dataesr/scientific-paragraphs-categorization huggingface dataset:
The quality of the agreement significantly deteriorates if the χ 2 evaluation neglects the PDF uncertainty. This effect is more pronounced for the CT10nlo and NNPDF3. 0 sets which include fewer data from the Tevatron. This indicates the significant constraining power of the Tevatron data. The CT10nlo and MMHT2014 PDFs are profiled according to Eq. (  4 ). The results of the profiling on the d-valence PDFs, and on their relative uncertainties, are shown in Fig. 6. The profiling affects the shape of the distribution more for the CT10nlo when compared to MMHT2014 set. Significant reduction of the uncertainties is observed for both sets, in particular in the low-and medium-x range. The NNPDF3. 0 PDFs are reweighted to the Tevatron data. The number of effect-ive replicas remaining after reweighting, N eff , is only 1 and hence the resulting PDFs are not shown.
Summary The HERAFitter framework is used to perform a QCD analysis of the DIS data from HERA, together with Wand Z-boson production measurements performed at the Tevatron collider in Run II. The correlation model of the systematic uncertainties of the Tevatron data is investigated, and a modification is proposed which accounts for the statistical nature of some of the systematic uncertainties. The Tevatron and HERA data are well described by a NLO fit with 15 free parameters, with a new parametrisation of PDFs which adds to the basic form a combination of linear and exponential terms. The impact of the Tevatron W -and Z-boson measurements is assessed by comparing PDF uncertainties from a fit to the HERA data alone, and a fit to the HERA and Tevatron data. A significant reduction of the uncertainties is observed in the latter case, for the valence quarks and d quarks in particular.
The Tevatron measurements are also compared to predictions evaluated with modern PDF sets, and the impact of the data on the PDFs is assessed using profiling and reweighting techniques. The profiling techniques take into account asymmetric PDF uncertainties. A good agreement between measurements and predictions is observed, if the PDF uncertainties of the predictions are taken into account. After the inclusion of the Tevatron data, the PDF uncertainties on the dvalence quarks are significantly reduced, especially for the PDF sets which include only the Z-boson data from the Tevatron, and the agreement between the various PDF sets is improved. These findings highlight the importance of the Tevatron W -and Z-boson production data to constrain d-quark and valence PDFs, and suggest that the data should be used in the future global PDF analyses.
Acknowledgements We thank  Juan Rojo  for useful comments on the manuscript, and  Hang Yin  for fruitful discussions on the experimental uncertainties of the D0 measurements. We are grateful to the  DESY IT department  for their support of the HERAFitter developers. This work is supported in part by  Helmholtz Gemeinschaft  under contract  VH-HA-101 , BMBF-JINR cooperation and  Heisenberg-Landau  programs as well as by the  Polish NSC  project  DEC-2011/03/B/ST2/00220.
According to the PYTHIA 8 and QGSJETII-04  [18]  generators, about 91-96% of the total inelastic cross section at √ s = 8 TeV is seen by T2  [4] , with the uncertainty coming mainly from low mass diffractive events. The present analysis follows the procedure described in Ref. [26] , where more details are given on the trigger, data selection, and correction procedures. Corrections for the contribution of background events triggered by T2 but without a charged primary particle in the T2 acceptance are estimated with simulated events from PYTHIA 8 and EPOS. These models were found to enclose the measured pseudorapidity distributions of charged particles in the forward region  [26]. The average corrections for the two models vary from 4% and 1% at p min T ≈ 1 GeV to 7% and 5% at p min T ≈ 45 GeV, for the track and trackjet analysis, respectively.
Also shown is the impact of turning off the regularisation of the cross section, labeled "PYTHIA 6 (default, MPI off, no sat)". At low p min T , the distribution predicted by this latter model differs by more than one order of magnitude from predictions with the regularised cross section. In Fig. 1  (right plots) the leading charged particle and leading jet data are compared with PYTHIA 8 with tunes 4C, CUET, and MONASH, HERWIG++ (version 2. 7. 0) with tune UE-EE-5C, EPOS (version 1. 99) with LHC tune, and QGSJETII-04. The leading charged particle and leading jet cross sections are best described by EPOS, which deviates only by up to 10% from the data at very low p min T and reproduces the data well for p min T > 4 GeV. The event generator HERWIG++ (UE-EE-5C tune) describes the leading jet cross sections fairly well, but does not reproduce the transition from large to small p T in the leading charged particle cross section.
Summary The integrated yields of events with a leading charged particle or a leading charged-particle jet with p T above a given p min T threshold, starting at p min T = 0. 8 and 1 GeV, respectively, have been measured in pp collisions at √ s = 8 TeV in a data sample corresponding to an integrated luminosity of 45 µb -1. The particles and jets are measured in the pseudorapidity ranges |η| < 2. 4 and 1. 9, respectively. The yields are found to be relatively flat in the p min T region around 1 GeV-where the fixedorder perturbative parton-parton cross section diverges in the absence of any mechanism that saturates or unitarises the pQCD scattering-followed by a steep decrease for p min T > 10 GeV. The flattening behaviour observed at very low p min T is best described by EPOS, which deviates by at most 10% from the data.
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. We are very grateful to the  TOTEM Collaboration  for making their trigger signal available to CMS and for providing the additional tools required to analyse the acquired data. 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) ;  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) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  MST (Taipei) ;  ThEPCenter, IPST, STAR  and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU  and  SFFR (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
Routine clinical care visits form the study visits for PASSPORT and take place approximately every 3 months (table  2 )  [12]. The first subject was enrolled in February 2012 and, as of the last interim database-lock in December 2013, 530 patients in the safety population had received at least one dose of pirfenidone. To date, the average exposure to pirfenidone is 6. 33 months, with a median of 5. 48 months and an overall exposure of 284. 1 patient years. As in the clinical trials and open-label extension study, the most common adverse drug reactions seen in these patients have been gastrointestinal symptoms, including nausea (15. 7%), fatigue (15. 3%), decreased appetite (10. 4%) and weight loss (10. 2%), and skin-related symptoms including rash (7. 5%) and photosensitivity reaction (4. 2%).
Over the past decades, the sea-ice extent has been shrinking causing a northward shift of the ice-edge and its associated primary production, with direct incidence to the export flux of particulate organic matter (POM) to the seafloor and the associated benthic carbon cycle. The present study aims at characterizing benthic mineralization along both the bathymetric transect and the latitudinal transect at the HAUSGARTEN observatory (Fig  1 ). The data set consists of benthic O 2 uptake rates quantified from O 2 concentration profiles obtained both in the laboratory and in situ during summer 2007 and 2008. Rather than focusing on the temporal variability inherent to the region, our study offers a spatial coverage of DOU rates in the Fram Strait at the interface between two regimes: i) from the continental shelf to the abyss, and ii) from the Atlantic to the Polar regime across the sea-ice front.
Oxygen profiles were used to calculate the diffusive oxygen uptake (DOU) rate of the sediment. The diffusive oxygen fluxes at the sediment-water interface (SWI) were assessed using Fick's first law: DOU ¼ À; Ds @O 2 @z ! z¼0 ; where Ds is the molecular diffusion coefficient in sediments at in situ temperature, @O 2 @z Â Ã z¼0 is the oxygen gradient at the SWI determined by linear regression over the 5 top mm of the sediment (selected as the minimum interval to cover the linear section of all gradients) and Ø is the porosity of the sediment. Ø was derived from the water content data and Ds was calculated using Archie's law as Ds = D 0 Ø 2. 5 , where D 0 is the molecular diffusion coefficient  [39].
644, p < 0. 05, Fig  6 ). This negative correlation with water depth is consistent with previous empirical relationships originating from compilation of data sets in the Arctic and the Atlantic Ocean (Fig  6 )  [22, 50, 53, 55, 56]. TOU, measured with an in situ benthic chamber on 3 stations only, displays the same behavior (P. Hall unpublished data) with a decrease by a factor of 2 between 1000 and 2500 m depth and an increase in the Molloy Deep compared to the site at 2500 m. Due to the limited number of TOU and thus the absence of a clear overview of the TOU/DOU distribution along the entire transect we used DOU as a proxy for carbon remineralization in this area. Nevertheless, we acknowledge that the decrease in oxygen consumption rates versus depth might hence be underestimated by ignoring the contribution of the benthic fauna.
Benthic mineralization along the latitudinal HAUSGARTEN transect The productivity and pelagic-benthic coupling of the Arctic Ocean largely rely on the extent, thickness and melting dynamics of sea ice, but also on the river discharges and inflow of Atlantic waters  [7]. Our study site, the HAUSGARTEN area, is located in the Fram Strait, a transition zone between the North Atlantic and the central Arctic Ocean: our dataset thus offers a unique opportunity to investigate the spatial variations of the benthic mineralization at a local scale in an ice-edge region. To investigate the effect of the ice-edge on the benthic degradation of organic carbon, we focused on a latitudinal transect along the 2500 m isobath, with stations at increasing distances to the sea ice. Overall, the DOU measured along this approx.
Singularly, the northern most station N4 seems to be characterized by low amounts of organic matter of good quality as indicated by slightly increased protein contents and higher proportions of chlorophyll contents (%Chl a). DOU and esterase activity represent respectively the total benthic carbon degradation activity, and the metabolic potential of bacteria, and are hence proxies for the degradation in the sediments of respectively total and intermediate-reactivity organic matter  [72, 73]. Both quantities showed larger values in the South compared to the Northern section of the transect, which indicates that the HAUSGARTEN benthic ecosystem along the latitudinal transect depends on the quantity rather than the quality of organic matter reaching the seafloor. Our benthic data hence suggests a larger deposition of organic matter of lower lability in the southern section of the transect and a lower quantity of organic matter with higher quality in the North, near the ice edge.
Acknowledgments We wish to thank the captains and crews of the  R/V Polarstern  and the  Quest ROV group  from  MARUM Bremen  for their help with sea work during the cruises. We thank  AWI Deep-Sea Research Group  for inviting us to the 2007 and 2008 arctic cruises on board Polarstern ( ARK-XXII/1c  and  ARK-XXIII/2 ). We would like to thank  A. Pappert  for her help in analyzing sediment properties and various biogenic sediment compounds. We thank  B. Bombled  who conducted part of the analysis on board in 2007. This work was supported by  LSCE. This is LSCE contribution number  5566  and publication "e36902" of the  Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaven, Germany.
It is therefore important to evaluate at the country level the current distribution and the genetic characteristics of the PUUV strains circulating in bank voles. To date, eight PUUV lineages have been described in Europe which show a strong geographical clustering  [8, 9]  the Central European (CE) lineage (including strains from Belgium, Germany, and Slovakia)  [10, 11] , the Alpe-Adrian (ALAD) lineage  [12] , the Latvian (LAT) lineage  [13] , the Danish (DAN) lineage  [9, 14] , the south-Scandinavian (S-SCA) lineage  [15] , the north-Scandinavian (N-SCA) lineage  [15, 16] , the Finnish (FIN) lineage  [9, 14]  and the Russian (RUS) lineage  [9]. Data are missing at the French level, only S and partial M segment sequences of viruses circulating in bank voles from the Jura region have been published, they clustered with the CE lineage.
[19]. Sequences of primers are available upon request. PCR-amplicons were purified from agarose gel and sequenced by the Sanger method. Complete S, M and L sequences of the six samples were deposited in GenBank database under accession numbers KT247592-KT247609 (Supplementary Table  S1 ). Datasets included in the study are constituted as follow. S dataset: We used a dataset composed of the complete coding S segment sequences (nucleoprotein) of the six newly sequenced French isolates from Ardennes, Jura and Orleans and of 181 PUUV and Asian PUUV-like sequences. The five PUUV sequences (KC676609, KC676611, KC676613, KC676614, and KC676615) from Croatia, the five PUUV sequences (AB433846, AB433847, AB433848, AB433842, and AB433844) from Russia and the three PUUV sequences (EU439969, EU439971, and EU439972) from Germany, for which the regions encoding the first 3, 14 and 18 amino acid residues, respectively, are lacking, were added to the PUUV group in order to improve the representativeness of these geographic areas.
The Asian PUUV-like sequences correspond to the Asian provisional species Hokkaido virus (HOKV), Muju virus (MUJV) and Fusong virus (FUSV) as reported in the 9 th ICTV Report  [20] , in order to include all known viruses with complete coding sequences for the S segments (S, open reading frame (ORF), 1293 bp). M dataset: We used a dataset composed by the partial (2484-3010 nt) M segment sequences of the six newly sequenced French isolates and of 49 PUUV and Asian PUUV-like sequences. L dataset: We used a dataset composed by the partial (577-989 nt) L segment sequences of the six newly sequenced French isolates and of 53 PUUV and Asian PUUV-like sequences. All sequences were obtained from the National Institute of Allergy and Infectious Diseases (NIAID) Virus Pathogen Database and Analysis Resource (ViPR)  [21, 22]  online through the website http://www.
viprbrc. org. The list of viruses and their geographic origin are displayed in Supplementary Table  S1. Multiple sequence alignments were prepared with the Clustal Omega alignment program implemented in SEAVIEW v4. 4. 2  [23]. Nucleotide sequences were translated into amino acid sequences and analyzed with SEAVIEW v4. 4. 2. Phylogenetic reconstructions were conducted using the Maximum Likelihood (ML) approach implemented in PhyML v3. 0  [24]  with a statistical approximate likelihood ratio test (aLRT) of branch support, using the Asian PUUV-like species as outgroup. The optimal substitution model was identified as the GTR+G+I model (General Time Reversible) for the three segments, using a function implemented in Mega v6. 0  [25]. The transition/transversion ratio was fixed to 4 and nucleotide frequencies were optimized from the data set.
Phylogenetic Analyses In order to elucidate if genetic differences in the PUUV viruses circulating in the different regions may explain the discrepancy in human transmission, we have compared viral isolates representative of the Orleans non-endemic region to those selected in the two main endemic areas of Charleville and Dole. This corresponds to the first description of the complete genome coding sequences of PUUV strains circulating in bank vole populations in France. Until now, only S and partial M segment sequences from PUUV circulating in the Jura region have been published  [27]. Complete coding sequences of the three genomic segments of two PUUV isolates for each of the three areas presenting the higher seroprevalence and number of positive rodents were determined (See Supplementary Table  S1  for their GenBank accession numbers).
Genetic Diversity of French Isolates Analyses of the complete coding sequence estimate that the evolutionary divergence between the PUUV lineages in France reaches up to 18% at the nucleotide level and 3% at the amino acid level for the S segment (Figure  2  and Table  2 ). This divergence is almost the same for the other segments with a global tendency to slightly more divergence for the M segments (19% nt and 4% aa) and slightly less divergence for the L segment (15% nt and 3% aa). As already documented for PUUV  [28, 29]  or other hantaviruses  [30] , only a few non-synonymous substitutions are observed, the majority of mutations are silent, suggesting strong purifying selection. PUUV nucleocapsid protein aa sequence visualized with Protter-visualize proteoforms  [31]. The used aa sequence corresponds to the consensus sequence of the S sequences dataset.
Amino Acid Specific Signatures All genetic lineages of PUUV possess specific amino acid "signatures" [9]. Concerning the French isolates, it is of note that within the CE lineage, only those from Ardennes possess the Q64 signature characteristic of the Belgian strains [9], outlining the close relationship between them. This residue is embedded in the major antigenic site of the N protein. On the other hand, sequences from Orleans have two specific amino acid residues ( V10  within the major antigenic site and  A294 ) at very conserved positions and share another one with the JU2 Jura isolate,  K258  located in the hyper variable region of the protein (Figure 4). Acknowledgments: J. B. , F. S. and D. P. are part of the  French Laboratory of Excellence  project  ECOFECT  ( ANR-11-LABX-0048 ;  ANR-11-IDEX-0007 ).
This study was funded by the  Anses (Afsset  grant  EST-2007-75 ) as well as by  EU  grants  FP7-261504 EDENext  and  FP7-278976 ANTIGONE. The manuscript is catalogued by the EDENext Steering Committee as EDENext401 (http://www. edenext. eu). The contents of this publication are the sole responsibility of the authors and don't necessarily reflect the views of the  European Commission.
Data Collected The questionnaire had five sections: n Demographic variables: Date and place of birth, sex, education level, and profession were collected from all participants. n Level of information about cancer: This series of questions was addressed to all participants involved in the truth-telling process. However, it was obvious that question 5, "Do you have information on cancer? And how," was not addressed to physicians. The data gathered in this section included information about cancer and the source of that information; disease curability; disclosure of the diagnosis to patients; the role of faith; acceptance of the truth by family, friends, and physicians; the patient's reaction after knowing the truth; factors that help to accept a cancer diagnosis; the importance of disclosing; the actual diagnosis and treatment side effects; ease of communication with the cancer patient (depending on awareness or unawareness of the diagnosis); and the percentage of patients who know their diagnosis.
Purpose The SAGIT instrument is a comprehensive clinician-reported outcome instrument assessing key features of acromegaly: signs and symptoms, associated comorbidities; growth hormone levels; insulin-like growth factor-1 levels; and tumor profile. The SAGIT instrument has been designed to assist endocrinologists managing acromegaly in practice. Here, we report on pre-testing (to assess ease of understanding and acceptability) and a pilot study (to assess relevance, ease of use, and utility in reallife conditions) (NCT02231593). Methods For pre-testing, 11 endocrinologists completed the SAGIT instrument using patient medical records and were also interviewed. They subsequently completed a PRAgmatic Content and face validity Test (PRAC-Test Ó ) to report their experiences using SAGIT, and feedback was used to revise the instrument.
Thus, there is a need for a comprehensive instrument that records biochemical, tumoral, and clinical aspects of acromegaly. Two such instruments are currently in development: SAGIT and ACRODAT (ACROmegaly Disease Activity Tool)  [15]. The SAGIT instrument is multidimensional, comprising five sections that assess key features of acromegaly  [6] : signs and symptoms (S), associated comorbidities (A), GH levels (G), IGF-1 levels (I), and the Tumor profile (T) (Fig. 1a ). The SAGIT instrument was developed by a steering committee comprising acromegaly experts from the Acromegaly Consensus Group, which has published guidelines and consensus papers  [16] [17] [18] [19] [20] ). The aim was to provide a reference instrument for acromegaly staging in clinical practice. A global development program, involving an iterative, 3-step process (NCT02231593), was implemented to develop and validate the original SAGIT instrument.
Characteristics of participating clinicians and their patients Of the 14 endocrinologists recruited, 13 participated in the pilot study, four from Brazil and the UK, and nine from other countries. Overall, 26 patients were included in the prospective pilot study; in the UK and Brazil (retrospective pilot study), the medical records of 12 patients were evaluated. The ages of the participating endocrinologists ranged from 34 to 56 years, with similar numbers working in outpatient clinics and hospitals (Table  2 ). The number of acromegaly patients encountered by the endocrinologists varied from 1-10 per month in the UK to 12-80 per month in Brazil (Supplemental Table  1 ). Of the 26 patients whose data were analyzed in the pilot study, nine had active/uncontrolled acromegaly, 10 had stable/controlled acromegaly, and seven were treatmentnaı ¨ve.
Acknowledgments The authors would like to thanks the following investigators for their participation in the work:  Felipe Henning Gaia Duarte ,  Raquel S. Jallad ,  Cesar Luiz Boguszewski ,  Antonio Ribeiro de Oliveira (Brazil) ;  Philippe Chanson ,  Christine Cortet ,  Francoise Galland, Sylvie Salenave (France) ;  Jens Aberle ,  Sylvere Sto ¨rmann (Germany) ;  Rita Berardelli ,  Silvia Grottoli ,  Gherardo Mazziotti ,  Teresa Porcelli  (Italy);  Ignacio Bernabeu ,  Fernando Cordido ,  Silvia Maraver ,  Isabel Salinas  (Spain);  Prakash Abraham ,  Daniel Flanagan ,  Robert Murray ,  Sam Philip (UK) ;  John Carmichael ,  Maria Fleseriu  (USA). The authors also thank  Watermeadow Medical  for assistance in preparing this manuscript (funded by  Ipsen ). Funding This study was sponsored by  Ipsen.