dataesr/scientific-paragraphs-categorization huggingface dataset:
Sampling and lab protocol Atmospheric total (wet + dry) insoluble deposition is collected at the five sampling sites over the period 2011-2013. For this study, a 1-week sampling duration was chosen as a compromise between maximising the opportunity of sampling a single dust plume deposition event and the long autonomy of the collector, i. e. up to 25 sampling weeks. The same sampling duration is programmed at the five sites, with an automatic change of the filter every Thursday at 12:00 UTC. In all, 537 weekly atmospheric deposition samples were collected. At least 1 year of continuous deposition measurements is available from every station, the longest time series being from the Frioul site (January 2011 to December 2013). Depending on the site, the data recovery rate of weekly atmospheric deposition samples ranges from 77 to 91 % for the sampling period and at least 1 year of continuous measurements is available for each station.
Conclusion A network of five sampling sites was deployed from 2011 on the western Mediterranean region to measure the insoluble atmospheric deposition fluxes. It included from south to north an Italian site (Lampedusa), a Spanish site (Majorca) and three French sites (Corsica, Frioul, and Le Casset in south-eastern France). The data recovery rate varied between 77 and 91 % depending on the station. The deposition data set acquired between 2011 and 2013 include 537 weekly samples. It allowed us to investigate Saharan dust deposition events in this region. At the three northern stations of the network, Le Casset (44 • 59 N, 6 • 28 E), Frioul (43 • 15 N, 5 • 17 E) and Corsica (43 • 00 N, 9 • 21 E), the maximum deposition fluxes measured on a weekly basis were 0. 17, 0. 34 and 0. 53 g m -2 , respectively.
Data availability To obtain the data of the CARAGA network, contact Gilles Bergametti or Benoit Laurent at LISA (http://mistrals. sedoo. fr/Database-Content/?project=ChArMEx). Acknowledgements. This study was funded by the PRIMEQUAL-ADEME programme on "Pollution atmosphérique longue distance" through the research project "Mesure du dépôt atmosphérique et validation de sa représentation dans les modèles régionaux" (DEMO project, contract no. 0962c0067). This project was also funded by the MISTRALS (Mediterranean Integrated Studies at Local and Regional Scales) programme as part of the Chemistry-Aerosol Mediterranean Experiment (ChArMEx) and by the Spanish Government project ChArMEx: aerosols deposition ref: CTM2011-14036-E. The development of the CARAGA collector was supported both by the Chemistry Faculty of the Paris Diderot University and the PRIMEQUAL-ADEME DEMO project.
5 can be explored, as well as the low-mass galaxies at low redshift. The paper is organised as follows. In Sect. 2 we describe our photometric and spectroscopic dataset. The photometric redshifts and galaxy classification are presented in Sect. 3, the stellar mass estimates in Sect. 4. We detail the measurements of the galaxy SMFs and the associated uncertainties in Sect. 5, where we also point out the effect of the photometric absolute calibration in the new generation of large surveys. We present the evolution of the stellar mass function and stellar mass density in Sect. 6. Finally, we discuss our results and their effects on the quenching channels in Sect. 7. Throughout this paper, we use the standard cosmology (Ω m = 0. 3, Ω Λ = 0. 7 with H 0 = 70 km s -1 Mpc -1 ). Magnitudes are given in the AB system  (Oke 1974).
Two independent photometric catalogues have been released to the community: the 7th and final release (noted T0007 3  ) of the CFHTLS produced by Terapix 4  , and the release from the CFHT Lensing Survey team (CFHTLenS 5  ). Both catalogues are based on the same raw images. The AstrOmatic software suite 6  has been used to generate the mosaic images (SWARP,  Bertin et al. 2002)  and to extract the photometric catalogues  (SExtractor, Bertin & Arnouts 1996). The two releases differ in several points, however. -In T0007, detection is based on gri -χ 2 images, while the galaxies in CFHTLenS are i-detected. -A point spread function (PSF) homogenisation is implemented in CFHTLenS (see  Hildebrandt et al. 2012 ) to improve the colour estimates. In practice, the PSF is homogenised across the field of view for each filter and degraded in all filters to the one with the highest PSF.
Final photometric catalogue The catalogue of sources comes from the T0007 release and is based on detection in the gri-χ 2 image. As mentioned above, the same procedure was applied to the K s images. Following  Erben et al. (2013)  and  Hildebrandt et al. (2012) , we used the T0007 isophotal apertures for the photometry to estimate the colours. The apertures are smaller than the Kron-like apertures  (Kron 1980) , which provides less noisy colours and leads to an improved photometric redshift accuracy  (Hildebrandt et al. 2012). We also confirmed this with our large spectroscopic dataset (see below), which is especially relevant for faint sources (i > 23. 5). To derive galaxy physical properties, we need to know the total flux in all wavelengths. Therefore, we rescaled the isophotal flux to the Kron-like flux, m f total = m f IS O + δ m , by adopting a unique factor, δ m , for each source to preserve the colours.
We finally note that the contribution of the stellar mass uncertainty (σ Φ,M ; cyan solid line) drives the total uncertainty of the SMF high-mass end. We recall that while the Poissonian uncertainty is always taken into account in the literature, the error bars may reflect different contributions to the SMF uncertainty depending on the study considered in Fig. 12  (as specified in the caption). The comparison with  Davidzon et al. (2013)  is straightforward since their observations were taken in the same two fields of the CFHTLS survey, covering an effective area of 5. 34 and 4. 97 deg 2 in W1 and W4, respectively. The authors derived the SMF between z = 0. 5 and z = 1. 3 using the VIPERS-PDR1 dataset (∼ 50,000 galaxies), that is, the main spectroscopic sample used to calibrate our redshifts (Sect.
Acknowledgements. We gratefully acknowledge the anonymous referee, whose advice helped much in improving the clarity of the paper. We wish to thank  J. -C. Cuillandre ,  H. Aussel ,  S. de la Torre  and  B. C. Lemaux  for helpful discussions. We would also like to thank  J. Moustakas  for providing the PRIMUS stellar mass estimates. This research is in part supported by the  Centre National d'Etudes Spatiales (CNES)  and the  Centre National de la Recherche Scientifique (CNRS) of France , and the  ANR Spin (e )  project ( ANR-13-BS05-0005 , http://cosmicorigin. org). L. G. acknowledges support of the  European Research Council  through the  Darklight ERC Advanced Research Grant  (#  291521 ). This paper is based on observations obtained with  MegaPrime/MegaCam , a joint project of  CFHT  and  CEA/DAPNIA , and with  WIRCam , a joint project of  CFHT, Taiwan, Korea, Canada and France , at the  Canada-France-Hawaii Telescope (CFHT).
The atmospheric deposition of mercury (Hg) occurs via several mechanisms including dry and wet scavenging by precipitation events. In an effort to understand the atmospheric cycling and seasonal depositional characteristics of Hg, wet deposition samples were collected for approximately five years at 17 selected GMOS monitoring sites located in the Northern and Southern Hemispheres in the framework of the Global Mercury Observation System (GMOS) project. Total mercury (THg) exhibited annual and seasonal patterns in Hg wet deposition samples. Inter-annual differences in total wet deposition are mostly 5 linked with precipitation volume, with the greatest deposition flux occurring in the wettest years. This data set provides a new insight into baseline concentrations of THg concentrations in precipitation worldwide, particularly in regions, such as the Southern Hemisphere and tropical areas where wet deposition as well as atmospheric Hg species were not investigated before, opening the way for future and additional simultaneous measurements across the GMOS network as well as new findings in future modeling studies.
, 2007; Selin, 2009; Zhang and Wright, 2009). Although a number of monitoring stations have been established to better understand the impact of Hg wet deposition on ecosystems in many countries in the Northern Hemisphere  (Wängberg et al. , 2007; Prestbo and Gay, 2009; Sanei et al. , 2010)  several regions of the world (i. e. , regions which are becoming increasingly impacted by anthropogenic activities in general), and prevalently the Tropical zone and the Southern Hemisphere, were lacking in wet deposition data available, in terms of concentrations and deposition Hg fluxes. To address this concern, seasonal and annual variations of Hg wet deposition and concentration at 17 ground-based sites in the Northern and Southern Hemispheres were monitored as a part of GMOS (www. gmos. eu). Here an overview of the seasonal/annual Hg wet deposition patterns across the 17 sites, is presented, briefly examining meteorological/climatological conditions, as well as indicators of anthropogenic air mass sources and/or atmospheric chemical conditions in relation to Hg 10 wet deposition results observed.
2 Sample collection, analytical procedure, and QA/QC Precipitation samples were collected across the sites primarily using wet-only collectors, (i. e. , N-CON MDN or the Eigenbrodt NSA 171 wet-only samplers). Where necessary, due to site constraints or operator availability, few GMOS sites (Table  1 ) alternatively collected bulk precipitation samples. Within GMOS special attention was paid in respect to protocols harmonization, data quality collection and data management in order to assure a full comparability of site specific observational datasets. During the implementation stage of the GMOS global network, harmonized Standard Operating Procedures (SOPs) as well as common Quality Assurance/Quality Control (QA/QC) protocols have been addressed  (Munthe et al. , 2011)  in accordance with the measurement practice adopted in well-established regional monitoring networks and based on the most recent literature  (Brown et al.
Considering the THg wet deposition from 2012 to 2014 at the European sites, there appears to be a geographical trend with an increase in Hg deposition from north (Arctic area, i. e. , Ny Alesund, Pallas etc. ) to south in the Northern Hemisphere (i. e. , Rao, Mace Head, Listvyanka, Col Margherita, Longobucco). At the Chinese sites as well as at lower latitude (i. e. , Tropical area and Southern Hemisphere) no spatial trend has been observed. However, it is important to point out that the sites in the Southern Hemisphere are limited in number compared to those in the Northern Hemisphere and the data coverage is less complete for each year considered. This makes detailed evaluation of spatial trends at the southern sites difficult. In addition, apart from Cape Point (CPT), no historical records of THg deposition exist for the new stations established in the GMOS project.
Acknowledgements. This work was funded by the  FP7  (2010)(2011)(2012)(2013)(2014)(2015) Global Mercury Observation System (GMOS) project. We thank all GMOS external Partners for providing high quality-controlled wet deposition measurements as well as we would like to acknowledge and thank all the site operators for the GMOS global network. AD, OM, HA thank the  French Polar Institute IPEV ( Program 1028 , GMOStral), the  LEFE CNRS/INSU  (program SAMOA) and the overwintering crew at Amsterdam Island. The  CNR-IIA  research staff thanks also  F. Cofone ,  A. Servidio , and  A. Rosselli  for their technical support for the laboratory work carried out on the samples from AMS, LON, CMA, and Mexican Stations. 28 Atmos. Chem. Phys. Discuss. , doi:10. 5194/acp-2016-517,2016 Manuscript under review for journal Atmos.
Outcomes The secondary end-points of EFS, OS, and safety were assessed at this clinical cut-off. EFS was defined as time from randomisation to the date of disease recurrence or progression (local, regional, distant, or contralateral), or death from any cause. OS was defined as time from randomisation to death and a final analysis will be carried out once 5 years of survival data have been collected. Adverse events and serious adverse events were recorded and graded according to standard criteria [17e19]. Safety for this analysis is focused on the treatment-free follow-up phase.
Discussion The HannaH phase III study provides data from the largest homogeneous population of patients with HER2-positive early breast cancer. In HannaH, the secondary long-term efficacy end-points, EFS and OS, at a median follow-up of more than 40 months, support the established non-inferiority of subcutaneous trastuzumab relative to intravenous trastuzumab as per the co-primary end-points, pCR and C trough. HannaH's results were robust and consistent across analysis populations, and in agreement with the neoadjuvanteadjuvant NeOAdjuvant Herceptin (NOAH) study of intravenous trastuzumab, where 3-year EFS was 71% for trastuzumab-treated patients  [20]. In general, results were consistent across subgroups (including demographic and disease characteristics). In particular, EFS results for both arms were similar in patients in the higher body weight patient quartiles, as compared with the overall population, which is important as higher body weight patients may have reduced trastuzumab exposure from the 600 mg every 3 weeks subcutaneous fixed dose compared with weightbased intravenous dosing.
In each of HannaH's two treatment arms, comprising approximately 300 patients per arm, tpCR was associated with improved long-term efficacy outcomes (EFS) in patients who received neoadjuvanteadjuvant therapy for HER2-positive early breast cancer. HannaH provides the largest clinical dataset from a single study in HER2positive early breast cancer to demonstrate the favourable association between tpCR and EFS to date, and these data add to the body of evidence on tpCR being associated with clinical benefit in HER2-positive early breast cancer.
Contributors All authors have reviewed the data analyses, contributed to data interpretation, contributed to the writing of the report, approved the final version of the submitted report, and agree to be accountable for all aspects of the report. CJ, S-TC, and MS contributed to the conception/study design. CJ, RH, DS, J-SA, BM, S-CC, S-BK, ML, ES, GK, SF, S-TC, and XP enrolled patients. CJ, J-SA, BM, ES, GK, S-TC, and DH collected data. CJ and DH undertook literature searches. DH, AC-F and MS contributed to generation of tables/figures. AC-F and MS collated data. A full list of study investigators can be found in the Supplementary Materials.
Implications of all the available evidence In each of HannaH's two treatment arms, comprising approximately 300 patients per arm, tpCR was associated with improved long-term efficacy outcomes (EFS) in patients who received neoadjuvanteadjuvant therapy for HER2-positive early breast cancer. These data add to the body of evidence on tpCR being associated with clinical benefit in HER2-positive early breast cancer. HannaH also confirmed no difference between subcutaneous and intravenous trastuzumab in terms of efficacy or safety with longer follow-up.
vectorbase. org; AgamP4;  [41] ) with a Wellcome Trust pipeline including Picard tools (https:// broadinstitute. github. io/picard/) to format the data, bwa (0. 7. 5a-r405  [69] ) for mapping, and other analysis tools providing optimized mapping data in SAM format. The Acerkis (RR, two individuals) samples were specifically sequenced for this project with the same sequencing technology (Illumina). The sequencing data consisted of 125 bp-read pairs separated by a 500 bp insert. The reads were then trimmed and mapped directly, using bwa, onto the same PEST reference genome. For the genomic analysis, we used the gene annotations from the AgamP4. 3 (https://www. vectorbase. org/organisms/anopheles-gambiae/pest/AgamP4. 3).
Resistance Measure Bioassays were used to assess mosquito resistance to three insecticides: one CX (bendiocarb, technical grade, 99. 5% purity), one OP (chlorpyrifos methyl, 99. 9% purity), and one PYR (permethrin, 98. 3% purity). We incubated 25 late third-instar larvae for 24 h at 27˚C ± 2˚C in plastic cups containing 99 ml of distilled water, to which we added 1 ml of insecticide solution at the required concentration (1 ml of ethanol in controls). Four replicates were performed for each concentration. Larval mortality was recorded after 24 h of exposure. Dose-mortality responses were analyzed with the BioRssay R script (v. 6. 2  [72] ) freely available from the ISEM website (http://www. isem. univ-montp2. fr/recherche/teams/genomic-adaptation/staff/ labbepierrick/?lang=en). This script computes the 50% or 95% lethal concentrations (LC 50 and LC 95 , i.
[73]. Optical density at 412 nm was recorded every minute for 15 min with an EL 800 microplate reader (Bio-Tek Instruments, Inc. ). The mean slope of each reaction was calculated with KCjunior v1. 41. 4 analysis software (Bio-Tek Instruments, Inc. ) and was used as a measurement of AChE1 activity. The first well (ethanol) was used to assess total AChE1 activity (A TOT ), whereas the second (propoxur) provided information about AChE1R activity (A R ) only. AChE1S activity (A S ) was deduced as = A TOT -A R. Note that activity in the second well was never equal to 0: a very shallow slope was observed even for susceptible individuals, due to the spontaneous degradation of DTNB. For comparisons of different strains or populations, samples of each were distributed on the same plate and analyzed simultaneously to avoid experimental artifacts.
Acknowledgments We would like to thank  Nicole Pasteur  for her helpful comments on the manuscript. Benoı ˆt S. Assogba was supported by a fellowship from the  Institut pour la Recherche et le Developpement (IRD). The Sanger sequences used in this work were generated by the technical facilities of the  Environmental Genomic Platform of the LabEx Centre "Mediterraneen Environnement Biodiversite" and GenSeq ISEM Platform. The genome sequences of the Acer-Kis strain were generated by MGX-Montpellier GenomiX. The genome sequences of the Acerduplikis and KisumuP strains were obtained thanks to  Pr. Martin Donnelly  through the  Wellcome Trust Sanger Institute. Contribution number  2016-246  of the  Institut des Sciences de l'Evolution de Montpellier ,  UMR 5554 CNRS-UM-IRD-EPHE.
For each site, the following information is given: year of collection, proportion of individuals belonging to each species, number of individuals for each ace-1 phenotype followed by the "-" or "+" symbols indicating the absence or presence of a duplication junction. Note that all [SS] mosquitoes gave negative results in the duplication test (225 individuals), whereas all [RS] or [RR] mosquitoes (173 individuals) gave positive results, regardless of the species considered. Underlying data can be found in DRYAD http://dx. doi. org/ 10. 5061/dryad. 4f7qg. doi:10. 1371/journal. pbio. 2000618. t001.
8 Expression of artificial chimeric RNAs composed of AluACA and canonical H/ACA RNA elements demonstrated that the suboptimal 5 0 hairpins account primarily for the poor accumulation of AluACA RNAs and that the BIO motif can significantly improve the inherently weak expression of AluACA RNAs. We detected perfectly conserved BIO motifs in more than 12% of the known 348 human AluACA RNAs. Usually, the BIO motif-containing RNAs were represented by high number of reads in our AluACA deep sequencing datasets,  8  providing further support to the idea that the BIO motif promotes H/ACA RNA accumulation in vivo. It has been proposed that the biogenesis-promoting element of hTR is composed of the C415, U416, G417 and U418 loop nucleotides following the CAB box. 50, 51 A detailed structural and functional analysis of the CR7 signal supporting hTR processing and CB-specific accumulation revealed that the hTR BIO motif comprises the terminal stem with 2 C-G bps at the top (C409-C410/G419-G420), a U.
Co-IP of AluACA7 and AluACA7-dm2 was monitored by RNase mappings. Interaction of Wdr79 with the endogenous U85 H/ACA scaRNA (positive control) and the U64 snoRNA (negative control) was also tested. Recovery of Wdr79 was confirmed by western blot analysis. Lane no Ab, control IP performed without antibody. computer folding of experimentally validated human H/ACA RNA sequences available in the LBME SnoRNA Database (https://www-snorna. biotoul. fr) confirmed that H/ACA RNAs carry fairly uniformly sized 5 0 -and 3 0 -terminal hairpins. We found that the H and ACA boxes are usually separated from the terminal loops of the preceding hairpins by 24-28 nts (Fig. 6 ). The very few RNAs with extended hairpins, e. g. E2 RNA, carry internal loops positioned 24-26 nts upstream of the H or ACA box. The H/ACA hairpins are tightly docked to the dyskerin/Nop10/Nhp2 protein scaffold that may function as a molecular ruler measuring the distances between the dyskerin-bound H or ACA box and the Nhp2-bound terminal loop.
Genome Analysis Protein-, rRNA-, and tRNA-encoding genes were identified as described  (Merga et al. 2013 ). The 1485E genome was annotated based on Cft strain 03-427 T (accession number CP006833)  (Gilbert et al. 2013; Fitzgerald et al. 2014 ) and the annotation of the 2463D genome was based on that of 1485E, with further annotation using Artemis  (Rutherford et al. 2000) , the identification of Pfam domains (v. 27. 0)  (Finn et al. 2014) , and BLASTP comparisons to proteins in the NCBI non-redundant (nr) database. CRISPR regions were identified using CRISPRFinder  (Grissa et al. 2007 ). The  values based on the whole genome sequences were calculated for these strains as a measure of genetic relatedness. The BLAST parameters were: X = 150, q = À1, F = F, e = 1eÀ15, and a = 2. To visualize genomic regions specific for Cig, the BLAST ring image generator (BRIG)  (Alikhan et al.
MLST Multilocus sequence typing (MLST) was performed for all Cig strains listed in table 1. The MLST loci were extracted from the genomes of 1485E and 2463D and sequenced as described previously for the other Cig isolates  (Miller et al. 2012). For HFglt, the annealing temperature was lowered to 46 C and 40 instead of 35 cycles were used. Sequences were trimmed and concatenated. In MEGA v. 6. 06, the concatenated sequences were aligned using MUSCLE and a Maximum likelihood dendrogram was created using 500 bootstraps. Accession numbers of the MLST sequence data can be found in table 1.
Features of theCampylobacter Strains Used in this Study Cff, C. fetus subsp. fetus; Cft, C. fetus subsp. testudinum; Cfv, C. fetus subsp. venerealis; Chh, C. hyointestinalis subsp. hyointestinalis; Chl, C. hyointestinalis subsp. lawsonii; Clan, C. lanienae. AR, Argentina; BE, Belgium; FR, France; NL, Netherlands; SE, Sweden; UK, United Kingdom; US, United States. MLST, multilocus sequence typing; WGS, whole genome sequencing. Cig strain 1485E has been deposited in GenBank under accession numbers CP009043 (chromosome) and CP009044 (megaplasmid) (Gilbert et al. 2014b). The complete annotated genome sequence of the Cig strain 2463D chromosome has been deposited in GenBank under accession number CP010995. Accession numbers of all genomes used in this study can be found in table 1. The C. iguaniorum strain 1485E genome was compared with the genome of strain 2463D and the completed genomes of the closely related taxa C.
fetus subsp. testudinum (strains 03-427 and SP3), C. fetus subsp. fetus (strain 82-40), C. fetus subsp. venerealis (strain 97/608), C. hyointestinalis subsp. hyointestinalis (strain LMG 9260), C. hyointestinalis subsp. lawsonii (strain CCUG 27631), and C. lanienae (NCTC 13004). For Campylobacter species outside the C. fetus clade, BLASTP comparisons to proteins in the NCBI non-redundant (nr) database were performed. A local BLAST was performed based on the predicted proteomes of all genomes and the results were screened for features specific for one or both Cig strains and the other members of the C. fetus clade. Using JSpecies v. 1. 2. 1 (Richter and Rossello-Mora 2009) and BLAST v. 2. 2. 26, average nucleotide identity (ANI).