dataesr/scientific-paragraphs-categorization huggingface dataset:
Construction of first-round mutagenesis libraries and screening The objective of the directed evolution approach was to improve enzymatic activities of PaMan5A and PaMan26A, two endo-mannanases from Podospora anserina. The error-prone PCR mutagenesis round was carried out using the wild type genes as templates (GenBank HM357135 and HM357136 for paman5a and paman26a, respectively) and with the conditions appropriate to reach a number of mutations in a range of 2 to 5 mutations per kb. Indeed, a very low number of mutations per kb (i. e. , below one mutation per kb) would result in too many active variants with unchanged activity, and a high number of mutations per kb would result in too many inactive clones as reported in  [17]  (. 70% inactive clones for a mutation rate of 10 mutation per kb).
3 unit (Figure  S1 ). This increase is likely to be due to the incorporation of an arginine residue. Circular dichroism analysis of all selected mutants was also carried out to check the relative content of secondary structures in each mutant. PaMan26A and PaMan5A variants displayed the same profile compared to parental enzymes, suggesting that the folding of mutants were similar to the parental enzymes (data not shown). Regarding the pH and temperature profiles, no significant difference was observed between variants and parental enzymes (data not shown). The kinetic parameters were determined at 40uC in sodium acetate buffer 50 mM, pH 5. 2 as described in the Methods section. Paired t test was used to compare the kinetic parameters of mutants versus native enzyme. The difference was considered statistically significant when p,0.
Acknowledgments The authors want to thank  M. Haon  and  S. Grisel  for their assistance in the purification of mutants. C. Montanier  and  C. Dumon  ( LISBP, INSA, Toulouse, France ),  P. M. Coutinho  ( AFMB, CNRS, Marseille, France ),  N. Lopes Ferreira  ( IFPEN, Rueil-Malmaison, France ) and  D. Navarro  ( INRA, Marseille, France ) are acknowledged for helpful discussions and  C. B. Faulds  for proofreading of the manuscript. The plasmids and strains for Yarrowia expression experiments were generously provided by  JM Nicaud (MICALIS, INRA-AgroParisTech, France)  and  A Marty  ( LISBP, INSA, Toulouse, France ). The high-throughput screening work was carried out at the  Laboratory for BioSystems & Process Engineering (Toulouse, France ) with the equipments of the ICEO facility, dedicated to the screening and the discovery of new and original enzymes.
ICEO is supported by grants from the  Region Midi-Pyrenees , the  European Regional Development Fund  and the  Institut National de la Recherche Agronomique (INRA). This work was carried out as part of the  FUTUROL PROJECT  and the authors want to thank  OSEO Innovation  for its financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgments Studies cited from the Mazel laboratory were funded by the  Institut Pasteur , the  Centre National de la Recherche Scientifique  ( CNRS-UMR3525 ), by the  European Union Seventh Framework Programme  ( FP7-HEALTH-2011 -single-stage) -Evolution and  Transfer of Antibiotic Resistance‖ (EvoTAR)  and the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence -Integrative Biology of Emerging Infectious Diseases‖  (grant n  ANR-10-LABX-62-IBEID ). ZB was supported by a  DIM Malinf postdoctoral fellowship  ( Conseil régional d'Île-de-France ). GG is the recipient of post-doctoral research fellowships from the  Fonds de Recherche Qué becois-Nature et Technologies  and from the  Roux, Howard and Cantarini Foundation (Institut Pasteur). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
MATERIAL AND METHODS Data on stage, diagnostic procedures, treatment and follow-up were collected for a representative sample of about 13 000 patients aged 15-99 years diagnosed with colorectal cancer (International Classification of Diseases, ninth revision (ICD-9) 5 codes 1530-1539, 1540-1549) in the USA and Europe during 1996-1998. A single protocol was used, derived from the EUROCARE high-resolution protocols. 6 he European data were provided by 14 populationbased cancer registries in nine countries, four with national coverage (denoted below with an asterisk (*)). For some analyses, the data were grouped into the four European regions defined by the United Nations (UN, http://unstats. un. org/unsd/methods/m49/m49regin. htm)-Northern Europe: Finland*; Western Europe: France (Côte d'Or) and the Netherlands (North East Netherlands); Southern Europe: Italy (Genova, Ragusa and Varese), Slovenia* and Spain (Granada, Navarra and Tarragona); Eastern Europe: Estonia*, Poland (Cracow and Kielce) and Slovakia*.
Estonia is classified by the UN as being in Northern Europe, but cancer survival has resembled that in Eastern European countries  7  and Estonia was included here with Eastern Europe. US data were provided by seven statewide registries (California, Colorado, Illinois, Louisiana, New York, Rhode Island and South Carolina) from the National Program of Cancer Registries (NPCR), based at the Centers for Disease Control and Prevention. For this study, cancer registries in the EUROCARE-3 high-resolution study 8 updated follow-up to at least 5 years after diagnosis for all patients. North East Netherlands was not included in EUROCARE-3, but the registry routinely collects high-resolution data and could provide such data on virtually all patients with colorectal cancer. Most registries provided a random sample of at least 500 patients diagnosed during 1996-1998 (1997 in the USA).
Statistical analysis We analysed the distribution of stage and the number of lymph nodes examined pathologically. 9 We report the proportion of patients resected with curative intent and the distributions of stage-specific treatment for colon or rectal cancer. Data sets were excluded if data on stage and/or treatment were missing for 25% or more of patients: Ragusa was excluded from stage-specific analyses, including those on treatment related to the stage at diagnosis. Net survival up to 5 years after diagnosis was estimated by geographical area (UN region of Europe, country, registry or US state), age and stage, using flexible parametric excess hazard models. 10 Net survival is the survival of patients with cancer in the hypothetical situation where the cancer may be assumed to be the only possible cause of death; it may be interpreted as cancer survival after controlling for competing causes of death.
Mesorectal excision was not used in Estonia before 1997, which may partly explain the low survival from rectal cancer. 22 he transatlantic 12% difference in the 3-year survival in colorectal cancer survival for patients diagnosed during 1990-1991  3  was mostly attributed to the differences in stage at diagnosis. In our study of patients diagnosed in the late 1990s, the overall 5-year net survival was still higher in the 7 US states (58%) than in the 14 European regions (42-56%). The widest differences with the USA were seen in Southern (49%) and Eastern Europe (42%). The two studies differed in design, however: data from the SEER public-use data set in the USA  23  were simply adapted to the EUROCARE-2 high-resolution protocol as far as possible. In contrast, data for this study were collected directly from clinical records on both sides of the Atlantic, with a standard protocol.
Acknowledgements Some of the data for this study were collected with the support of the  Compagnia di San Paolo, Turin, Italy. Alleanza Contro il Cancro , the  Italian Cancer Network  (http://www. alleanzacontroilcancro. it) supported a CONCORD Working Group meeting for this study in London, 29-30 September 2010. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the  US Centers for Disease Control and Prevention. Contributors CA, MS, GG  and  MPC  contributed to the study design. CL, JF, TA, EA, MBL, SB, RC, ME, JPF, JG, SG, TH, MPZ, JR, CSD, MJSa, MJSc, TS, GT, RT, MV, HJW and XCW contributed to data collection. CA performed data quality control. PB prepared the life tables; CA, BR and MPC performed the data analyses.
We conducted a retrospective study on behalf of the Group of Research in Adult Acute Lymphoblastic Leukemia (GRAALL). Centers from the GRAALL were asked about patients having received nelarabine as salvage therapy because of relapse after transplantation. We recorded data concerning characteristics of the disease (leukocyte count, presence of tumoral syndrome, karyotype, molecular biology) at diagnosis and at relapse. Transplantation procedure (conditioning regimen, graft-versus-host disease [GVHD] prophylaxis) and complications (GVHD, in particular) were also investigated. Relapse was defined as the presence of more than 5% lymphoblasts as shown by bone marrow aspiration, more than 20% in the peripheral blood, or   Between 2004 and 2010, 11  patients from 5 centers received nelarabine as salvage therapy of 14 patients with T-ALL/LL relapsing after HSCT.
Classification and features 16S rRNA analysis A representative genomic 16S rRNA sequence of strain Z-7692 T was compared using NCBI BLAST  [3, 4]  under default settings (e. g. , considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  [5]  and the relative frequencies of taxa and keywords (reduced to their stem Standards in Genomic Sciences  [6] ) were determined, weighted by BLAST scores. The most frequently occurring genera were Spirochaeta (91. 1%), Treponema (5. 8%) and Cytophaga (3. 1%) (29 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 99. 6%, whereas the average coverage by HSPs was 99. 0%. Regarding the 19 hits to sequences from other members of the genus, the average identity within HSPs was 89.
1%, whereas the average coverage by HSPs was 78. 9%. Among all other species, the one yielding the highest score was Spirochaeta asiatica (NR_026300), which corresponded to an identity of 96. 6% and an HSP coverage of 98. 8%. (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 AF454308 (Greengenes short name 'spirochete clone ML320J-13'), which showed an identity of 90. 6% and an HSP coverage of 99. 3%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were 'microbi' (10. 5%), 'mat' (8. 8%), 'hypersalin' (6. 3%), 'new' (4. 2%) and 'world' (4. 1%) (221 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found, indicating that this species is rarely found in environmental sequencing.
Lineages with type strain genome sequencing projects registered in GOLD  [13]  are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks (see  [14] [15] [16] [17] [18] [19] [20]  and CP003155 for Sphaerochaeta pleomorpha, CP002903 for Sphaerochaeta thermophila, CP002696 for Treponema brennaborense, CP001841 for T. azotonutricium and CP001843 for T. primitia. Note: Spirochaeta caldaria, S. stenostrepta and S. zuelzerae were effectively renamed to T. caldaria, T. stenostrepta and T. zuelzerae in  [15] , however, the names have not yet been validily published. Table  1. Classification and general features of S. africana Z-7692 T according to the MIGS recommendations  [21]  and the NamesforLife database  [22].
Genome project history This organism was selected for sequencing on the basis of its phylogenetic position  [36, 37] , and is part of the Genomic Encyclopedia of Bacteria and Archaea project  [38]. The genome project is deposited in the Genomes On Line Database  [13]  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI) using state of the art sequencing technology  [39]. A summary of the project information is shown in Table  2.
Genome sequencing and assembly The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website  [43]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 511 contigs in one scaffold was converted into a phrap  [44]  assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (459. 3 Mb) was assembled with Velvet  [45]  and the consensus sequences were shredded into 1. 5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 234. 5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters areconsed -a 50 -l 350 -g -m -ml 21.
The Phred/Phrap/Consed software package  [44]  was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [43], Dupfinisher  [46] , or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J. -F. Chang, unpublished). A total of 132 additional reactions were necessary to close some gaps and to raise the quality of the final contigs. Illumina reads were also used to correct potential base errors and increase con-sensus quality using a software Polisher developed at JGI  [47]. The error rate of the final genome sequence is less than 1 in 100,000.
Genome annotation Genes were identified using Prodigal  [48]  as part of the DOE-JGI genome annotation pipeline  [20] , followed by a round of manual curation using the JGI GenePRIMP pipeline  [49]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes -Expert Review (IMG-ER) platform  [50].
Phylogenomic analyses According to the results from 16S rRNA gene analysis (Figure  1 ), for a comparative analysis the genome sequences of S. africana (GenBank ID CP003282), S. alkalica (GenBank ID PRJNA169743), S. caldaria (CP002868) and S. smaragdinae (CP002116) were used. The genomes of S. caldaria (3. 2 Mb, 2,928 protein-coding genes), S. africana (3. 3 Mb, 2,874 protein-coding genes) and S. alkalica (3. 4 Mb, 2,938 proteincoding genes) have a similar size, whereas the genome of S. smaragdinae (4. 7 Mb, 4,363 proteincoding gene) is significantly larger in size. S. caldaria and S. smaragdinae have similar G+C contents, 46% and 49%, respectively. The G+C con-tents of S. alkalica and S. africana are significantly higher, 61% and 58%, respectively. An estimate of the overall similarity between the genomes of S.
Acknowledgements We would like to gratefully acknowledge the help of  Helga Pomrenke  for growing S. africana cultures and  Evelyne-Marie Brambilla  for DNA extraction and quality control (both at DSMZ). This work was performed under the auspices of the  US Department of Energy's Office of Science, Biological and Environmental Research Program , and by the  University of California ,  Lawrence Berkeley National Laboratory  under contract No. DE-AC02-05CH11231 ,  Lawrence Livermore National Laboratory  under Contract No. DE-AC52-07NA27344 , and  Los Alamos National Laboratory  under contract No. DE-AC02-06NA25396 ,  UT-Battelle  and  Oak Ridge National Laboratory  under contract  DE-AC05-00OR22725 , as well as  German Research Foundation  ( DFG) INST 599/1-2.
Achieved results were contrasted with results from the removal of uranium  [31, 33] , discoloration of methylene blue  [34]  and removal of arsenic  [35]. Available data validate the suitability of the EDTA test to characterize the intrinsic reactivity of Fe 0 materials. The present study extends this effort by relating the intrinsic reactivity, the Fe 0 particle size/shape and the hydraulic conductivity of Fe 0 filters for three selected materials. A total of 9 Fe 0 materials making up 10 samples (ZVI1 through ZVI10) have been characterized by the EDTA test. Three selected Fe 0 materials (ZVI1, ZVI9, ZVI10) were then used in column studies to characterize the evolution of (i) Fe release, (ii) methylene blue (MB) discoloration and (iii) hydraulic conductivity. A 2. 0 mg L -1 MB solution was used as an indictor for the impact of iron corrosion on the filtration process.
Metallic iron (Fe 0 ) A total of 10 samples (ZVI1 through ZVI10) from 9 Fe 0 materials were tested. The materials were obtained from various sources, in different forms and grain sizes. The main characteristics of these materials are summarised in Tab. 2. Fig. 1  depicts micrographs of 500 mg of each sample using a portable camera (Keyence VHX-500F). No information about manufacturing processes (e. g. , raw material, heat treatment) was available to assist with subsequent data interpretation. The average elemental composition of the materials as specified by the suppliers are well-documented in the literature  [25, 26, 41]  and are not repeated here. the efficiency of three of them for the discoloration of methylene blue in column studies. A part from the Rheinfelden material (iPutcec GmbH & Co) which was tested in two fractions, all other materials were used in their typical state and form ('as received' state) in which they might be used for field applications.
Acknowledgements For providing the iron materials investigated in this study the authors would like to express their gratitude to iPutec  GmbH (Rheinfelden, Germany) ,  Ann-Marie Gottinger  from  Mainstream Water Solutions Inc. (Regina, Canada ) and  Paolo S. Calabrò  from the  University Calabria (Italy). Mohammed Saad  ( Leesu, Ecole des Ponts ParisTech, Marne La Vallée ),  Mehmet A. Oturan  and  Hugo Gonzales  ( LGE, Institute IFI, Marne la Vallée ) are thanked for their help, their grateful discussion and the possibility to use their spectrophotometer. Tanja Stegemann  ( Geoscience Museum -University of Göttingen ) is acknowledged for the micrographs. This work was partly supported by the " Service de Coopération et d'Action Culturelle" (SCAC)  from the  France Embassy in Yaoundé (Cameroun).
At least one track should have p T > 1. 7 GeV/c and IP χ 2 with respect to the primary interaction greater than 16. The IP χ 2 is defined as the difference between the χ 2 of the primary vertex (PV) reconstructed with and without the considered track. A multivariate algorithm is used for the identification of secondary vertices consistent with the decay of a b hadron  [10]. The results presented in this paper use the full 2011 dataset corresponding to an integrated luminosity of 1. 0 fb -1 of pp collisions at √ s = 7 TeV. Candidate B 0 decays are formed by combining a D * -→ (D 0 → K + π -)π -candidate with either a single bachelor or triple-bachelor combination. All final state tracks are required to have p T in excess of 500 MeV/c 2 , except for the slow pion produced in the D * -decay, which must have p T in excess of 100 MeV/c.
In the simulation, pp collisions are generated using Pythia 6. 4  [12]  with a specific LHCb configuration  [13]. Decays of hadronic particles are described by EvtGen  [14]  in which final state radiation is generated using Photos  [15]. The interaction of the generated particles with the detector and its response are implemented using the Geant4 toolkit  [16]  as described in Ref. [17]. The simulated events are passed through an emulation of the hardware trigger and then through the full software trigger as run on data. The total kinematic efficiency, kin , is determined from the simulation as the fraction of events that pass all reconstruction and selection requirements and the trigger. The fraction of selected events that pass the particular trigger selection relative to the total number of selected events is taken to be the trigger pass fraction, f trig.
Search for excited charm resonances Using the same dataset, a search for orbital excitations of charm resonances (D * * ) contributing to the B 0 → D * -π + π -π + final state is performed. The selection is identical to that presented above, except the lower p T cut on bachelors is reduced to 300 MeV/c. Events that have been triggered via tracks not associated with the B 0 → D * -π + π -π + candidate are also included. The signal purity is only slightly reduced as a result of the looser selection. The corrected mass M (D * -π + ) = m(D * -π + ) -m(D * -) + m(D * -) PDG MeV/c 2 is computed for each D * -π + combination, in which the contribution to the mass resolution from the D * -mass measurement is removed. To statistically subtract the background, each event is weighted using sWeights  [22]  obtained from the B 0 → D * -π + π -π + invariant mass fit.
ACKNOWLEDGMENTS This work was supported by a  Hartwell Foundation Individual Biomedical Research Award , a  Basil O'Connor Starter Scholar Award  from the  March of Dimes Foundation , and a  National Institutes of Health   Director's New Innovator Award  ( DP2-OD008586 ) to C. A. G. ; a  Canadian Institute of Health Research  grant to J. P. T. ; and support from the  Association Française contre les Myopathies  to V. M. D. G. O. is supported by the  Duke Biomedical Engineering Howard Clark Fellowship  and an  American Heart Association Predoctoral Fellowship. P. I. T. is supported by a  Graduate Research Fellowship  from the  National Science Foundation  and M. T. B. is supported by a  Pratt Undergraduate Research Fellowship. KamelMamchaoui assisted in the development of the cell lines and the platform for immortalization of human cells at the  Myology Institute in Paris.
76), the EFSA considered 26 sulphur-containing heterocyclic compounds evaluated by the JECFA at its 59 th meeting. Since publication of FGE. 76, one substance, thiazole. 028], is no longer supported by Industry for use as a flavouring substance in Europe and will therefore not be considered any further. The present revision is made due to inclusion of one additional substance,. 004], cleared for genotoxicity concern in FGE. 224. Additionally, new toxicity data have become available  for 5, 4, 3,. Therefore, the present revision of FGE. 76, FGE. 76Rev1, considers 26 flavouring substances evaluated by the JECFA. The Panel concluded that all 26 Register substances in the JECFA flavouring group of sulphurcontaining heterocyclic compounds are structurally related to the 59 thiazoles, thiophenes, thiazoline and thienyl derivatives from chemical group 29 and miscellaneous substances from chemical group 30 evaluated by EFSA in the Flavouring Group Evaluation 21, Revision 3 (FGE.
Conclusion on genotoxicity It is concluded that the genotoxicity data are limited and that genotoxicity could not be assessed adequately for the flavouring substances in the present revision of FGE. 21, Revision 3. However, except for the two dihydrothiazines For a summary of in vitro genotoxicity data considered by EFSA, see Table  3. In vitro data on. 004] Bacterial Reverse Mutation Assay 5-Methyl-2-thiophenecarbaldehyde was tested for the induction of gene mutations in the Salmonella typhimurium strains TA98, TA100, TA1535, TA1537 and TA102 both in the absence and in the presence of Aroclor induced rat liver S9-mix. Three independent experiments were performed  (Beevers, 2009 ). An initial toxicity range-finding experiment was carried out in the absence and presence of S9-mix in strain TA100.