/6J), CAST/EiJ has lost 20 ORs and gained 37 gene family members; 12 novel and 25 supported by published predictions based on mRNA derived from CAST/EiJ whole olfactory mucosa (Figure  2a , Supplementary Table  13 )  55. Many gene family loci, particularly immune loci, are characterised by variable copy number among individuals within a population (e. g. MHC  56  ). Complete sequencing and annotation of multiple inbred strains in parallel enabled us to accurately predict the underlying structure of many of these gene family loci.
Methods See separate online materials and methods document. The genome sequencing reads are available from the European Nucleotide Archive and the assemblies are part of NCBI BioProject PRJNA310854 (Supplementary Table  17 ). The genome assemblies and annotation are available via the Ensembl genome browser, and the UCSC genome browser. Sequence accessions for the three immune related loci on Chr11 are available from the European Nucleotide Archive (Supplementary Table  18 ).
Acknowledgements This work was supported by the  Medical Research Council  [ MR/L007428/1 ],  BBSRC  [ BB/M000281/1 ] and the  Wellcome Trust. DJA is supported by  Cancer Research-UK  and the  Wellcome Trust. We thank members of the  Sanger Institute Mouse Pipelines teams (Mouse Informatics ,  Molecular Technologies ,  Genome Engineering Technologies, Mouse Production Team, Mouse Phenotyping ) and the  Research Support Facility  for the provision and management of the mice. We thank  Valerie Vancollie  for assistance with phenotyping data.