dataesr/scientific-paragraphs-categorization huggingface dataset:
Renal transplants performed The overall number of renal transplants performed in 2011 among all registries reporting to the ERA-EDTA Registry was 22 814 (37 pmp). Of those, a total of 16 118 (26 pmp) renal transplants were performed using deceased     Based on data from Austria, Bosnia and Herzegovina, Denmark, Finland, France, Greece, Iceland, Norway, Romania, Serbia, Spain (Andalusia), Spain (Aragon), Spain (Asturias), Spain (Basque Country), Spain (Catalonia), Spain (Extremadura), Spain (Galicia), Spain (Valencian region), Sweden, the Netherlands and UK (Scotland). donor kidneys, 6 059 (9. 9 pmp) using a living donor kidneys and for 637 (1. 0 pmp) transplants the donor type was unknown. Tables  9  and 10  report that the highest overall transplant rates were reported from Spain, Cantabria (81 pmp) and Spain, Catalonia (77 pmp).
Rates of living donor kidney transplants were highest in Turkey (39 pmp), Iceland (35 pmp), the Netherlands and UK, Northern Ireland (both 26 pmp). The transplantation activity reflects 70% of the total transplantation activity in the country, because there is underreporting of pre-emptive transplants. Patient and graft survival Survival analysis was performed using the data from 22 registries in 12 countries that provided individual patient records for the period from 2002 to 2009. The results of the unadjusted and adjusted survival analyses for all countries combined for all patients and for those aged 65 years and older are presented in Figure  4  and Table  11. The adjusted analyses for the total group of patients used fixed values for age, gender and distribution of primary renal disease, while the adjusted analyses in the group of patients ≥65 years were not adjusted for age.
A more detailed description of the methods used for the survival analyses can be found in the Appendix. For the calculation of the expected remaining lifetimes, we used data from 18 national and regional renal registries in 11 countries that provided individual patient records for the period from 2000 to 2011. As is illustrated in Figure  5 , the expected remaining lifetime for patients on RRT is much lower than for the general population. Particularly, the expected remaining lifetime of dialysis patients is strongly reduced when compared with that of transplant recipients, and it represents approximately    one-third of the expected remaining lifetime of the general population. In addition to the RRT modality, age plays an important role: with a higher age, the reduction in expected remaining lifetime is less pronounced.
Acknowledgements. The ERA-EDTA Registry would like to thank the patients and staff of all the dialysis and transplant units who have contributed data via their national and regional renal registries. In addition, we thank the persons and organizations listed in the Appendix for their contribution to the work of the ERA-EDTA Registry. The ERA-EDTA Registry is funded by the  European Renal Association-European Dialysis and Transplant Association (ERA-EDTA ).
A plasmid par-titioning gene, parA, was detected, which suggests the occurrence of a plasmid. This draft genome, along with the additional draft sequences of N. ulvanivorans  (10)  and two Alteromonas spp. (  14 ), will allow a better understanding of the utilization and exploitation of the Ulvales biomass. A BLAST search of the known ulvan lyase and the GH105 against the draft genome has found no matching sequences. Since the PLSV strain is able to degrade ulvan, it most likely contains genes coding for a distinct set of enzymes that participate in the degradation process. Identifying these enzymes will shed new light on alternative ulvan breakdown pathways. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no.
Ethics statement The research protocol was implemented with the approval of the Vice-Presidency of Agriculture, Fisheries and Environment of the Union of Comoros. No endangered or protected species were involved in the survey. Farmers in each zone gave their verbal consent to be included in the study. Permissions for the blood sample collection were obtained. The animals were bled without suffering. Regarding the trade survey, no personal data were collected, and only information concerning the number of animals travelling from one island to another was taken into account.
RFEv2/. est_ prcp/), with a spatial and temporal resolution of 11 km and 10 days respectively. DLST, NLST and rainfall values were extracted within a 5-km radius buffer around each farm corresponding to the maximum daily distance for cattle (grazing and watering). For each sampled animal that became RVFV antibody positive, MODIS and MEWS data recorded at the time of the seroconversion in the zone concerned were compared with MODIS and MEWS data recorded at the same time in the other zones.
Trade survey The aim of the trade survey was to estimate the movement of live animals between continental Africa and the Comoros archipelago and among the islands of the archipelago themselves. To date, only approximate figures are known without any quantitative data available  [17]. The number of imported ruminants was collected monthly between November 2010 and August 2011 as follows i) the local veterinary authorities provided records of animal movements through the official ports of Moroni (Grande Comore), Fomboni (Moheli), and Mutsamudu (Anjouan), ii) one interviewer per island had the task of identifying undeclared animal arrivals on the coast, either in the field or from information provided by village chiefs.
Txi~N umber of seroconverted animals Number of animals in an at-risk period The incidence rate was determined using an Access database in the Laser format (available at http://livtools. cirad. fr/) [30] [31] [32]  by calculating the instantaneous risk of infection (the risk that an animal will be infected in a given period)  [30]  taking into account the risk of seroconversion, death or lost animals. The number of animals in an at-risk period represents the total number of animals in a susceptible period of RVFV infection. Incidence and seroprevalence analysis. To assess whether location had an effect on the RVFV antibody prevalence, different zones with specific ecosystems were included in the follow-up study. A Fisher's exact test was used to compare the difference in incidence of RVFV antibody acquisition and RVFV antibody prevalence between zones and islands.
Incidence was analyzed and hypotheses were proposed about relationships with environmental and climate conditions. Analysis of entomological data. A trapping session with no rain and/or wind was included in the data analysis even if no blood-sucking insects were collected. Student's t-Test was used for statistical analysis. Trade survey. The movements of animals recorded between the three islands of the Union of Comoros were mapped, as well as their potential connection with continental Africa, Mayotte and Madagascar.
Livestock longitudinal survey in relation with environmental data A total of 191 ruminants (88 cattle and 103 goats) were included in the livestock longitudinal survey: 135 animals in Grande Comore, 27 in Moheli and 29 in Anjouan. Detection of RVFV antibodies (IgM and IgG) was performed by ELISA for a total of 849 serum samples over the duration of study. Table  1  presents by date and per zone the number of animals that acquired RVFV antibodies over the duration of the livestock longitudinal survey. A total of 15 animals out of the 191 sampled acquired RVFV antibody during the study. Each of the 13 RVFV IgG ELISA positive samples were confirmed by VNT. Only one RVFV IgM ELISA positive sample was not confirmed by VNT (July 200, Moheli). This animal was confirmed RVFV IgG ELISA positive and VNT positive four months later in November 2010.
Trade survey The study highlighted movements of live ruminants between the three islands of the Union of Comoros, the African mainland, Mayotte and Madagascar (Figure  2 ). Data recorded by veterinarians and technicians showed movements of live ruminants from i) the east coast of Africa to Union of Comoros and ii) between the three islands of the Union of Comoros (Figure  2A. ). Animals were observed being landed on beaches without any controls or in secondary ''ports'' like Chindini in the south of Grande Comore. Figure  2B  represents the dynamics of live animal importations in Union of Comoros from May 2010 to July 2011. We recorded up to ten fold more ruminants imported in Grande Comore than in Moheli or Anjouan.
Acknowledgments This study was conducted in the framework of  AnimalRisk-OI , a research program on emerging animal diseases in the Indian Ocean. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the  European Commission. We thank all the Comoros farmers, veterinarians and veterinary technicians for their participation in the fieldwork as well as  S. Girard. We thank  R. Lancelot  for his help with the Laser database and incidence calculation. We thank  W. Wint ,  D. Rogers  and  D. Benz  of the  Spatial Ecology and Epidemiology Group (University of Oxford ) for providing MODIS data. We also thank  L. Cavalerie  for her personal remarks on RVF circulation in the  Union of Comoros ,  C. Sutter  for providing the striking image and  T.
This study was conducted in the framework of  AnimalRisk-OI , a research program on emerging animal diseases in the Indian Ocean, funded by  FEDER POCT (European Union ,  Regional Council of Reunion  and the  French government). The study was partially funded by  EU  grant  FP7-261504  EDENext and is catalogued by the EDENext Steering Committee as EDENext000 (http://www. edenext. eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Materials and methods Observational analytical retrospective anonymized study based on the informations contained in the Lille MH Database. The criteria of inclusion were: 1) anesthetic probands classified as MHS according to the IVCT and/or the presence of a MH mutation in the RYR1 gene in at least one family member and 2) existence of sufficient clinical information concerning the crisis. The severity of the MH crisis was classified as: death, survival after stay in intensive care unit ICU, survival without stay in ICU. The results of the IVCT: maximal force of contracture at halothane 2%, caffeine 2mmol/L, halothane 3%. The statistical analysis was carried out with a test of Chi-2 for the comparisons of frequency and a test of Mann Whitney for the nonparametric variables with p<0,05 significant.
© 2014 Krivosic-Horber et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons. org/licenses/by/4. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons. org/publicdomain/zero/1. 0/) applies to the data made available in this article, unless otherwise stated.
Acknowledgments The study was supported by the  Instituto de Salud Carlos III ,  Centro de Investigación Biomédica en Red de Salud Mental ,  CIBERSAM , as well as grant  SAF 2012-35183  to  FA (Spanish Ministry of Economy and Competitiveness , co-financed by  European Regional Development Fund, ERDF). The authors would like to thank  Bradley Londres  for his contribution in preparing the manuscript.
and discussions. Some strains were provided by the Caenorhabditis Genetics Center (CGC), which is funded by National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440). Our laboratories are supported by the Swiss National Science Foundation (SNF assistant professor grant PP00P3_133744), the Swiss Foundation for Muscle Diseases Research, and the University of Bern (to P. M. ); the French Centre National de la Recherche Scientifique and the Ecole Normale Sup erieure de Lyon (to C. V. and D. J. ); the Spanish Ministry of Economy and Competitiveness (BFU2010-15478), the European Regional Development Fund (to P. A. ); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)-Aard en Levenswetenschappen (ALW) Veni (to J. K. ); and ZonMW (Medische wetenschappen)-TOP (to B.
Acknowledgments We thank members of the  Meister and Ochsenreiter laboratories  for numerous discussions,  Sonia Karaz  and  Julie Campos  for expert technical help, Myl ene Docquier and the iGE3 genomics platform of the  University of Geneva  for next-generation sequencing (NGS) and advice, and  Iskra Katic  and the  Friedrich Miescher Institute (FMI) C. elegans laboratories  for help.
The threshold cycle value (Ct), computed for each of these genes as the average of 2 determinations was used to measure the amount of PCR product. The mean ΔCt was calculated by subtracting the mean Ct of duplicated np9 and gag measurements from the mean Ct of duplicated GAPDH measurements. The ΔΔCt values were calculated with the mean ΔCt of the 6 healthy donors. The expression factor difference was calculated by the formula 2 À ΔΔCt. Thus, the calculated relative expression provides data on how much np9 and gag gene expression differs from that found in healthy donors.
Classification and features 16S rRNA gene analysis Figure  1  shows the phylogenetic neighborhood of R. mesophilum in a 16S rRNA gene sequence-based tree. The sequence of the single 16S rRNA gene in the DSM 19309 T genome does not differ from the previously published 16S rRNA gene sequence (EF547368), which contains four ambiguous base calls. The genomic 16S rRNA gene sequence of R. mesophilum DSM 19309 T was compared with the Greengenes database for determining the weighted relative frequencies of taxa and (truncated) keywords as previously described  [7]. The most frequently occurring genera were Paracoccus (45. 3%), Loktanella (30. 3%), Rubellimicrobium (14. 0%), Methylarcula (8. 4%) and 'Pararubellimicrobium' (2. 0%) (58 hits in total). Regarding the five hits to sequences from other members of the genus, the average identity within HSPs was 94.
9%, whereas the average coverage by HSPs was 99. 3%. Among all other species, the one yielding the highest score was 'Pararubellimicrobium aerilata' (EU338486), which corresponded to an identity of 96. 3% and a HSP coverage of 98. 0%. (Note that the Greengenes database uses the INSDC (=EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification). The highestscoring environmental sequence was JF417792 (Greengenes short name 'microbial structures coalbeds located Eerduosi Basin China coalbed clone QQSB73'), which showed an identity of 98. 7% and a HSP coverage of 99. 6%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'skin' (10. 6%), 'fossa' (5. 9%), 'poplit' (4. 2%), 'forearm, volar' (3. 3%) and 'sea' (2.
Genome project history The genome of strain R. mesophilum DSM 19309 T was first selected for genome sequencing in phase I of the one thousand microbial genomes (KMG-I) project  [20] , an extension of the Genomic Ency-clopaedia of Bacteria and Archaea (GEBA)  [21] , but ultimately sequenced within the DFG funded project "Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a globally Important Clade of Marine Bacteria". The strain was chosen for genome sequencing according to a phylogenydriven target selection procedure for large scale genome-sequencing (and other) projects as routinely used for the KMG-I project  [20, 22]. The project information can be found in the Genome OnLine Database  [8]. The Whole Genome Shotgun (WGS) sequence is deposited in GenBank and the Integrated Microbial Genomes database (IMG)  [23].
Genome sequencing and assembly The genome was sequenced using a combination of two libraries (Table  2 ). The paired-end library contained inserts of an average of 420 bp in length. Illumina sequencing was performed on a GA IIx platform with 150 cycles. The first run on the Illumina GA IIx platform delivered 3. 6 million reads. In order to increase the sequencing depth, a second Illumina run was performed, providing another 7. 0 million reads. Error correction and clipping were performed by fastq-mcf  [26]  and quake  [27]. The data was assembled using Velvet  [28]. The first draft assembly from 5,400,234 filtered reads (median read length of 132 nt) resulted in more than 143 unordered contigs. To gain information about the contig arrangement an additional 454 run was performed. The paired-end jumping library of 3 kb insert size was sequenced on 1/8 of a lane.
Pyrosequencing resulted in 102,695 reads with an average read length of 199 bp, assembled with Newbler (Roche Diagnostics). The resulting assembly consisted of 261 scaffolds. Both draft assemblies (Illumina and 454 sequences) were fractionated into artificial Sanger reads of 1,000 nt in length plus 75 bp overlap on each site. These artificial reads served as an input for the phred/phrap/consed package  [29]. By manual editing, 138 contigs could be assembled on 127 scaffolds. The combined sequences provided a 129× coverage of the genome.
Genome annotation Genes were identified using Prodigal  [30]  as part of the JGI genome annotation pipeline. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Identification of RNA genes was carried out by using HMMER 3. 0rc1  [31]  (rRNAs) and tRNAscan-SE 1. 23  [32]  (tRNAs). Other non-coding genes were predicted using INFERNAL 1. 0. 2 [33]. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes -Expert Review (IMG-ER) platform  [34]. CRISPR elements were detected using CRT  [35]  and PILER-CR  [36].
Insights into the genome Plasmids The identification of plasmids is difficult because typical replication modules comprising the characteristic replicase and the adjacent parAB partitioning operon are missing  [36]. However, comprehensive BLASTP searches with plasmid replicases from Rhodobacterales revealed the presence of one RepB gene (rumeso_01479), whereas RepA-, RepABC-type and DnaA-like replicases are absent from the genome. The localization of the chromosomal replication initiator DnaA documents that scaffold 15 is part of the chromosome (Table  5 ). The 119 kb RepB type plasmid contains a postsegregational killing system (PSK) consisting of a typical operon with two small genes encoding a stable toxin and an unstable antitoxin (rumesco_01477/78  [37] ;).
Subject area Biology, parasitology More specific subject area Proteomics on the endomembrane system of Entamoeba histolytica Type of data Proteome Discoverer and Maxquant results (. txt) and list of identified proteins as tables (. xls) How data was acquired Liquid chromatography mass spectrometry in tandem (LC-MS/MS). Proteins from the internal membrane fraction of E. histolytica trophozoites were treated to obtain tryptic peptides. These were separated by HPLC coupled to an LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific) Data format.
Proteomic data analysis Data analysis was performed using Thermo Proteome Discoverer software suite (version 1. 4). For the search engine SEQUEST, the peptide precursor mass tolerance was set to 10 ppm, and fragment ion mass tolerance was set to 0. 6 Da. Carbamidomethylation on cysteine residues was used as fixed modification, and oxidation of methionine along with N-terminal acetylation was used as variable Fig. 1. Scheme of the procedure used for separation of endomembrane enriched fraction. Entamoeba histolytica subcellular fraction separation was performed as described before  [4]  from a trophozoite pellet corresponding to 2 Â 10 8 cells. The final yield of internal membrane proteins was of 50 μg/ml. modifications. Spectra were queried against the E. histolytica uniProt database. In order to improve the rate of peptide identifications percolator node in proteome discoverer was utilized with the false discovery rate (FDR) set to 1% for peptide and protein identifications.
In order to determine the absolute abundance of different proteins within a single sample we used iBAQ feature of MaxQuant version 1. 4. 0. 5 software using default search parameters  [5, 6]. The results of proteome discoverer and Maxquant searches were arranged together. The mass spectrometry proteomics data have been deposited to the open access library of ProteomeXchange Consortium (http://www. proteomexchange. org) via the PRIDE partner repository  [2]  with the dataset identifier PXD000770.
Bioinformatic analysis Proteome discoverer annotation node, which is connected to ProteinCenter web based application, was used to download categorical GO database information in the form of biological process (BF), molecular function (MF), and cellular component (CC). Maxquant and Perseus were utilized for protein identification and assignment of Interpro, KEGG, Prosite annotations along with their iBAQ values. The iBAQ values were obtained by Maxquant software and are represented in. txt files representing protein and peptide identification results of the endomembrane enriched fractions. A list showing dynamic range of internal membrane proteome of E. histolytica are represented as iBAQ values in Figs. 3 4 5. Maxquant results and analysis are found as a folder in Supplemental material 2 (Fig.
Acknowledgments This work is supported by grants to NG from the  French National Agency for Research  ( ANR-10-INTB-1301-PARACTIN ) and from the  French Parasitology Network of Excellence ParaFrap  (Grant  ANR-11-LABX0024 ). DP was supported by fellowships from the  French Ministère de la Recherche et la Technologie (MRT)  and from  Fondation pour la Recherche Médicale (FRM). GDJ is supported by the  Wellcome Trust-DBT India Alliance  (Grant  500080/Z/09/Z ).
Re-analysis of publicly available whole genome and exome massively parallel sequencing datasets Exome and whole genome sequencing data for 1293 tumours were obtained from The Cancer Genome Atlas (TCGA) and other published studies  [3] [4] [5] [6] [7] [8]. Processed variant calls reported in these studies were annotated using the Ensembl Variant effect predictor  [17]  and mutational gene frequencies computed. Binary alignment mapping (BAM) files of SF3B1 mutant tumours available in TCGA were used to assess the heterozygosity at the SF3B1 locus using ASCAT  [18].
Four indexed samples were pooled at equimolar concentrations and sequenced on a single lane of a HiSeq 2500 using SBS v3 chemistry (Illumina, San Diego, CA, USA) (2 × 76 cycles). Samples were aligned to the human genome (hg19 build 37) using TopHat version 2. 0. 8b. Raw counts of reads mapped to genes were calculated using HT-Seq (http://wwwhuber. embl. de/users/anders/HTSeq/doc/overview. html) and used as input for differential exon usage analysis using DEXSeq  [24] , with an adjusted p-value cut-off of ≤0. 1. FASTQ files from available TCGA RNA-sequencing data from SF3B1 K700E mutant (n = 8) and ER, PR, HER2 status, and PIK3CA and TP53 mutational status, and randomly matched controls (n = 16) were downloaded from the Cancer Genomics Hub (CGHub; https://cghub. ucsc. edu) and processed as above (TCGA project access number 6223).
Ethic Statement The study was approved by our Institutional Review Committee (Comitede Protection des Personnes ''Ile de France II'' # 2009-A00359-48) and all subjects provided written informed consent. The study was registered at ClinicalTrials. gov #NCT01293019 on February 9, 2011 (http://clinicaltrials. gov/ct2/show/ NCT01293019). The delay in registering the study was due to a change in the statistician responsible for the study. The authors confirm that all ongoing and related trials for this intervention are registered.