dataesr/scientific-paragraphs-categorization huggingface dataset:
Fungal strains The 90 reference filamentous fungus strains corresponding to 30 distinct species that were used to construct the eight distinct reference mass spectrum libraries are detailed in Table  6. Of the 90 reference strains, 63 strains were graciously provided by the BCCM/IHEM (Belgian coordinated collection of microorganisms, Scientific Institute of Public Health, Mycology and Aerobiology Section, Brussels, Belgium), and 3 strains were provided by the Pasteur Institute (Paris, France). The remaining 24 strains were clinical isolates from the Marseille University Hospital mycology laboratory, which were accurately identified via DNA sequence analysis as described below. All strains used to construct the reference database are preserved in the BCCM/IHEM collection. The identification performance of each reference library was tested using 200 clinical isolates from the Marseille University Hospital mycology laboratory.
Each deposit was then covered with 1 μL of a freshly prepared solution of α-cyano-4-  Constructing the reference mass spectra (RMS) The RMS were established by combining i) 4 raw spectra obtained from one subculture (RMS4); ii) 10 raw spectra obtained from one subculture (RMS10); iii) 20 raw spectra, 10 from two subcultures each (RMS20); or iv) 40 raw spectra, 10 from four subcultures each (RMS40) of a given reference strain using the "MSP creation" function of the MALDI Biotyper v2. 1 software (Table  7 ). The following settings were applied (Bruker's default parameters): Max. Mass Error of each single spectrum: 2000; Desired Mass Error of the MSP: 200; Desired Peak Frequency Minimum: 25%; and Max. Desired Peak Number of the MSP: 70. The modulation of the number of peaks and desired peak frequency minimum of the MSP creation parameters has been tested regarding the B1 library, and the modified parameters were tested on the B7 database (Table  4 ).
MALDI-TOF MS-based identification of clinical isolates Raw mass spectra were obtained from clinical isolates using the same procedure as for the reference strains with the exception that the supernatant were deposited in quadruplicate. The deposits, referred to as spots 1, 2, 3, and 4, correspond to the first, second, third, and fourth extraction supernatant deposit of each sample, respectively. The raw MS data for each spot was successively matched to the eight reference libraries, and the resulting "best match" LS values were calculated using MALDI Biotyper software. An alternate identification process was assessed by constructing an MSP with the four spots corresponding to each of the clinical isolates and comparing isolate MSP with each of the RMS in the libraries. The interpretation of the results was initially performed independently of the LS value.
Statistical analysis The concordant and non-concordant identification results were compared two by two using the paired and non-parametric McNemar's test. The results of the quantitative variable LS analysis were compared using the non-parametric rank sum test of the Kruskall-Wallis test. When the results of the Kruskall-Wallis test indicated a statistical difference between the LS values derived from the different mass spectral libraries, a post hoc statistical analysis was performed, which involved a pairwise comparison of the LS values obtained from each library using the Wilcoxon signed-rank test with Bonferroni adjustment. These analyses were performed using R software (http://www. r-project. org/) with the MASS and ROCR packages. To further examine the influence of library architecture on the probability of obtaining a correct identification, a multivariate analysis was conducted with the Genmod procedure of the SAS 9.
Experimental manipulation of pH The experiments were performed in a temperature-controlled room (between 26 and 27°C) under fluorescent lights on a 12:12 h light:dark regime. A CO 2 mixing system, developed by  Munday et al. (2009) , was used to bubble CO 2 through seawater at 3 concentrations chosen to match the projections of the Intergovernmental Panel on Climate Change (2007) over the next 80 yr. pH was measured on the National Bureau of Standards (NBS) scale with a portable meter (Hach HQ11D), calibrated daily with pH 4 and pH 7 buffers. Temperature, pH, oxygen concentration and total alkalinity were monitored daily at 11:00 h  (Moya et al. 2012). Experimental calcite and aragonite saturations, as well as actual pCO2 (µatm) were calculated from average total alkalinity data (TA), salinity, temperature and pH NBS using CO2SYS with dissociation constants of  Mehrbach et al.
Acknowledgements. We thank  P. Munday  for the original design of the CO 2 manipulation system and  JCU Marine  and  Freshwater Aquarium  research assistants for technical assistance. We thank  E. Woolsey ,  L. Huisman ,  P. Cross  and  G. Torda  for field assistance and  L. Harrington  for CCA identification. This project is funded by an  ARC   Linkage grant  to W. L. , an  ARC   Future Fellowship  to A. H. B. and a  Ministry of Higher Education of Malaysia PhD  scholarship to C. M. C. Author contributions: A. H. B. , C. M. C. , B. L. and A. M. designed the study; C. M. C. and A. M. collected the data; A. H. B. and C. M. C. wrote the paper; and W. L. and A. M. edited the manuscript.
Experimental Datasets Case data were collected prospectively by trained public health staff using a standardized questionnaire. The following information was obtained via patient interview: the patient's sex, date and country of birth, nationality, immigration status (if applicable), number of years of residence in Hamburg (Germany), current address (or whether the patient was homeless), whether the patient was living in a health-care or any public institution, education level and/or professional training (as far as this could be ascertained), the nature of the patient's current employment (if any), details of any previous known exposure to other persons with TB (especially within the 6 mo before the first appearance of symptoms), and the names of the patient's household contacts and/or any close contacts in occupational or crowded settings.
The sociodemographic and clinical data of each index person acquired from standardized patient questionnaires in the first interview were reassessed immediately after the interview-independently of the cluster study and before the patient's isolate was subjected to RFLP fingerprinting-in order to determine the patient's epidemiologic context, especially his/her possible membership in a high risk group. This profile was intended to help clarify the route of infection and to establish whether the patient's contact information was adequate and whether further Mtb infection could have been transmitted but remained undetected through the omission of probable contact persons. When a patient was recognized to be a cluster member, additional interviews were conducted if possible, i. e. , if one or more patients of the same clusters diagnosed earlier were still alive and with known domicile.
Genome Sequencing Isolated genomic DNA of the Mtb strain 7199/99 was sequenced using 454 pyrosequencing with both standard and paired-end runs. Assembly with GS De Novo Assembler software yielded 124 contigs in five scaffolds. Gap closure was achieved by PCR and Sanger sequencing of the amplicons. The closed genome was corrected for sequencing errors using reads generated by the Illumina platform, and the refined sequence was automatically annotated using the annotation system GenDB  [17]  and H37Rv as the reference genome (GenBank ID: NC_000962. 2)  [18]. All detected differences from the H37Rv annotation were curated manually. The genome was submitted to the ENA EMBL-Bank (accession number HE663067).
Resequencing Isolated genomic DNA of individual strains was sequenced on the Illumina platform. Resulting reads were mapped to the Mtb H37Rv genome (GenBank ID: NC_000962. 2) using the exact alignment program SARUMAN  [20]. Genomic coverage by at least one read ranged from 92. 7% to 99. 9% (mean: 96. 4%), with a coverage of 99. 2% for isolate 7199/99. Single nucleotide polymorphisms (SNPs) were extracted from mapped reads by customized Perl scripts using a minimum coverage of ten reads and a minimum allele frequency of 80% as thresholds for detection. We screened for SNPs present in at least one but not all clinical isolates (i. e. , variants discriminating the outbreak isolates). The drop of sequencing quality in genomic regions featuring high GC content or repetitive elements can lead to false positive detection of polymorphisms.
Calculation of Evolutionary Rates Evolutionary rates and divergence times were computed on the basis of an alignment of 3,663,090 sequenced base pairs from each of 86 Mtb isolates using the BEAST software  [21]. Sequences were dated based on the dates of isolation of Mtb isolates. We used the HKY model of nucleotide substitution and a strict clock model. The strict clock was justified because a likelihood ratio test did not indicate a statistically significant difference between likelihood scores for maximum-likelihood trees calculated using PAUP with or without a strict clock enforced  [22]. BEAST ran for 10 8 iterations after a burn-in of 10 6 iterations. Usage of alternative tree priors (i. e. , prior probability distributions) in the Bayesian analysis resulted in very similar mutation rates and divergence times.
Based on the observed accumulation of sequence variation in 86 Mtb genomes reflecting clonal expansion over at least 14 y (Figure  S3 , upper panel), we determined a time scale for the evolution of Mtb in its natural host. Coalescence-based analyses estimated the nucleotide substitution rate at 1610 27 substitutions per nucleotide site per year (95% confidence interval, 0. 6610 27 to 1. 5610 27 ), i. e. , approximately 0. 4 mutations per Mtb genome per year. When analyses were rerun on datasets with sampling dates permutated across isolates, divergence dates were much older and credible intervals much larger (Figure  S3 , middle panel), suggesting our rate calculations were based on a genuine temporal signal in the sequence data. The rate calculations were also supported by a linear regression of root-to-tip distances from a maximum-likelihood tree against dates of isolation (Figure  S3 , lower panel).
Discussion Our study demonstrates that WGS-based typing provides epidemiologically relevant resolution of large, longitudinal Mtb outbreaks much more efficiently than classical genotyping. Genome-based analysis correlated better with contact tracing information and spatio-temporal patterns of the pathogen's spread. In addition, we were able to determine a timescale of evolution of Mtb during clonal expansion over more than a decade, in a population of. 80 patients. We estimated a maximum variation of three SNPs in definite human-to-human transmission events as a benchmark for interpreting WGS data for future genome-based molecular epidemiology. The efficiency of TB surveillance relies on the capacity to accurately detect outbreaks in the community and to track ongoing transmission chains, which requires the characterization of clinical isolates with high discriminatory power, at strain level  [9].
This work was supported by the  Schleswig-Holsteinische Gesellschaft zur Verhu ¨tung und Beka ¨mpfung der Tuberkulose und der Lungenkrankheiten e. V. , the  EU   FP7 TB-PAN-NET  ( FP7-223681 ),  EU   FP7 Patho-Ngen-Trace  ( FP7-278864-2 ),  ATM Museum National d'Histoire Naturelle ''Biodiversiteet role des microorganismes dans les ecosystemes actuels et passes '' and the  BMBF funded TBornotTB network  ( 01KI0784 )  project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
PCR products were purified using the QIAquick Gel extraction Kit (Qiagen) and cloned into a pGEMH-T Easy Vector (Promega). For all genes, plasmids were sequenced as a routine control prior to RNA probe synthesis. Phylogenetic analyses of the sequences were systematically performed (see procedures and trees in File S1). The gene sequences are available from the GenBank database under the following reference numbers: PpiWnt6: FQ001620. 1; PpiWntX: CU420621. 1; PpiWntA: KF758439; PpiWnt9: KF758438; PpiFzA: FQ005841. 1; PpiFzB: FP991039. 1; PpiDvl1: CU416561. 1; PpiDvl2: FQ013569. 1; PpiGSK-3b: CU418898. 1; Ppib-cat: CU421890. 1; PpiTcf: FP990243. 1.
Acknowledgments We thank the director and staff of the  ''Station Biologique'' in Roscoff (France)  for welcoming us and  Sylvie Mazan  ( UMR 7150 ) for providing lab facilities. We are grateful to the sailors of the Roscoff zoological station, in particular  Gilles Maron  and  Laurent Le  ´veque, for their help in animal collection. Elvire Antajan  is acknowledged for providing hints about P. pileus collection in Graveline, and  Salah el Mestikawy  for providing the anti-Vmat2 antibody. EST sequencing was performed by the '' Consortium National de Recherche en Genomique'' at the Genoscope (Evry, France). Alexandre Alie  ´contributed to the P. pileus picture of Fig. 1 and provided the drawing of Fig. 4C. We thank  Karen Pottin  for useful technical advice concerning cryo-sectionning and for manuscript re-readings.
A second amplification product is observed at a lower size than expected between loci Ccel_1239 and Ccel_1240 (Figure  1C , lane 11RT); this product may be due to a secondary structure that mRNA could undergo during cDNA synthesis. In addition, weak amplifications were obtained between Ccel_1240 and Ccel_1241 (Figure  1C , lane 12RT) and between Ccel_1242 and Ccel_1243 (Figure  1C , lane 14RT) suggesting the presence of more or less weak terminators located downstream of Ccel_1240 and Ccel_1242 or processing events in these regions. It may be relevant to note that the intergenic sequence between loci Ccel_1240 and Ccel_1241 is the largest one found in the cluster. In this intergenic sequence, the use of FindTerm and BPROM programs (http://linux1. softberry. com) allowed to find a putative terminator downstream of locus Ccel_1240 and to predict a promoter with its -35 and -10 sequences downstream of this terminator and upstream of locus Ccel_1241 (Figure  1D ).
Modification of xyl-doc Gene Expression by in vivo Overproduction of the XydR Regulator In order to investigate the involvement of XydR in the regulation of the expression of xyl-doc genes, we first chose to overproduce a derivative of XydR in C. cellulolyticum and to analyze the effect on cellulosomes composition. From primary sequence analysis, XydR is predicted to be a response regulator belonging to COG4753 over all its sequence. It consists of 532 amino acids with an N-terminal conserved CheY-like receiver domain of 122 amino acids belonging to the REC super family (clo09944 in Conserved Domain Database, CDD, http://www. ncbi. nlm. nih. gov/Structure/cdd/cdd. shtml)  [20] , and in its C terminus, a 42 amino-acid DNA binding domain belonging to helix-turn-helix motif of AraC family (clo2815 in CDD).
cellulolyticum) thereby generating pSOS954D116 (Table  1 ), which was then used to transform wild-type H10 C. cellulolyticum strain. Two independent clones isolated from strain H10(pSOS954D116) (Table  1 ), as well as a H10(pSOSzero) strain, which contains the expression vector with no expression cassette (Table  1 ), and H10 strain were grown in cellulose-or straw-based medium for cellulosomes preparation. The secreted cellulosomal proteins (harboring dockerin or cohesin modules) obtained in each culture conditions, were firstly separated using SDS-PAGE and secondly identified with liquid chromatography coupled to tandem mass spectrometry (LC MS/ MS). Comparison of the compositions of the cellulosomes obtained from H10 strain grown on straw-based medium and from H10(pSOSzero) strain, grown on cellulose-based medium confirmed our previous results  [11]  (data not shown).
Only partial recovery of the expression of the gene at loci Ccel_1229, however, was observed in MTL1228 strain complemented by xydR in trans. We hypothesize that this partial complementation could be due to the disruption of xydR (at locus Ccel_1228) in strain MTL1228 leading to i) a polar effect as expression of genes at loci Ccel_1228 and Ccel_1229 is linked, or ii) a modification of the DNA conformation of the binding site of XydR. Electromobility shift assays results have shown that the effector domain of XydR binds to DNA regions upstream to loci Ccel_1229 and Ccel_1656. The binding occurs between minus 327 bp and minus 599 bp, and between minus 237 bp and minus 483 bp from the start codons of the genes at loci Ccel_1229 and Ccel_1656, respectively. In these regions, promoters were predicted by BPROM program with clear 235 consensus and 210 consensus sequences located at minus 415 bp (for 210 consensus) and at minus 299 bp (for 210 consensus) from the start codons of these genes, respectively.
qRT-PCR Quantification of cDNAs was carried out with the SsoFast Evagreen Supermix 2X kit (BioRad), according to the manufacturer's protocol. Complementary DNA was mixed with 0. 5 mM of each primer in 15 ml final volume. Pairs of primers used (1229qRT-F/1229qRT-R, 1656qRT-F/1656qRT-R; Table  S1 ) were designed to specifically amplify part of each targeted gene Ccel_1229 and Ccel_1656, respectively. Real-time PCR was carried out on a CFX96 Real-Time System, C1000 Thermal cycler (BioRad). Thermal cycler was programmed for an initial step at 95uC for 5 s, 55uC for 10 s and 72uC for 1 s. Specificity of accumulated products was verified by using the melting-curve analysis. The Relative Expression Software Tool (REST) was used to calculate the relative expression of each gene in each condition using rpoD-like gene (locus Ccel_0541, amplified with primers RPO-F and RPO-R, table  1S ), predicted to encode Sigma70 RNA-polymerase subunit.
Precursors were dynamically excluded for 30 s, and unassigned charge states as well as singly charged ions were rejected. The mass spectrometric data were subjected to database searching via Sorcerer and Sequest  [44]. Charge state deconvolution and deisotoping were not performed. All MS/MS samples were analyzed using Sequest (Thermo Fisher Scientific, San Jose, CA, USA; version 27, revision 11). The searched database contained the target sequences, which include the complete proteome set of C. cellulolyticum H10 extracted from UniProtKB (http://www. uniprot. org/uniprot/ ?query = Clostridium+cellulolyticum&sort = score) and a set of common laboratory contaminants as well as a decoy data database. The precursor tolerance was set to 10 ppm, and tolerance for fragment ions was set to 1 atomic mass unit (amu).
In these searches, we only allowed fully tryptic peptides, two missed cleavage sites, and methionine oxidation (+15. 9949) as differential modification. Only b-and y-ion series were included in the database search. Data were merged in Scaffold (version 3. 6. 4). Filters in Scaffold were set as follows: XCorr scores of 1. 9, 2. 5, 3. 8 and 3. 5 for singly, doubly, triply and quadruply charged peptides, respectively and DeltaCn of 0. 1. Only proteins identified with at least two peptides were included. Quantification was done using spectral counts  [45].
Data analysis Demographic, clinical, parasitological and attendance data were double-entered independently in an Access database (ver. 7 1995). Data were analysed using Stata V11 software. Only one blood sample per person per monitoring period was considered for the analysis. When a pathological condition was detected, it was the blood sample taken during the clinical episode that was considered for the analysis. When several blood samples from an asymptomatic period were available, one of them was randomly selected for the analysis. Parasitological data were analysed separately in terms of (1) prevalence of Plasmodium falciparum, Plasmodium malariae and Plasmodium ovale asexual blood forms, (2) density of P. falciparum asexual blood forms in parasite-positive thick smears, and (3) prevalence of P.
Acknowledgements This study was undertaken within the framework of the WARDA/WHO-PEEM/ IDRC/DANIDA/Government of  Norway Health Research Consortium on the Association between irrigated Rice Ecosystems and Vector-Borne Diseases in West Africa. The Consortium received technical assistance from the  International Development Research Centre (IDRC) ,  Ottawa ,  Canada  and financial support from the  International Development Research Centre (IDRC) ,  Ottawa ,  Canada , the  Danish International Development Agency (DANIDA)  and the  Royal Government of Norway. We thank  Elena Akodo , the Danané and Guiglo District Health Officers. We also thank the village chiefs and population for their warm welcome during each of our visits. Finally, we are grateful to the team of nurses, health workers and microscopists who made this study possible.
A3A isoforms p1 and p2 The cDNAs encoding the two A3A isoforms were those corresponding to the sequence Genbank Accession Number NM_145699. Primers were designed to equip both A3A isoforms with adequate and strong Kozak motifs respectively. For one construction the SV40 TAg nuclear localization signal (NLS, residues PPKKKRKV) was added to the C-terminus. Full-length cDNAs were subcloned in the pcDNA3. 1D/V5-His-TOPO expression vector (Invitrogen). All constructs were transformed and amplified in E. coli DH5α strain. Catalytically inactive A3A mutants were made by engineering C101S or C106S substitutions into active site residues, following manufacturer's recommendation (GeneArt Site-Directed Mutagenesis System, Invitrogen).
Following secondary antibodies were: 1:500 diluted Alexa Fluor 633 F(ab') 2 fragment of goat anti-mouse IgG (H+L) (Invitrogen), 1:100 diluted FITC goat anti-mouse IgG (Sigma) or 1:100 diluted FITC goat antirabbit IgG (Sigma) for 45 min. All incubation steps were performed on ice. Cells were analysed on FACSCalibur (BD Biosciences) using CellQuest Pro (BD Biosciences, version 5. 2) or FlowJo software (Tree Star, Inc. , version 8. 7. 1). For each sample 10,000 cells were counted.
ImageStream analysis At 24 h post transfection HeLa cells were fixed, permeabilized and stained as described for flow cytometry. After staining of nuclei with DAPI, cells were analyzed on an ImageStream multispectral flow cytometer and images were analyzed using IDEAS image-analysis software (Amnis Corporation). Ten thousand events were collected in each sample and single stained controls were used to compensate fluorescence between channel images on a pixel-by-pixel basis. The instrument combines the features of classic fluorescence microscopy and flow cytometry so allowing multiparametric analyses  [59]. The machine enabled gating around single cells, allowing detailed morphological analysis based on acquired cellular images. Nuclear translocation of A3A was determined by using the similarity feature in the IDEAS software.
Cell cycle analysis HeLa cells were transfected for 24 h. RNA was removed with RNase A and DNA was stained with propidium iodide (PI) according to manufacturer's instructions of Cell Cycle Kit (Genscript). Cells were analysed with FACSCalibur using Cell Quest Pro or FlowJo software. For each sample 10,000 events were collected. Cellular aggregates and debris were excluded from analysis by proper gating. Data were fit to define the G1, S, and G2/M phases by using the Dean-Jett-Fox mathematical model of the FlowJo software.
FACS analysis of apoptosis Annexin V possesses high affinity for the phospholipid phosphatidylserine (PS) thus identifying cells undergoing apoptosis  [60]. At 24 h after transfection, HeLa cells were resuspended in binding buffer (BD Pharmingen) and stained with FITC-labelled Annexin V antibody (1 µg/ml) (BD Pharmingen). Cells were counterstained 5 µg/ml PI (BD Pharmingen) to distinguish between early apoptotic and late apoptotic or necrotic events. Cells were analysed with FACSCalibur using CellQuest Pro or FlowJo software. For each sample 10,000 events were collected.