dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods A total of 109,179 individuals of European descent from 36 studies were included in the analysis (Online Table  1 ), comprising 19 in general populations and 10 studies in patients with ACS. In addition, we included 4 case control studies of coronary artery disease, 1 cohort of patients with established arterial vascular disease or risk factors for cardiovascular disease (SMART [Second Manifestations of ARTerial disease] study), and 1 nested case-control study of coronary artery restenosis in patients with ACS undergoing percutaneous coronary intervention (GENDER [GENetic Determinants of Restenosis] study). These additional studies did not contribute toward the analyses set in general population or ACS studies, and were analyzed and reported separately (Online Appendix). Finally, tissue samples from 1 cohort of patients undergoing aortic valve surgery (ASAP [Advanced Study of Aortic Pathology]) were used to investigate the association of single-nucleotide polymorphisms (SNPs) in PLA2G2A with mRNA expression in liver, mammary artery, aorta, and heart with an external data source comprising 206 transplant donor liver samples used for replication  (14).
Second, given the impact of the SNP The observational analyses were adjusted for age, sex, BMI, BP, T2D, LDL-C, HDL-C, and TG in general population cohorts (corresponding to Model 3 in Fig. 1 ) and for age, sex, BMI, and BP in ACS cohorts (corresponding to Model 2 in Fig. 1 ). Abbreviations as in Figure  1. JACC Vol. 62, No. 21, 2013  Holmes et al. November 19/26, 2013 November 19/26, :1966-76 -76  Secretory Phospholipase A 2 -IIA and Cardiovascular Disease on sPLA 2 enzyme activity was more modest than its effect on sPLA 2 -IIA mass, our genetic analyses do not exclude a possible causal role of other isoforms such as sPLA 2 -III, -V, and -X in cardiovascular disease. However, our genetic data do provide clear evidence against a causal role of sPLA 2 -IIA mass in incident MVE in the general population.
761. 70), and the Dutch Inter University Cardiology Institute Netherlands (ICIN). GP is supported by the Canada Research Chair in Genetic and Molecular Epidemiology. The EPIC-NL study was funded by the Europe Against Cancer Programme of the European Commission (SANCO), Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, Dutch Cancer Society; ZonMW the Netherlands Organisation for Health Research and Development, World Cancer Research Fund (WCRF) (the Netherlands). Genotyping was funded by IOP Genomics grant IGE05012 from Agentschap NL. Folkert W. Asselbergs is supported by a clinical fellowship from the Netherlands Organisation for Health Research and Development (ZonMw grant 90700342). The FAST-MI study is sponsored by the French Society of Cardiology and has been supported by a grant from La Caisse Nationale de l'Assurance Maladie (CNAM) and unrestricted grants from Pfizer and Servier.
The WHII study has been supported by grants from the Medical Research Council; British Heart Foundation; Health and Safety Executive; Department of Health; National Heart, Lung, and Blood Institute (NHLBI: HL36310) and National Institute on Aging (AG13196), U. S. , NIH; Agency for Health Care Policy Research (HS06516); and the John D. and Catherine T. MacArthur Foundation Research Networks on Successful Midlife Development and Socio-economic Status and Health. Heart and Health Study is supported by funding from the British Heart Foundation (BHF) and the Department of Health Policy Research Programme (England). Human CVD genotyping of the BWHHS was funded by the BHF.
( PG/07/131/24254 ). D. A. L. , T. M. P. , T. R. G. , and I. N. M. D. work in a center that receives funds from the  UK Medical Research Council  ( G0600705 ) and  University of Bristol. The EAS has been supported by grants from the  British Heart Foundation. Recruitment of the CAD cases for the  BHF-FHS Study  was funded by the  British Heart Foundation. Controls were collected as part of the  Wellcome Trust Case Control Consortium Study. Genotyping was funded by the  British Heart Foundation  and the  European Union FP6 Cardiogenics Study. Recruitment and genotyping of the  GRAPHIC Study  was funded by the  British Heart Foundation. N. J. S. holds a Chair funded by the  British Heart Foundation  and is an NIHR Senior Investigator. Z. M. holds a Chair funded by the  British Heart Foundation.
Support for genotyping was provided by the  Netherlands Organisation of Scientific Research NWO Investments  (nr. 175. 010. 2005. 011 , 911-03-012 ), the  Research Institute for Diseases in the Elderly  ( 014-93-015 ;  RIDE2 ), the  Netherlands Genomics Initiative (NGI) / Netherlands Consortium for Healthy Aging (NCHA)  project nr. 050-060-810. Jacqueline Witteman  is supported by  NWO  grant (vici,  918-76-619 ). Abbas Dehghan is supported by  NWO  grant (veni,  916. 12. 154 ) and the  EUR Fellowship. The research of the PROSPER study has been funded by the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement n  HEALTH-F2-2009-223004. GRACE-Scotland  was supported by an unrestricted educational grant from sanofi-aventis,. KAROLA: The study was supported in parts by the  Association of German Pension Fund Agencies , the  German Federal Ministry of Education and Research  (# 01GD9820/0 ), and the  Pitzer Foundation (Bad Nauheim, Germany ).
UDACS was supported by a clinical training fellowship (JWS:BDA: RD 01 / 0001357 ) from  Diabetes UK. GENDEMIP: supported by the project ( Ministry of Health, Czech Republic ) for development of research organization  00023001  ( IKEM, Prague, Czech Republic )-Institutional support. UCP: The project was funded by  Veni grant Organization for Scientific Research (NWO) , Grant no. 2001. 064Netherlands  Heart Foundation (NHS) , and  TI Pharma  Grant  T6-101  Mondriaan. S Yusuf  holds the  Heart and Stroke Foundation/ Marion W Burke Chair  in cardiovascular diseases. PROCARDIS was supported by the  British Heart Foundation ; by the  European Community Sixth Framework Programme  (grant number  LSHM-CT-2007-037273 ); and by  AstraZeneca. A. B. , M. F. , and H. W. are supported by the  British Heart Foundation Centre for Research Excellence in Oxford  and the  Wellcome Trust   core award  ( 090532/Z/09/Z ).
Anders Hamsten  obtained support for this project from the  Swedish Heart-Lung Foundation ; from the  Swedish Medical Research Council  (grant number  8691 ); from the  Knut and Alice Wallenberg Foundation ; from the  Karolinska Institute ; and from the  Stockholm County Council  (grant number  560183 ). Dr. Schwartz , through his institution, has received research grants from  Anthera ,  Resverlogix ,  Roche , and sanofi-aventis. The MIRACL study was supported by  Pfizer. CCHS: Supported by The  Danish Medical Research Council and The Research Fund at Rigshospitalet ,  Copenhagen University Hospital. The Whitehall II study is supported by the  UK Medical Research Council  ( K013351 ), the  British Heart Foundation , the  ESRC , the  U. S. NIH  ( R01 HL036310 ;  R01 AG034454 ) Health and Safety Executive; the  Department of Health ; the  National Heart, Lung, and Blood Institute (NHLBI ;  HL36310 ); the  National Institute on Aging  ( AG13196 ); the  Agency for Health Care Policy Research  ( HS06516 ); and the  John D.
The WHII study has been supported by grants from the Medical Research Council; British Heart Foundation; Health and Safety Executive; Department of Health; National Heart, Lung, and Blood Institute (NHLBI: HL36310) and National Institute on Aging (AG13196), U. S. , NIH; Agency for Health Care Policy Research (HS06516); and the John D. and Catherine T. MacArthur Foundation Research Networks on Successful Midlife Development and Socio-economic Status and Health. Heart and Health Study is supported by funding from the British Heart Foundation (BHF) and the Department of Health Policy Research Programme (England). Human CVD genotyping of the BWHHS was funded by the BHF The ASAP study was supported by the Swedish Research Council (12660: P. E. ), the Swedish Heart-Lung Foundation (20090541: P. E.
), the European Commission (FAD, Health F2 2008 200647: P. E. ), a donation by Fredrik Lundberg (A. F. C. and P. E. ). Dr. Swerdlow is supported by a Medical Research Council Doctoral Training Award. M. Scholz was funded by LIFE-Leipzig Research Center for Civilization Diseases (LIFE Center, Universität Leipzig). LIFE-Leipzig Research Center for Civilization Diseases is funded by means of the European Union, by the European Regional Development Fund (ERFD) and by means of the Free State of Saxony within the framework of the excellence initiative. This publication is supported by LIFE-Leipzig Research Center for Civilization Diseases, Universität Leipzig). LIFE is funded by means of the European Union, by the European Regional Development Fund (ERFD) and by means of the Free State of Saxony within the framework of the excellence initiative.
Implementation of CTMC-COB physics models using the Geant4-DNA extension In a private version of the Geant4-DNA extension, ionizing processes for protons and neutral hydrogen atoms in liquid water and DNA nucleobases were implemented. These processes include single electron capture, single ionization, double ionization and transfer ionization for protons as well as single ionization and stripping for hydrogen atoms. Each process computes the total cross section of the corresponding physical interaction and fully describes the final state of the system (incident projectile energy loss, production of secondary electrons. ) according to the CTMC-COB approach described above. Molecular binding energies for DNA bases have been extracted from  [4, 5]. CTMC-COB cross sections have been pre-tabulated and are directly interpolated -step by step -by the Geant4-DNA software for projectile energies ranging from 10 keV up to 1 MeV.
Acknowledgments The  Geant4-DNA  project has received funding from the  French Agence Nationale de la Recherche  contract number  ANR-09-BLAN-0135-01  and from the  European Space Agency  under contract number  AO6041-22712/09/NL/AT. This work was also supported by the  International Associated Laboratory ''France Korea Particle Physics Laboratory'' (FKPPL) , by the  France-Korea Partenariat Hubert Curien (PHC) STAR program  ('' PROTEUS '' project) and by the  National Nuclear R&D Program  through the  National Research Foundation of Korea  ( 2011-0020782 ).
Acknowledgements The authors are indebted to  Prof. B. Szewczyk  for providing the HA gene and  Prof. K. Jaszczak  for samples of hen blood. We are grateful to  Dr A. Anielska-Mazur  for help with confocal microscopy and to  A. Krzewski  for technical assistance. This work was in part supported by grant  N N302 505738  from the  Polish National Science Centre  and by the  CLG  grant no. 982385  from the  NATO.
16S rRNA data analysis The sequences were assigned to samples as a function of their sample-specific barcodes. The sequences were then checked for the following criteria  [14] : (i) an almost perfect match with the barcode and primers; (ii) at least 240 nucleotides in length (not including barcodes and primers); and (iii) no more than two undetermined bases (denoted by N). By "an almost perfect match", we mean that one mismatch/deletion/insertion per barcode or per primer was allowed. Each pyrosequenced dataset that passed quality control was assigned to a family with the RDP classifier (version 2. 1, http://rdp. cme. msu. edu) with a confidence threshold > 80%. The Chao richness estimate was calculated with the Mothur software package (for more details, see http://www. mothur. org/wiki/Chao).
Denaturing gradient gel electrophoresis (DGGE) The variable V3 region of the 16S rRNA gene was amplified using the universal bacterial primers F357-GC and R518  [15, 16]. The PCR and temperature program have been described elsewhere  [17]. The resulting 16S rRNA amplicons were analyzed by DGGE fingerprinting analysis (the D-Code System from Bio-Rad, Nazareth, Belgium) using 35% to 70% denaturing gels, as previously described  [16]. Each lane received 30 μl of PCR product and electrophoresis was performed at 70 V for 990 min. Next, the DGGE gels were stained for 30 min with 1 X SYBR Gold nucleic acid gel stain (S-11494; Invitrogen, Merelbeke, Belgium) in 1 X TAE buffer (Bio-Rad), and the band profiles were digitized and visualized with a charge-coupled device (CCD) camera and Quantity One software (Bio-Rad).
A more in-depth analysis of the cecal and fecal microbiome was carried out via 454 pyrosequencing of the V5-V6 region of the 16S rRNA (Table  1 , Figures  3  and 4 ). We generated a dataset consisting of 197,143 filtered, high-quality 16S rRNA gene sequences (mean ± SD number of sequences per sample: 11,596 ± 6060). With operational taxonomic unit (OTU) cut-offs of 0. 03, 0. 05 or 0. 10, the samples from the Cd, Pb and control groups did not differ significantly in terms of microbial richness (as estimated by the Chao richness index) or biodiversity (assessed by a nonparametric Shannon index). With an OTU cut-off of 0. 03, the mean number of clusters was 1244 ± 381. The abundance of the two major phyla (the Firmicutes and Bacteroidetes) was similar in all three groups, whereas there were few Actinobacteria (Figure  3 ).
Immunoreactivity was visualized by chemiluminescence (GE Healthcare). The amount of PrP present in each fraction was determined by the GeneTools software after acquisition of chemiluminescent signals with a GeneGnome digital imager (Syngene, Frederick, Maryland, United States). The PrP sedimentation profiles obtained by immunoblot were normalized to units and decomposed using multiple Gaussians fits procedures with a maximum entropy minimization approach.
Acknowledgments We thank  J. Castilla ,  C. Soto  ( University of Texas Medical Branch, Galveston, USA. ),  O. Andreoletti  ( INRA-ENVT, Toulouse, France ) for initiating us to PMCA and the staff of  Animalerie Rongeurs  ( INRA, Jouyen-Josas, France ) for excellent animal care. We thank  S. G. Victoria  ( Pasteur Institute, Paris ) for helpful comments.
5, 2, 3, 4 and 8 hours; n = 3 mice per time point (population PK). Compound 9. dose level: po dose, 50 mg Kg 21 , 20 ml Kg 21 vol. adm. ; vehicle po PK (suspension): Water-1% methylcellulose (1% MC); sampling scheme: 15, 30 and 45 minutes, 1, 2, 4, 8 and 24 hours; n = 3 mice (individual PK). Analytical method, sensitivity: LC/MS, LLQ = 1-5 ng mL 21 in 25 mL blood; data analysis: Non-compartmental analysis (NCA) with WinNonlin Phoenix 6. 3 (Pharsight, Certara L. P); supplementary analysis with GraphPad Prism 5 (GraphPad Software, Inc).
The cytotoxicity of the compounds was determined using both Human hepatocarcinoma (HepG2) and normal African green monkey kidney epithelial (Vero) cells. Although compounds 5, 6 and 7 gave MICs 1-2 dilutions higher than the parent compounds (0. 3 mM for 5 versus 0. 16 mM for 2, 0. 6 mM for 6 versus 0. 2 mM for 3, 0. 6 mM for 7 versus 0. 16 mM for 4, see Tables  1  and 3 ), these values were counterbalanced by moderate reductions in the HepG2 cytotoxicity data (20. 08 mM for 5 versus 24. 01 mM for 2,. 25 mM for 6 versus 15. 2 mM for 3, 32. 9 mM for 7 versus 5. 9 mM for 4, see Tables  1  and 3 ). For all the tested compounds, the MICs in the LORA were higher than those obtained under aerobic conditions (. 13. 4-72. 47 mM versus 0. 3-0. 6 mM, see Table  3 ), a common result for many known anti-TB drugs including isoniazid  [11].
Acknowledgments We gratefully acknowledge  Leticia Huertas  for pharmacokinetic studies, Veronica  Sousa Morcuende  and  Iliana Mir Casamayor  for efficacy studies,  Antonio Martı  ´nez and team for essential animal lab upkeep and maintenance,  Esther Pe  ´rez-Herran,  Carolina Gonzalez , and  Pedro Alfonso Torres  for in vitro biology,  Marı ´a Teresa Fraile  for formulation, Ana A ´lvarez for physical chemical evaluations,  Sophie Huss ,  A ´ngel Santos , and  O ´scar Atienza  for in vitro DMPK studies, and  Raquel Ferna  ´ndez for helpful discussions.
This work was supported by  Istituto Pasteur Fondazione Cenci-Bolognetti (Italy) ,  MIUR-PRIN 2008  (Italy),  MIUR 2011 (Progetti di Ricerca di Ateneo) (Italy)  and  Tres Cantos Open Lab Foundation. The research leading to these results also received funding from the  European Union 's 7th framework programme ( FP7-2007-2013)  under grant agreement no  261378. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Furthermore, little or no information is currently available regarding the stability of export complexes in the cell nucleus. This is important in the context of viral export, as continuous dissociation and reassociation of Rev to the viral RNA would allow spliceosome assembly and splicing of the RNA. We used FRAP to measure the mobility of Rev and CRM1 in the nucleus and at the viral sites of transcription. Fitting the data showed that two exponentials correctly described the recovery of Rev, whereas that of CRM1 required three exponentials. Comparison with the mobility of the proteins in the nucleoplasm indicated that the fast component corresponded to the free protein, whereas the slow component represented the RNA-bound form. Moreover, the slow component of Rev and CRM1 nicely overlapped with each other and with the recovery of the RNA itself.
ACKNOWLEDGMENTS The help of  Maria Carmo-Fonseca ,  José Rino , and the members of the Bertrand and Kjems teams are gratefully acknowledged. We thank the  Montpellier RIO Imaging (MRI)  facility for the microscopy support and advice. This work was supported by the  Danish Research Council for Independent Research, SIDACTION  and  ANRS. I. N. was supported by  Aarhus University  and an  EMBO  fellowship. FRM supported F. M. and Sidaction supported U. S. Received January 7, 2013; accepted September 13, 2013.
All studies were approved by local ethics committees and all participants provided written informed consent. Each study performed genome-wide association testing for age at menarche or menopause across 2. 5 million imputed SNPs, based on linear regression under an additive genetic model. Individual study data were meta-analysed using the METAL software package; genomic control (GC) adjustments were applied. We considered P-values of ,5 × 10 28 to indicate genome-wide significance.
denticariosi, V. dispar, V. montpellierensis, V. parvula, V. ratti and V. rogosae, that were used as reference data (Figures  4  and 5 ). The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, 100 peaks at most were taken into account and compared with the spectra in the database. The MALDI-TOF score enabled the predictive identification and discrimination of the tested species from those in a database: a score > 2 with a validated species enabled identification at th0e species level, and a score < 1. 7 did not enable any identification. No significant score was obtained for strain NP3 T against the Brüker database, suggesting that our isolate was not a member of a known species. We added the spectrum from strain NP3 T to our database for future reference (Figure  4 ).
Genome project history The organism was selected for sequencing on the basis of its phenotypic differences, phylogenetic position and 16S rRNA similarity to other members of the genus Megasphaera, and is part of a study of the human digestive flora aiming at isolating all bacterial species within human feces  [1, 2]. It was the third genome of a Megasphaera species and the first sequenced genome of M. massiliensis sp. nov. The GenBank ID is CAVO00000000 and consists of 106 large contigs. Table  3  shows the project information and its association with MIGS version 2. 0 compliance  [47].
Genome annotation Prodigal  [48]  with default parameters was used to predict the Open Reading Frames (ORFs). The predicted ORFs were excluded if they spanned a sequencing gap region. Protein functional assessment was obtained by comparison with sequences in the GenBank  [49]  and Clusters of Orthologs Groups (COG) databases using BLASTP. The rRNA and tRNA were identified using RNAmmer  [50]  and tRNAscan-SE 1. 21  [51]  respectively. SignalP  [52]  and TMHMM  [53]  were used to predict signal peptides and transmembrane helices, respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans.
Artemis  [54]  was used for data management and DNA Plotter  [55]  was used for visualization of genomic features. PHAST was used to identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids  [56]. To estimate the mean level of nucleotide sequence similarity at the genome level between M. massiliensis and another 5 members of the family Veillonellaceae, orthologous proteins were detected using the Proteinortho software with the following parameters: e-value 1e-5, 30% percentage of identity, 50% coverage and algebraic connectivity of 50%  [57] , and genomes compared two by two. For each pair of genomes, we determined the mean percentage of nucleotide sequence identity among orthologous ORFs using BLASTn.
Weak reactions observed for amygdaline and potassium 2-cetogluconate production, and glycerol and D-arabinose fermentation. Cells are susceptible to amoxicillin, amoxicillin-clavulanic acid, ceftriaxone, imipenem and doxycycline, but resistant to vancomycin, erythromycin, rifampicin, trimethoprim/sulfamethoxazole, metronidazole, and ciprofloxacin. The G+C content of the genome is 50. 2%. The 16S rRNA and genome sequences are deposited in Genbank under accession numbers JX424772 and CAVO00000000, respectively. The type strain NP3 T (= CSUR P245 = DSM 26228) was isolated from the fecal flora of an HIV-infected patient in Marseille, France.
subtilis subsp. subtilis and belongs to a clade demarcated as the putative ecotype 10 (3). Strain PS216 resides in the same quorum-sensing pherotype group as 168  (4, 5). The genome sequence of B. subtilis PS216 was generated as described in Koren et al. (6). Briefly, 274 Mb of PacBio long-read data were error corrected with 150 bp MiSeq data using the pacBioToCA pipeline, resulting in approximately 71 Mb of corrected long reads that were then assembled by the Celera assembler. This assembly contained 146 contigs, 90% of the assembly being in 26 contigs that are Ͼ42 kb. The initial assembly yielded a total of 112 single-nucleotide changes compared to the reference strain 168 (accession no. NC_000964) and 140 single-nucleotide polymorphisms (SNPs) compared to strain NCIB3610 (accession no. NZ_CM000488).
We anticipate that this sequence information for PS216 will facilitate comparative studies of the development and physiology in Bacillus species. Nucleotide sequence accession numbers. This Whole-Genome Shotgun project has been deposited at DDBJ/EMBL/ GenBank under the accession no. AQGR00000000. The version described in this paper is the first version, accession no. AQGR01000000.
Patient population The use of resected lung tissues was approved by the regional investigational review board (Comité de Protection des Personnes Ile de France VIII, Boulogne-Billancourt, France; accession numbers: DC 08 09 45 and DC 11 10 05) and written informed consent was obtained from each patient. Lung tissues were obtained from 25 patients (mean±SD age: 63±3 years; M/F=18:7; FEV 1 /FVC ratio: 0. 86±0. 06; smokers/exsmokers: 14:11, pack-years: 41±5) undergoing surgical lung resection. None of the patients had undergone prior chemotherapy or radiotherapy.