dataesr/scientific-paragraphs-categorization huggingface dataset:
Computed tomography Samples were drilled from the sediment plates from Tungurahua in order to investigate grain size variations at the lamina scale with computed tomography (Fig. 5 ). Two subsets were created, the larger ones for 2 cm diameter samples (Fig. 5a-c ) and a second set was subsequently re-drilled within the large ones at 0. 5 cm diameter (Fig. 5d-e ). Computed tomography measurements using a GE phoenix nanotom m scanner system provided a resolution of 6 μm and 2. 4 μm pixel size for the 2 and 0. 5 cm diameter samples, respectively. For smaller samples individual clasts are well recognized and 2D grain size distribution was computed automatically using several workflows using the software Avizo. Preliminary comparison with manual segmentation shows that 2D automatic segmentation is reliable and is consequently applicable to compute 3D grain size distribution.
Exhibition and further usage Part of the sediment plate dataset from Tungurahua was used for a special exhibition in summer 2016 at the Mineralogy Museum in Munich (G'Schichten vom Tungurahua,  Douillet et al. 2016). Over 1500 visitors were registered during the 30-day exhibition. The plates mainly served as a dissemination tool for an introduction to sedimentology and were used to illustrate several concepts including: -The granular nature of deposits from explosive volcanic eruptions, -The difference between massive and stratified deposits, -The links between time and stratal aggradation, -The phases of a flow, -sedimentation, erosion, hiatus-, and. -The three "Steno" principles of stratigraphy: lateral continuity, superposition, deposition following existing surface (demonstrated by "the great Islamic scholar Avicenna or Îbn-Sînâ", 980 to 1037, see Fisher and Garrison 2009).
Regarding teaching, the dataset was presented during lectures, as an actual example of real volcanic deposits. Although geology and sedimentology concepts had been taught theoretically during classes, it became clear that when discussing these principles in front of the sediment plates, applying this knowledge and using it for interpretation was typically not fully grasped. Exercises involving the description, correlation, and interpretation of the dataset can be carried out. Fine-scale features of the plates also initiated student research projects. The dataset has also been used in Munich as contribution to meetings (Physics of Volcanoes 2017) and short courses  (Melts, Glasses, Magmas 2016 , 2017).
Acknowledgements This project is supported by the  Deutsche Forschungsgemeinschaft  grant  DO1953/1-1  to GAD. GAD acknowledges financial support by the  Bavarian grant  " Thesis" as well as BayLat  (project  CoCotE ). GAD and UK were supported by the  Deutsche Forschungsgemeinschaft  grant  KU2689/2-1. QC was supported by the  Alsacian grant  " Boussole" and the European grant program  "Erasmus". I. H. P. W. and R. R. were supported by the  LMU  student support " Studi_forscht@LMU ". GAD and UK thank  Sandro di Vito  of  Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Napoli , for logistical help during fieldwork in the Astroni crater, and members of the  Instituto Geofísico  for help at Tungurahua. M. A. CK® is acknowledged for their support and shipping the epoxy to  Ecuador.
Sampling Locations and Sample Description A total of 505 samples including 237 shellfish batches, 40 surface sediments, 12 seawaters and 216 waters from nine sampling points upstream of shellfish-harvesting areas described in  Balière et al. (2015)  were analyzed. These samples came from three shellfish-harvesting sites located on the English Channel coast and in their catchments. On the catchment of the Brittany site (site 1, La Fresnaye), four rivers flow with their outlet in the bay: Frémur (1A, 50 km long, sub-catchment: 77. 4 km 2 ), Le Rat (1B, 10. 5 km, sub-catchment: 19. 2 km 2 ), Le Clos (1C, 7 km, subcatchment: 13. 3 km 2 ) and Kermiton (1D, 2. 3 km, sub-catchment: 6. 3 km 2 ) (Figure  1 ). Cattle, swine and poultry are intensively bred on this catchment (Supplementary Data S1). The Normandy site 2 (Regnéville sur mer) is characterized by the intensive breeding of cattle and sheep and by the presence of poultry and swine, while its neighboring site 3 (La Vanlée) rather hosts cattle, sheep, and swine (Supplementary Data S1).
Detection and Characterization of E. coli and Enterococci Escherichia coli and enterococci from water samples were enumerated by  ISO-9308-3:1998 ISO-9308-3: (1998) )  and  ISO-7899-1:1998 ISO-7899-1: (1998) )  methods, respectively, and E. coli from shellfish batches by impedance method according to AFNOR-NF-V-08-106:2010 (2010). In addition, E. coli and enterococci were isolated as described in Supplementary Data S2. DNAs were extracted using Instagene matrix (Bio-Rad) after mechanical lysis of the bacteria with glass micro-beads. Escherichia coli isolates were classified into the four main phylogenetic groups A, B1, B2, or D using a method based on the detection of two genes, chuA and yjaA and of a DNA fragment designated TSPE4. C2  (Clermont et al. , 2000). Detection of these elements was performed by quantitative PCR (qPCR) using SYBER Green precision melt supermix (Bio-Rad) and primers described in Supplementary Data S3.
, 1999) , an extracellular zinc metallo-endopeptidase  (Su et al. , 1991) , and an aggregation substance  (Kreft et al. , 1992) , respectively] was determined by multiplex qPCR using SYBER Green precision melt supermix and primers described in Supplementary Data S3. Antimicrobial susceptibility testing of a selection of 556 E. coli and 446 enterococci (213 E. faecalis and 233 E. faecium) isolates was based on the disk diffusion method on Muller-Hinton medium (AES-chemunex, Bruz, France). Plates were incubated at 37 • C for 24 h.
Detection, Isolation and Characterization of Campylobacter Campylobacter spp. were detected and isolated as described in Supplementary Data S2. Genomic DNA was extracted from colonies suspended in water using Nuclisens protocol (BioMérieux). Isolates were confirmed as Campylobacter spp. by detecting 16S rRNA gene by qPCR  (Leblanc-Maridor et al. , 2011). Species were identified by mass spectrometry using a MALDI-TOF Bruker Microflex apparatus (MALDI-TOF Bruker Microflex, Billerica, MA, United States) and following the protocol described by the supplier.
Detection, Isolation and Characterization of Vibrio Detection and isolation of V. parahaemolyticus, V. cholerae, and V. vulnificus in a selection of samples including shellfish and seawater were performed as described in Supplementary Data S2. DNA was heat-released from APW-enriched cultures and presence of total and haemolysin-producing V. parahaemolyticus and of V. cholerae and V. vulnificus was detected by qPCR and PCR. Presumptive V. parahaemolyticus, V. vulnificus and V. cholerae colonies were selected from PCR-positive APWenriched cultures streaked (previously) onto chromogenic (CHROMagar TM Vibrio, Humeau) and selective (Thiosulfate Citrate Bile Salts Sucrose, TCBS, Difco) media plates and incubated 24 h at 37 • C. These colonies were analyzed by qPCR and PCR using the primer sets described in Supplementary Data S2.
Environmental Data and Statistical Analysis Rainfall data (2-days cumulative rainfall before sampling date) were provided by the meteorological stations from Meteo France at Pleurtuit (site 1) and at Coutances (sites 2 and 3). On-site water temperature, and salinity were measured using a multi sensor probe 3430 (WTW) equipped with a FDO 925 electrode and a pH-electrode Sentix 940 (site 1) or an EcoSence EC300 apparatus (VWR) (sites 2 and 3). Data on temperature and precipitation were categorized into three groups whose boundaries were defined to have a number of samples compatible with a reliable statistical analysis in each category. Comparisons of prevalence and microorganism's characteristics between samples type, site, season, temperature and precipitation were analyzed by the chisquare test using the CHISQ.
TEST function of the Excel software (Microsoft). A P-value of <0. 05 was considered statistically significant. In case sample was positive for multiple pathogens of interest, it was considered positive for each of the pathogens in question. The Shannon diversity index [H = -S i=1 Pi log 2 (Pi)] was calculated using the Biodiversity Calculator tool 4. Odds ratios (OR) and relative risk (RR) were calculated using MEDCALC 5  and considered statistically significant when P-values were less <0. 05. OR is the odds of a positive sample for a given parameter among positive samples for a second parameter while RR is the probability that a sample is positive for a given parameter among samples positive for a second parameter relative to the probability that it is positive for the given parameter among samples negative for the second parameter.
0). Four hundred and forty nine E. coli strains were analyzed to evaluate their level of resistance against a panel of 16 antibiotics or combinations of antibiotics (Supplementary Data S4). The results showed that a higher proportion of E. coli from Les Hardes river (sub-catchment of site 3) were resistant to cefoxitin, amoxicillin + clavulanic acid, and amoxicillin when compared to isolates from the other rivers. On the other hand, isolates from Le Frémur river (sub-catchment of site 1) were statistically more frequently resistant to doxycycline. Boxplots show the minimum, the 25th percentile, the median, the 75th percentile and the maximum concentration. For water samples, 1E, 2D, and 3C correspond to seawater and others to river or brackish water. For shellfish samples, 1F, 1H, 2E, and 3D correspond to oysters, 1G, 1I, 2F, and 3E to mussels, and 1J and 2G to cockles.
Characterization of Enterococci A total of 4,344 enterococcal strains were isolated, of which 3,887 were identified by mass spectrometry. These strains belong to 26 different species where E. faecalis (32. 9%), E. faecium (23. 2%), E. hirae (13. 7%), E. casseliflavus (8. 5%) E. mundtii, (7. 4%), and E. durans (6. 5%) represent the predominant species (Figure  4 ). The H biodiversity index of Shannon was similar for the three sites (2. 5, 2. 9, and 2. 7, respectively, for sites 1, 2, and 3). These species were also the most abundant in water samples (E. faecalis: 29. 1%, E. faecium: 23. 6%, and E. hirae: 14. 0%) and in shellfish (E. faecalis: 39. 0%, E. faecium: 22. 6%, and E. hirae: 12. 9%). Two thousand and sixty-nine strains (1,200 E. faecalis and 869 E. faecium) were analyzed for the presence of three virulence genes (esp, gelE, and agg) (Supplementary Data S4).
These genes were more frequently detected within E. faecalis than E. faecium species. Their occurrence was comparable from one site to another, except for gelE, which was more frequently detected in E. faecalis from site 1 (56. 3%) than from sites 2 and 3 (45. 8%). Susceptibility of 213 E. faecalis and 233 E. faecium strains to 16 antibiotics was also determined (Supplementary Data S4). Interestingly, the percentage of E. faecium resistant to levofloxacin, ampicillin, and streptomycin was higher for strains isolated from water samples than from shellfish. Analysis of isolates from rivers, revealed that 64. 3% of E. faecium strains from La Sienne river (sub-catchment of site 2) and 55. 5% from La Soules (sub-catchment of site 2) were resistant to ampicillin, whereas all strains from the other rivers were sensitive to this antibiotic.
DISCUSSION This original study aims to detect and characterize a large panel of micro-organisms from fecal contamination (Salmonella spp. , Campylobacter spp. , E. coli and enterococci strains and HuNoVs) as well as some marine bacteria such as Vibrio spp. For this study samples were collected from shellfish-harvesting areas and their catchments, but also from seawater. This has rarely been performed, most of other reporting data on these pathogens specifically relate either in shellfish or in water samples. The enumerations of the FIB showed that water from all three catchments is characterized by fecal pollution that is variable and can reach relatively high levels at certain periods. Classification of E. coli into phylogenetic groups revealed that isolates belonging to phylogroup A or B1 were more predominant than clones from group B2 or D.
ACKNOWLEDGMENTS We thank  Marie-Paule Caprais ,  Jean-Claude Le Saux ,  Emmanuelle Quenot ,  Céline Hubert ,  Pascal Garry ,  Antoine Véron  from  Ifremer ,  Clémence Balière ,  Isabelle Rincé ,  Quentin Bruet  from the  University of Caen-Normandy , and  Emilie Jardé ,  Loïc Harrault  and  Laurent Jeanneau  from  Geosciences Rennes  for their participation in the sampling and/or technical assistance. We are especially grateful for the assistance of  Julien Chevé  from  Ifremer (Dinard)  for the analysis of catchment data on the Brittany site, and for the permission of the local stakeholders (Dinan agglomeration;  Elvis Desnieuls  and  Michel Eldejam ) to take samples and to share catchment characteristic data.
Introduction The ensemble Kalman filter (EnKF,  Evensen, 1994)  and its variants are currently among the most popular data assimilation (DA) methods. Because EnKF-like methods are simple to implement, they have been successfully developed and applied to numerous dynamical systems in geophysics such as atmospheric and oceanographic models, including in operational conditions (see for example  Houtekamer et al. , 2005; Sakov et al. , 2012a). The EnKF can be viewed as a subclass of sequential Monte Carlo (MC) methods whose analysis step relies on Gaussian distributions. However, observations can have non-Gaussian error distributions, an example being the case of bounded variables, which are frequent in ocean and land surface modelling or in atmospheric chemistry. Most geophysical dynamical models are nonlinear yielding non-Gaussian error distributions  (Bocquet et al.
Acknowledgements. The authors thank the editor,  Olivier Talagrand , and three reviewers,  Stephen G. Penny  and two anonymous reviewers, for their useful comments, suggestions and thorough reading of the manuscript. The authors are grateful to  Patrick Raanes  for enlightening debates and to  Sebastian Reich  for suggestions. CEREA is a member of  Institut Pierre-Simon Laplace (IPSL). Edited by: Olivier Talagrand Reviewed by:  Stephen G. Penny  and two anonymous referees.
Signal modeling Simulated signal samples are generated at leading order and their cross sections are scaled to next-to-leading order with a K-factor of 1. 25  [22, 23]  appropriate for our signal mass range of interest. All signal samples are generated using the COMPHEP  [24]  4. 5. 2 package according to the following lowest-order effective Lagrangian  [22] : L = V f i f j 2 √ 2 g W fi γ µ a R (1 + γ 5 ) + a L (1 -γ 5 ) W µ f j + h. c. , (1) where V f i f j is the Cabibbo-Kobayashi-Maskawa matrix if f is a quark and V f i f j = δ ij if f is a lepton, g W is the SM weak coupling constant, and a R and a L are the coupling strengths of the W to right-and left-handed fermions, respectively. We consider values of a L and a R that range from 0 to 1, and any signal with a L > 0 takes into account interference with the SM W boson.
Acknowledgments We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centres and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES  and  CSF (Croatia) ;  RPF (Cyprus) ;  SENESCYT (Ecuador) ;  MoER ,  ERC IUT , and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NIH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  MSIP  and  NRF (Republic of Korea) ;  LAS (Lithuania) ;  MOE  and  UM (Malaysia) ;  BUAP ,  CINVESTAV ,  CONACYT ,  LNS ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New.
Accepted Article. January 2014. The relationships between overall survival and the following parameters were studied: gender, age at HCC diagnosis, AFP level, HIV and HCV viral loads, diabetes mellitus, type (infiltrative or nodular) of tumour, venous portal thrombosis, alcohol and tobacco consumption. Univariate and multivariate Cox regression models were used to assess prognostic factors for survival. All analyses were performed using SAS v9. 3 software (SAS Institute, Inc, Cary, NC). A P value <0. 05 was considered to denote statistical significance.
Follow-up was ensured every 3 months until death, loss to follow-up, or liver transplantation (LT) in the Carcinovic collaboration. At each visit, a physical Accepted Article examination, Model for End-Stage liver Disease (MELD) score, Child-Turcotte-Pugh (CTP) score, CDC score, and virological, immunological, biochemical and drug toxicity assessments were carried out. The treatment histories and patient's responses to previous treatments of HIV and HCV infections were recorded at the diagnosis of HCC and during follow-up. Twenty-six Infectious Diseases or Hepatology units in France participated in the Carcinovic collaboration. A common database with, patients' demographics, radiological and biological features, modality of therapy and survival, was created, which represented the support for analysis.
Acknowledgements Ť This study is dedicated in the memory of  Prof. Jean-Claude  Trinchet The authors thank  Prof. Jean-François DELFRAISSY  who supported the project and all members of the  ANRS HC EP 25 Prethevic ,  ANRS CO13 HepaVih , and  ANRS CO12 CirVir Study Groups ,  Laetitia JOHNSON  and  Messad OULD RABAH  ( Clinical Research Assistants ),  Anne PERSOZ  (senior data manager).
No conflict of interest by authors for this study Financial support: This study was sponsored and funded by the  French National Institute for Health and Medical Research -French National Agency for Research on Aids and Viral Hepatitis (Inserm-ANRS ). Author's contributions: study concept and design, study supervision, obtained funding (JCDV); acquisition of data, administrative, technical, or material support (MGS, MO); analysis and interpretation of data (MGS, JCDV, ML, MO, TB, MBS, LM, PN, RL, FRT); drafting of the manuscript (MGS, JCDV, ML, MO);.
Inflammatory parameter measurements Concentrations of IL-6, IL-1β and TNF-α in synovial fluids were quantified using a Milliplex MAP Human Cytokine/Chemokine Magnetic Bead Panel kit (Millipore, Billerica, MA). The assays were performed according to the manufacturer's instructions. Standards and samples were analyzed on a LuminexR 1 apparatus (Bio-Plex 200, BioRad, Mu ¨nchen, Germany) using the BioPlex Manager Software (Version 5, BioRad, Hercules, CA). Net mass concentrations of LPS were measured in synovial fluids through the direct quantitation of 3-hydroxmyristate by liquid chromatography-mass spectrometry (LC-MS) according to the general procedure previously described  [26].
8; 2% glycerol; 2% SDS and 1% glycerol, β-mercaptoethanol and 0. 001% Bromophenol blue) was added directly to the cells for 5 min followed by cell scratching. An equal amount of cell lysates was resolved by 10% polyacrylamide gel, and immunoblot analysis was performed. An ECL plus detection system (RNP2232; GE Healthcare) was used to detect specific protein bands. Blots were developed, scanned and densitometric signals were determined using the NIH image J 1. 63 software. PLTP was normalized to β-actin levels. Expression level of PLTP was expressed as a ratio relative to the mean expression of PLTP in all FLS tested (RAFLS and OAFLS). To detect PLTP, mouse monoclonal antibodies to PLTP (2μg/ml; ab57273; Abcam) or antiβ-actin (1/10,000; A5441; Sigma) and horseradish peroxidase-conjugated rabbit anti-mouse IgG (1:10,000; P0260; Dako) were used.
Statistical analysis Results were expressed as means ± standard deviations (SD). Mann-Whitney U test (nonparametric) for unpaired set of data and Wilcoxon matched pairs test for paired set of data were used. Unless when indicated, two-tailed p values were calculated. Correlations were determined by Spearman correlation. All statistical analyses were calculated using GraphPad Prism version 4. 00 (GraphPad Software, San Diego, CA).
Acknowledgments We thank  Pr Chammas ,  Pr Canovas  and  Dr Moussali  for providing synovial tissues and fluids. We acknowledge the imaging facility MRI, member of the national infrastructure  France-BioImaging  supported by the  French National Research Agency  ( ANR-10-INBS-04 ,  «Investments  for the future»). We also thank  Sumaiya Hoque  for editing English.
This work was supported by  PASSERELLE 2013 (Pfizer ) grant. This work was also supported by  INSERM  ( Institut National de la Santeet de la Recherche Medicale ), the  Regional Council of Bourgogne , the  European Regional Development Fund , the  University of Bourgogne , proliferation, independently of its lipid transfer activity. These results suggest a pro-inflammatory role for PLTP in RA. the  Fondation de France , and by a  French Government  grant managed by the  French National Research Agency (ANR)  under the program " Investissements d'Avenir " with reference  ANR-11-LABX-0021-01-LipSTIC LabEx. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ration of the manuscript.
Background Gestational weight gain is an important predictor of adverse maternal and child health outcomes  [1]. Insufficient weight gain is associated with increased risks of preterm birth and delivering a low birth weight infant, whereas excessive weight gain is associated with increased risks of gestational hypertension, preterm birth, delivering a high birth weight infant, cesarean delivery, and childhood overweight  [2] [3] [4] [5]. Appropriate gestational weight gain charts are necessary to monitor the progress of weight gain and to enable risk selection. Gestational weight gain charts have been derived from country-specific studies that varied in sample selection, study design, and methods of data collection and statistical analysis  [6]. A study of the INTERGROWTH-21st Project among 3097 normal weight women from Brazil, China, India, Italy, Kenya, Oman, UK, and USA described the patterns in maternal gestational weight gain from 14 weeks onwards in healthy pregnancies with good maternal and perinatal outcomes  [7].
We used individual participant data from 218,216 pregnant women from 33 European, North American, and Oceania pregnancy cohort studies to assess the pattern of weight gain and to construct gestational weight gain charts for underweight, normal weight, overweight, and grades 1, 2, and 3 obese women. Additionally, we compared these charts to those obtained in 138,517 pregnant women from 26 cohorts who had uncomplicated term pregnancies.
Inclusion criteria and participating cohorts This study was embedded in an international collaboration on Maternal Obesity and Childhood Outcomes (MOCO). Pregnancy and birth cohort studies participated if they included mothers with singleton live-born children born from 1989 onwards, had information available on maternal pre/early-pregnancy BMI and at least one offspring measurement (birth weight or childhood BMI) and were approved by their local institutional review boards. We identified 50 cohorts from Europe, North America, and Oceania selected from the existing collaborations on childhood health (EarlyNutrition Project, CHICOS Project, www. birthcohorts. net assessed until July 2014). We invited these cohorts, of which 39 cohorts agreed to participate, providing data of 239,621 singleton births.