dataesr/scientific-paragraphs-categorization huggingface dataset:
Band 4 contained the highest concentration of Wolbachia, very low levels of host nuclear DNA, and no detectable mitochondrial contamination, and this band was therefore chosen for genomic DNA extraction and sequencing. Genome Sequencing, Assembly, and Annotation Initial genome sequencing was performed by the Australian Genome Research Facility. The wMelCS genome was sequenced using Illumina, while wMelPop, wMelPop-CLA, and wMelPop-PYGP were sequenced using 454 (Roche) pyrosequencing (see table 1 for details). Subsequent Illumina resequencing of wMelPop and wMelPop-PGYP was performed by the Ramaciotti Centre, University of New South Wales. The wMelPop, wMelPop-CLA, and wMelPop-PGYP genomes were each assembled using Newbler v2. 6. The initial assemblies contained a substantial number of homopolymer errors, which we corrected for wMelPop and wMelPop-PGYP using Illumina sequencing data generated from the same DNA material that was used for the original 454 sequencing.
Phylogenetic Analysis To construct a whole-genome phylogeny of wMel, wMelCS, and wMelPop, we used the corrected wMelPop genome assembly, the published wMel genome  (Wu et al. 2004 ), eight of the wMel consensus genomes and the two wMelCS consensus genomes called by  Richardson et al. (2012) , and a consensus genome generated from our wMelCS/Canton-S sequencing data using the same method as  Richardson et al. (2012). Briefly, we mapped the wMelCS reads to the reference wMel genome using BWA  (Li and Durbin 2009) , then generated a -PE, paired ends. Approximate mean sequencing depth is estimated by mapping the sequence reads to the wMel genome using default mapper settings and calculating mean total per-site coverage. Complete lists of accession numbers for all data types are given in supplementary information (Supplementary Material online).
Identification of Sequence Variants between Genomes We identified sequence differences between each of the genomes analyzed here (wMel, the three wMelCS genomes, wMelPop, wMelPop-CLA, and wMelPop-PGYP) using three main techniques: 1. For the three popcorn genome assemblies, we used Mauve  (Darling et al. 2004 ) to create pairwise alignments of each draft assembly to the other assemblies and to the wMel genome, and then exported the core alignments using the stripSubsetLCBs script (provided by Mauve developers at http://gel. ahabs. wisc. edu/mauve/snapshots/, last accessed November 19, 2013). We then used custom Perl scripts to identify mismatches in the alignments. 2. To identify variants between the three popcorn genomes, and between the three wMelCS genomes and the popcorn genomes, we mapped the reads of each of the six data sets to each of the popcorn assemblies, and called variants as described later.
To attempt to identify these changes, we mapped the three sets of wMelCS reads to the wMelPop draft assembly and searched for differences between them. We found a small number of variants between the wMelCS/DGRP335 and wMelCS/DGRP338 sequences and wMelPop (table  2 ), but at these sites, wMelCS/Canton-S always matched the sequence of wMelPop, indicating that these differences could not be associated with pathogenesis. The wMelPop draft genome assembly contains collapsed repeats and could possibly contain other errors that might impede the detection of sequence variants. To ensure that we were not missing true variants, we therefore also mapped the sequencing reads from each of the three wMelCS data sets and the wMelPop, wMelPop-CLA and wMelPop-PGYP data sets against the wMel genome, and compared the variants that were called.
aegypti. Using primers that spanned the gene boundaries WD0512-WD0513 and WD0513-WD0514, and normalizing against the single-copy gene wsp, we found that these genes amplify approximately three times as highly in wMelPop as in wMelCS (fig. 4 ). These results are consistent with earlier data serendipitously examining expression of these genes using Southern blots  (Iturbe-Ormaetxe et al. 2005) : in those data, the hybridization signal for these genes, and in particular for WD0514, is stronger in wMelPop than in wMel or wMelCS, whereas the other genes tested, including wsp, produced similar signal intensities for the different strains. It seems unlikely, however, that the triplication of one or all of these genes could be directly responsible for pathogenesis, as the region that is triplicated in wMelPop is completely deleted in wMelPop-CLA and wMelPop-PGYP (confirmed by mapping of sequencing reads to the wMel genome for both substrains, fig.
Acknowledgments The authors are very grateful to  Nicola Petty ,  Nouri Ben Zakour ,  Torsten Seemann , and  Paul Harrison  for discussion and advice, and to the  Victorian Bioinformatics Consortium  for access to computational resources. They also thank past and present members of the  O'Neill and McGraw labs  for assistance and discussion of results, attendees of the International Wolbachia conferences for comments on earlier stages of these analyses, and two anonymous reviewers for valuable suggestions to improve the manuscript. This research was supported by grants from the  Australian Research Council  and the  Foundation for the National Institutes of Health  through the  Grand Challenges in Global Health Initiative of the Bill and Melinda Gates Foundation.
Questionnaire-construction Process The first step of the questionnaire-construction process used focus-group methodology  [18]. This qualitative phase, conducted between September and December 2008, involved 12 adult patients, nine parents of children with AD, and 15 health professionals (8 general practitioners and 7 pharmacists) in the collect of data on patients' behaviors, beliefs, cognitions, sensations and perceptions of TCP. Five focus-group meetings were held and interviews were transcribed. In addition, four telephone interviews sufficed to reach the data saturation threshold. Analysis was completed by an examination of the literature. The qualitative phase was previously reported in details  [15]. The second step enabled us to generate a 51-item questionnaire with an additional 18 items concerning sociodemographic characteristics and health status.
Score Calculation Four response choices were offered, from totally disagree to totally agree, with points attributed to each one (0, 1, 2 or 3), with higher values corresponding to more severe TCP. Individual scores for all patients who responded to at least half the items plus one in a dimension were calculated by summing responses to items and then dividing that value by the number of items completed, yielding a maximal score of 36, expressed as a percentage. The mean score for a dimension was the sum of individual scores divided by the number of respondents. TOPICOPß scores ranged from 0 to 100. All study analyses were computed using R 2. 9 and SPAD 5. 6. Structural equation modeling used SAS v9. 1 (SAS Institute, Cary, NC) and its ''PROC CALIS'' procedure.
Study population We used data from a large, prospective, single-hospital cohort of patients with meningitis enrolled over a 25-year period at the Hospital de la Santa Creu i Sant Pau (Barcelona, Spain). This institution is a 620-bed tertiary university hospital providing care for an urban area with an estimated population of 450,000 inhabitants. From 1982 through 2006 all consecutive adults (defined as patients 14 years or older) in whom acute bacterial meningitis was diagnosed at our hospital were prospectively identified. The diagnosis of meningitis caused by a specific bacterial pathogen was based on compatible clinical findings (sudden onset of headache, fever, nausea, vomiting, neck stiffness and/or altered mental status) and one of the following: a positive cerebrospinal fluid (CSF) culture, or a negative CSF culture with a finding of neutrophilic pleocytosis (defined as pleocytosis of at least 100 neutrophils per cubic millimeter) and at least one of the following: a positive CSF antigen test, a positive blood culture, or identification of gram-negative diplococci on Gram's staining of CSF in patients with a petechial or purpuric rash and a fulminant course (these last cases were considered to be caused by Neisseria meningitidis)  [21].
Statistical analysis Qualitative variables were summarized with absolute numbers and percentage and quantitative variables with means and standard deviation (SD) or medians and interquartile range (IQR) (depending on their homogeneity). Continuous variables were compared using t Student or the Mann-Whitney U test when appropriate. We analyzed categorical data using the χ 2 test or Fisher's exact test when indicated. Logistic regression was used to determine characteristics of GNBM among patients with spontaneous acute bacterial meningitis. Additionally, we used logistic regression to examine the association between GNBM and the likelihood of death. Covariates were chosen based on previous research and clinical judgment. Proportions of the variation of the outcome explained by the model were assessed by the Nagelkerke's R 2.
Candidate genes Together, the four QTL regions, identified from mapping only with the Singer markers and following fine mapping of QRps. JIC-3. 1, included a total of 616 predicted genes identified using the TAIR seqviewer (Table  1 ). The Singer marker set was used in this analysis because the QTL peaks were located in the same positions whether the NASC or Singer markers were used in mapping, but there are no missing genotype scores in the Singer data. All 616 genes were analysed for the presence of polymorphisms between the sequences of the parental accessions, Ler and Col, using the GBrowse Viewer (http://gbrowse. weigelworld. org/cgibin/gbrowse/polymorph/), which examines the open reading frame of all genes and the promoter region of well-annotated genes. Polymorphic genes were then cross-referenced to a list of 421 genes annotated by the microarray software Mapman 2.
1. 1  (Thimm et al. , 2004)  as being involved in biotic stress, and with genes shown to be significantly up-or down-regulated in response to a PAMP, the bacterial flagellin protein flg22 (supplementary data in  Zipfel et al. , 2004). This approach focused on genes that may alter expression levels during an attack by pathogens, and therefore may contribute to partial resistance, but did not check every gene within each QTL interval. In addition, therefore, all the genes within the QTL regions were viewed as annotated loci on the TAIR website to see whether further genes should be included, based on their function reported elsewhere as being related to a resistance or stress response. A shortlist of candidates for partial resistance genes in the region of the major QTL, QRps. JIC-3. 1, is given in Table  2  and a list of possible candidates at the three minor QTLs in Table  S2  (see Supporting Information).
maculicola ES4326, with annotations from The Arabidopsis Information Resource (TAIR) database. The numbers of polymorphisms between loci from Columbia and Landsberg erecta are as shown on the Polymorph GBrowse viewer. Bold type: genes reported to be involved in biotic stress. Italic type: genes reported to be involved in pathogen-associated molecular pattern (PAMP) recognition. QTLs accounting for substantial fractions of partial resistance to P. syringae in Arabidopsis have been reported, in addition to several mapped, minor QTLs distributed throughout the genome and an unknown number of genes with small effects. QTL analysis has been used in research on the relationship of defence pathways to resistance to P. syringae in Arabidopsis. A QTL on chromosome 4 regulating PR-1 expression induced by salicylic acid (SA) was associated with basal resistance to P.
QTL mapping Analysis and mapping of QTLs were performed using the software MapQTL 5  (Van Ooijen, 2004). The data in the genotype (. loc) and mapping (. map) files are available as supplementary data in  Singer et al. (2006)  and at the NASC website: http://arabidopsis. info/new_ri_map. html. A Kruskal-Wallis (KW) rank test was used to identify candidate regions of the Col ¥ Ler map linked to partial resistance. Interval Mapping (IM) was then used to test the genetic effect of QTLs postulated by the KW test, using the logarithm of the likelihood ratio (LOD). A permutation test  (Churchill and Doerge, 1994)  with 1000 replicates was used to determine that the P < 0. 05 significance threshold for the identification of QTLs was a LOD score of 3. 3. Markers closely linked to QTLs were selected as co-factors for MQM mapping.
Fine mapping After identifying the region on chromosome 3 in which the most potent QTL was located, markers from the NASC database were added and new markers were designed to fill the gaps between existing markers. The Sequence Viewer tool http://www. arabidopsis. org/servlets/sv enabled the scanning of the sequence to identify single nucleotide polymorphisms between Columbia and Landsberg which were used to design new markers. Restriction endonucleases (REs) predicted to cut at the site of each polymorphism were identified with NEBcutter V2. 0 (http:// tools. neb. com/NEBcutter2/index. php) (Vincze et al. , 2003). Primer3 was used to design primer pairs (Sigma, Gillingham, UK; Table  S1 , see Supporting Information) for these regions (http://frodo. wi. mit. edu).
Phenotypic Analysis by X-Ray, Scanning Electron Microscopy (SEM), and Microcomputed Tomography (µCT) Analysis For X-ray and µCT analysis, 1-month-and 3-month-old mouse skulls of control and cKO mice were dissected, cut symmetrically in half, fixed in 4% paraformaldehyde, and stored in phosphate buffered saline (PBS). X-ray analysis was performed using the Faxitron MX20 (Faxitron Bioptics, Tucson, AZ) as described earlier in  [8]. Morphological analysis and measurement of enamel mineralization of the mandibular molars were further performed using a cone beam µCT scanner (SMX-100CT; Shimadzu, Kyoto, Japan). The X-ray tube was operated at 75 kV, 200 µA, with brass filter of 0. 1 mm thickness. The image scans were performed at a 10 µm/voxel resolution setting. The three-dimensional images were reconstructed and measured by software (TRI/3D-BON software; RATOC System Engineering, Tokyo, Japan).
Altered Localization of ECM Proteins in in TGF-ß RII cKO Enamel To investigate the possible cause of tooth defects that led to the dental attrition phenotype in the cKO enamel, we analyzed enamel matrix proteins by immunostaining with specific antibodies. At P7, more intense staining was observed for amelogenin, enamelin, and ameloblastin in the cKO enamel as compared to the control (Figure  4A ). To determine how deletion of TGF-ß signaling affects the ameloblasts, we performed qPCR analysis specifically for enamel matrix and enamel processing proteins such as amelogenin, enamelin, ameloblastin, KLK4, and MMP-20 in P2 and P7 molars. MMP-20 and KLK4 expression in the cKO teeth were unaffected at P2 (data not shown), but at P7 we observed a slight increase in MMP-20 and significant reduction in KLK4 expression (Figure  4B ).
Primers were designed using Primer Express (Applied Biosystems/Life Technologies, Foster City, CA, USA) or obtained commercially from Applied Biosystems. Real-time quantitative PCR on 10 ng of amplified complementary DNA (cDNA) from each sample was performed on the Fluidigm BioMark system (Fluidigm, Foster City, CA, USA). Ubiquitin levels were measured in a separate reaction and used to normalize the data by the d-d Ct method.
ACKNOWLEDGMENTS We thank  Steve Jungers ,  Scott Turner ,  Fran Shen , and  Bela Desai  for performing the FACS and maintaining the FACS facility;  Eddie Bowman ,  Rene De Waal Malefyt , and  Sarah Gaffen  for helpful discussions; and  Debbie Law  and  Jean-Michel Lecerf  for critical readings of the manuscript. All authors except S. M. A. are current or previous employees of  Merck.
Experimental results The proposed experimentations are based on the Ant Colony System (ACS) applied to the Travelling Salesman Problem (  [34] ). Both implementations have been experimented on ROMEO II in the Centre de Calcul de Champagne-Ardenne. ROMEO II is a parallel supercomputer of cluster type, consisting of 8 Novascale SMP nodes dedicated to computations. Each node includes 4 Intel Itanium II dual-core processors running at 1. 6 GHz with 8MB of cache memory, for a total number of 8 cores, as well as from 16 GB to 128 GB of memory. Each execution is performed on a single node using from 1 to 8 cores. Application code is written in C++ with OpenMP directives for parallelization. The chosen TSP instances range in size from 783 cities to 13 509 cities. For a more detailed version of the experimental setup and results, the reader may consult Delisle et al.
It contains 14 SMs, 32 SPs per SM, 48 KB of shared memory per SM and a warp size of 32. The CPU code runs on one core of a 4-core Xeon E5640 CPUs running at 2. 67 Ghz and 24 GB of DDR3 memory. Application code was written in the "C for CUDA V3. 1" programming environment. The implementation uses a number of blocks equal to the number of ants, each one of them being composed of a number of threads equal to the size of candidate lists, in that case 20. Also, the number of iterations is set with the intent of globally keeping the same global number of tour constructions for each experiment. For more details on the experimental setup, the reader may consult Delévacq et al. (  [10] ). A first step in our experiments is to compare solution quality obtained by sequential and parallel versions of the algorithm.
Most sites were positively influenced by CO 2 mole fraction (i. e. there was a positive correlation between phosphorylation and photosynthetic activity), except for eIF4G, eIF4A and eIF5A (Figure  4A ). That is, the components of eIF4F were either not phosphorylated in our conditions (eIF4E) or responded negatively to photosynthetic conditions (eIF4G, eIF4A). 17 and 5 sites in ribosomal proteins and eIFs, respectively, were Table  1. Eukaryotic ribosomal protein and initiation factor phosphopeptides identified by nanoLC-MS/MS. S2. b-A phosphorylation site is considered as new when absent from refs. [8]  and  [11]  and PhosPhAt 4. 0 database(http://phosphat. mpimp-golm. mpg. de/). c-Phosphorylation patterns are presented in Figures  3  and 4. d-By 'punctually', we mean occasional detection of phosphorylation, with no clear pattern.
Identification of Peptides and Phosphorylation Sites Database searches were performed using X!Tandem CY-CLONE (http://www. thegpm. org/TANDEM). Cys carboxyamidomethylation and light and heavy dimethylation of peptide Ntermini and lysine residues were set as static modifications while Met oxidation and phosphorylation of tyrosine, serine or threonine residues were set as variable modifications. Precursor mass tolerance was 10 ppm and fragment mass tolerance was 0. 02 Th. Identifications were performed using the TAIRrelease 8 database (http://www. uniprot. org/http://www. arabidopsis. org/). Identified proteins were filtered and grouped using the X!Tandem pipeline v3. 2. 0 (http://pappso. inra. fr/bioinfo/ xtandempipeline/). Data filtering was achieved according to a peptide E value smaller than 0.
Quantification of Peptides and Phosphorylation Sites Relative quantification of non-phosphorylated peptides and phosphopeptides was performed using the MassChroQ software  [20]  by extracting ion chromatograms (XICs) of all identified peptides within a 10 ppm window and by integrating the area of the XIC peak at their corresponding retention time. LC-MS/MS chromatogram alignment was performed by using common MS/ MS identifications as landmarks to evaluate retention time deviations along the chromatographic profiles. Alignments were performed within groups of LC-MS/MS runs originating from similar SCX fractions. For each peptide detected in the heavy and light form in a single LC-MS/MS run, a light-to-heavy ratio was computed. To compensate for possible global deviations to 1:1 of the light/heavy ratio (i.
The authors thank the  Institut Federatif de Recherche 87  for its financial support for phosphoproteomics. E. B. -F. thanks the  Labex Saclay Plant Science  for its support through a post-doctoral grant. GT and MH thank the  Agence Nationale de la Recherche  for supporting running costs of this study, thanks to a project  Jeunes Chercheurs , under contract no. 08-330055. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Entamoeba histolytica PCR of the pus aspirate of the abscess is a very useful tool to diagnose ALA. According to case reports, serodiagnostic may lacks sensitivity when compared to PCR, as false positive serologies have been reported in endemic area  [5, 28]. PCR has been evaluated in a few studies for imported ALA and should become a gold standard to diagnose ALA when invasive explorations are performed. Table  2. Cont. At least, our study collected data from 13 hospitals with different types of healthcare management. Longitudinal follow-up studies could better describe recovery and also evaluate factors associated with abscess persistence. Similarly, clinical trials are needed to assess percutaneous aspiration and to perform guidelines for its use in the treatment of ALA, something which can often be adequately treated using drugs alone.
Acknowledgments The  ALA Study Group is composed of: Helene Gros (Garches ),  Catherine Buffet and Jean-Francois Delfraissy (Bicetre) ,  Eric Dannaoui ,  Laurence Weiss  and  Loı ¨c Capron (Paris, Hopital Europeen Georges Pompidou) ,  Philippe Marteau  ( Paris, Hopital Lariboisiere), Thierry Poynard (Paris, Hopital de la Pitie-Salpetriere ),  Patricia Roux  and  Pierre-Marie Girard  ( Paris, Hopital Saint-Antoine ),  Annie August 2013 | Volume 7 | Issue 8 | e2333 Sulahian ,  Jean-Michel Molina  and  Emile Sarfati  ( Paris, Hopital Saint-Louis ),  Gilles Pialoux  ( Paris, Hopital Tenon ),  Nadine Godineau  ( Saint-Denis ),  Daniel Vittecoq ,  Denis Castaing  (Villejuif) We thank  Jude Sweeney  for the English revision and editing of the manuscript.
In brief, cells were incubated 12 h with BrdU-labeling solution in EBM-2 medium in the absence or presence of rsCD146 and fixed. Cellular DNA was partially digested by nuclease treatment, and incorporated BrdU was detected with a peroxidase-conjugated anti-BrdU primary antibody. The absorbance was measured at 450 nm using a microplate reader. Results were expressed as arbitrary units. Experiments were performed in triplicates. Wound Healing Assay-A reproducible wound was performed with a pipette tip on a confluent monolayer of EPC cultured on 24-well plates. The surface of the wound was measured at 400ϫ magnification using an Olympus inverted microscope and acquired with the Biocom Visiolab image analysis software (Les Ulis, France). The medium was removed, and EPC were incubated for 6 h with EBM-2 medium containing or not rsCD146.
Protein Expression Profiling-Total cell lysates were prepared from cultured late EPC treated or not for 24 h with 50 ng/ml rsCD146. Antibody arrays were performed according to the manufacturer's instructions (Tebu-Bio; Le Perray en Yvelines; France). Spot signals were quantified using the Tebu-Bio software. Subtraction of background was done for the signal mean intensities in both test and reference spots. Quantitative RT-PCR-Total cellular RNA was isolated from late EPC using the RNeasy kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions, including the DNase digestion step. 5 g of total RNA were reverse-transcribed into cDNA in a 50-l reaction containing 40 units of RNaseOUT (Invitrogen), 150 ng of random hexamers (Roche Applied Science), 10 mM dNTPs (Invitrogen), and 200 units of Superscript II (Invitrogen).