dataesr/scientific-paragraphs-categorization huggingface dataset:
Shape and pigmentation The Gram reaction of cells of strain L21-RPul-D2 T was determined with air-dried smears of liquid cultures that were fixed with methanol and stained with DIFCO kit reagents. For electron microscopy, exponentially grown cells were negatively stained with 1% sodium phosphotungstic acid (pH 7. 2). Whole cells and cross-sections were observed with a Zeiss EM 912 electron microscope at an accelerating voltage of 75 kV. The cross-sections were obtained by fixation of cells with 10% glutaraldehyde and 0. 1 M cacodylate buffer, a post fixation staining with 2% osmium tetroxide and subsequent inclusion in epoxy resin (EMbed 812). The presence of spores was Figure  1  Phylogenetic tree highlighting the position of strain L21-RPul-D2 T within the family Spirochaetaceae. The dendrogram is based on almost complete 16S rRNA gene sequences and was reconstructed with a neighbor-joining distance matrix program as implemented in the ARB package using phylogenetic distances calculated with the algorithm of Jukes and Cantor.
No filter or weighting masks were used to constrain the used positions of the alignment. In addition, trees were reconstructed using the PHYLIP maximum parsimony program of ARB and the RAxML maximum likelihood program. Support of a distinct branching by bootstrap analyses is indicated by symbols. Closed circles at a distinct node indicate that bootstrap values of 80% or above (percentages of 1000 resamplings) were obtained with three different reconstruction methods, while open circles indicate that values of 80% or above were obtained with only two reconstruction methods. Stable clades of Spirochaeta species formed by two or more type strains are marked with brackets. The sequence of Leptospira interrogans (acc. no. Z12817) was used as outgroup (not shown). Type strains with genome sequencing projects registered in GOLD  [20]  are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks (see  [21] [22] [23] , CP002541 for S.
Genome project history The genome of strain L21-RPul-D2 T was sequenced within the DFG funded project "Microbial control of mineralization processes in non-marine biofilms and microbial mats". The strain was chosen for genome sequencing according to its low 16S rRNA gene sequence identity value to related type strains. Project information is available from the Genomes OnLine Database  [20]  and the complete genome sequence can be found at GenBank. A summary of the project information is shown in Table  2.
Genome sequencing and assembly The genome was sequenced using a combination of three genomic libraries ( Length 40, Overlapper K-mer 14. Thus, one final contig could be obtained, which was trimmed, circularized and adjusted to dnaA as first gene. A total coverage of 365× has been calculated within the long read assembly process. Quality check of the final consensus sequences regarding overall coverage as well as SNPs was performed using IGV  [40]  after mapping of Illumina and 454 short read data onto the draft genome using BWA  [41].
Genome properties The genome of strain L21-RPul-D2 T is represented by one circular chromosome that has a total length of 3,782,798 bp and a G + C content of 51. 86 mol%. The genome sequence has been deposited in GenBank nucleotide database under the accession number CP006939. 1. The genome statistics are provided in Table  3  and Figure  3. Of the 3,500 genes predicted, 3,450 were identified protein-coding genes and 50 RNAs. Around half of the protein-coding genes were assigned a putative function (56. 9%) while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table  4.
Comparative genomics To date genome sequences of the following type strains of Spirochaeta species are available in public databases (accession numbers in parentheses): S. africana DSM 8902 T (CP003282)  [21] , S. alkalica DSM 8900 T (AREC01000000), S. bajacaliforniense DSM 16054 T (ARJU01000000), S. cellobiosiphila DSM 17781 T (AUFW01000000), S. smaragdinae DSM 11293 T (CP002116)  [22]  and S. thermophila DSM 6578 T (CP002903). The percentage of conserved genes among genomes was determined using the phylogenetic profiler function of the IMG-ER system  [32]  with default adjustments, except that the minimal percent identity for homologous genes was set to 40%. Values of percentages of conserved genes were calculated according to the POCP formula proposed by Qin et al. [33]. The shared gene content among the novel strain L21-RPul-D2 T and genome-sequenced Spirochaeta species is shown in Table  5  along with corresponding 16S rRNA gene identity values.
Acknowledgements The authors gratefully acknowledge the help of  Sabine Wellnitz  and  Regine Fähnrich , DSMZ, for growing cells of strains DSM 8901 T , DSM 8902 T , and  DSM 23605  T. Evelyne Brambilla , DSMZ, is acknowledged for DNA extraction and quality control of DNA. We thank  Simone Severitt  and  Nicole Mrotzek  for excellent technical assistance regarding SMRTbell™ template preparation and sequencing. We are grateful to the  Genome Analytics group (HZI Braunschweig)  for providing Illumina sequence data of DSM 27196 T. The ID service of the DSMZ is acknowledged for peptidoglycan, cellular fatty acid and polar lipids analyses. This study was funded by the  German Research Foundation , project  Kl 1000/2-2  of the  Research Unit 571 "Geobiology of Organo-and Biofilms ".
Behavioral data analysis A behavioral analysis was performed on the subjects' performances, their reaction time and responses to questionnaires. For the performance, the 200 trials were divided into 10 blocks of 20 trials. In each block, the net score was calculated by subtracting the number of disadvantageous decks from the number of advantageous decks selected. Hunch and conceptual phases were separated from the calculation of the net score. The last blocks where the net score remained stable were considered a part of the conceptual phase. In order to specifically examine the neural mechanisms underpinning the elaboration of a successful long-term strategy in the present task, the net scores from the conceptual phase were used to categorize participants. Indeed, it is only in that phase that some subjects developed a conscious strategy to succeed in the IGT.
EEG recording and data analysis During the task, all EEG channels were recorded using the OSG digital equipment (BrainRT, OSG bvba, Rumst, Belgium) with two Schwarzer AHNS epas 44 channels amplifiers (Natus, Munich, Germany). EEG signals were acquired from 64 electrodes at the positions of the 10/10 systems using a 64-channel electrode cap (Easycap, easycapGmbh, Ammersee, Germany). EEG data were continuously recorded with a band pass of 0. 05-100Hz, and a sampling rate of 1000 Hz. Signal processing was performed using Cartool Software (http:/brainmapping. unige. ch/ Cartool. php). In addition to a criteria artifact rejection of ± 100 μV, data were visually inspected in order to reject epochs with blinks, eye movements or other sources of transient noise. There were 20. 7% of rejected trials for the analysis of the DPN and 23.
6% for the P200/P300. Data on electrode artifacts from each participant were interpolated using a 3-dimensionalspline algorithm (average: 0. 78% interpolated electrode;  [48] ). Analyses were conducted during three temporal intervals: The first temporal interval started before deck selection, while subjects were fixating on a cross or a letter, to measure the anticipatory DPN component. A time interval from 600 ms before to 200 ms after the selection was chosen on the basis of past experiments  [3, 28]. In agreement with previous studies the first 10 trials corresponding to the pre-punishment phase were excluded from the analysis of the anticipation component. The condition studied was defined by the choices made by the subject, i. e. if they choose advantageous (C or D) or disadvantageous (A or B) decks.
Psychometric and socio-demographic data As evidenced by the self-rating scales, volunteers had no addictive disorders, anxiety or depression. Four healthy participants were reported to occasionally gamble. South Oaks Gambling Screen confirmed a good game control with a score of 1 for only one participant, the others having a score of 0. All subjects had scores compatible with the absence of impulsivity on the BIS-10 both generally and at sub-score level. In our group of subjects, all scores for each dimension of the Big Five Inventory were similar those conventionally found in the general population  [47]. Groups did not differ either by age (t = -1. 31; p = 0. 21), or by educational level (t = 0. 65; p = 0. 62).
001), whereas no effect was noted in the Undecided group. The answers in the questionnaire completed at the end of the task were analyzed for each sub-group, taking into account if at least one advantageous or disadvantageous deck was identified as such. The differences in the answers between sub-groups were significantly different, with the identification of at least one advantageous deck for 100% of the Favorable group as opposed to 45. 4% of the Undecided group (chi 2 = 7. 01; p < 0. 01), and the identification of at least one disadvantageous deck for 100% of the Favorable group as opposed to 63. 6% of the Undecided group (chi 2 = 4. 09; p < 0. 05). Furthermore, 80% of the subjects said they enjoyed the game, without difference between groups. Student's-t-tests were used to compare the selfrating scales in the psychometric data which did not show any significant difference between each group.
Decision preceding negativity (DPN). Based on behavioral and literature data only trials from the pre-hunch and hunch phases were analyzed for the DPN, i. e. trials 11 to 140. Data  The source localization confirmed the activation of frontal, parietal and occipital regions for both advantageous and disadvantageous conditions during anticipation (Fig  3B ). To accurately determine which region was responsible for the frontal surface differences between both conditions, a Student's-t-test was performed in several regions of interests which were right and left inferior frontal gyri, right and left superior frontal gyri. A significant difference was found in the right superior frontal gyrus (t (19) = 2. 14; p<0. 05). Similar tests carried out on parietal and occipital regions did not show any significant difference between both conditions.
Acknowledgments The authors thank all the healthy volunteers for participating in the study. We are also grateful to  Richard Medeiros , Medical Editor of  Medical Editing International  for editing the manuscript. This study was supported by a grant from the  French Ministry of Health  ( PHRC n°2 009-A00806-51 , 2009). The Ministry played no role in the study design, collection, analysis and interpretation of the data, writing of the manuscript, or the decision to submit the paper for the publication.
(2007). They analysed transcripts from autumn and winter buds on a 15K oligonucleotide chip designed using sequences from available expressed sequence tag (EST) libraries. Microarray analyses revealed a significant number of genes up-and downregulated during winter. However, no inferences were made from these data from the perspective of functional genomics. One reason for this could be that, at the time of the study, there was insufficient literature on the molecular control of bud dormancy, as well as a relatively low availability of databases for apple and other temperate fruit trees. Since then, the number of resources for high-throughput functional genomics analyses has grown exponentially, including for apple  (Troggio et al. , 2012). In 2010, a genome sequence of apple was made publicly available, which greatly accelerated apple genomics research  (Velasco et al.
, 2010). Apple genome data analysis estimated a number of 57K genes, which was the basis for the design of a full genome microarray chip for apple, the AryANE chip  (Celton et al. , 2014). This work aimed to identify differential expression of apple genes across bud dormancy stages. Closed terminal buds exhibiting distinct dormancy status were screened for differential gene expression using the AryANE chip. These results were analysed by singular enrichment analysis, and differential expression for 15 selected transcripts was confirmed by reverse transcription followed by quantitative PCR (RT-qPCR). Cold-treated buds exhibited a great number of differentially expressed (DE) genes when compared with buds in the field. DE genes were enriched in Gene Ontology (GO) terms related to photosynthesis, the citrate cycle, ribosome biogenesis, and flavonoid biosynthesis.
Hybridizations RNA samples were screened for differential gene expression by hybridization with the AryANE chip (INRA), according to  Celton et al. (2014). Approximately 400 ng of total RNA was amplified using an Ambion messageAmp II kit (Ambion, Austin, TX, USA). Amplified RNAs (5 μg) were used for sample labelling by RT in the presence of Cy3-or Cy5-CTP. After purification and quantification, labelled samples were combined as 30 pmol for each dye and co-hybridized to the AryANE 12 × 135K arrays. After washing and drying, the fluorescence signals were read by a MS200 scanner (NimbleGen, Madison, WI, USA). NimbleScan Software v. 2. 4 was used to extract pair-data files from the scanned images. For each comparison, two biological replicates, one from each growth   S1 ), were analysed in a dye-switch design, as described in  Depuydt et al.
(2009). All statistical analyses were performed using the R language (R Development Core Team, 2014). The data were normalized using the LOWESS method, the differential expression analyses were performed using the lmFit function, and the Bayes moderated t-test was performed using the package LIMMA  (Smyth, 2005)  from the Bioconductor project. Genes considered to be DE showed transcript level variation greater than 1. 5-fold in at least one comparison, for P<0. 01. The normalized microarray data were deposited at NCBI's Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) under accession code GSE64717. Comparisons were designed in the most comprehensibly form possible in order to follow transcript accumulation changes during dormancy entrance and release. Because each sample had a particular set of properties (bud break rate, cultivar, etc.
Singular enrichment analysis DE genes (>1. 5-fold change, P<0. 01) were tested for enrichment in GO functional classifications using the Blast2GO program  (Götz et al. , 2008). GO term annotations were downloaded from the apple genome and validated in the program (i. e. only the most specific terms for each ontology branch were kept). DE genes were also tested for enrichment in KEGG metabolic pathways using the KOBAS software  (Xie et al. , 2011).
Validation by real-time PCR Gene-specific primers for each selected transcript were designed using Primer3  (Rozen et al. 2000)  and checked for stable putative secondary structures with IDT's OligoAnalyzer (http://www. idtdna. com/analyzer/applications/oligoanalyzer). From each RNA sample, cDNAs were synthesized using a GeneAmp RNA PCR Core kit (Life Technologies) following the manufacturer's instructions. The amplification reactions were performed in a StepOnePlus TM Real-Time PCR System (Life Technologies) as follows: 10 μl of diluted cDNA (1:100), 200 nM of each primer, 50 μM of each dNTP, 0. 25 units of Platinum TM Taq DNA polymerase (Invitrogen, Carlsbad, CA, USA), 1× Buffer Solution (Invitrogen), 1. 5 mM MgCl 2 , 1× SYBR Green TM (Invitrogen), and 1× ROX reference dye (Invitrogen). The reactions were performed in technical quadruplicates for each sample.
Two subgroups of photosynthesis-related genes showed differential regulation during dormancy Hierarchical clustering of photosynthesis-related gene expression results found a group of 11 genes, most of them encoding components of photosystem I and II, with transcriptional induction in RcRcB, CcCcB, and, to a lesser extent, RfRcD (Fig. 2 ). Promoter sequences (1 kb upstream of the predicted translational start site) for eight of these genes were available in the apple genome database  (Velasco et al. , 2010) , as well as for 166 of the remaining DE photosynthesis-related genes. In an attempt to identify candidate signalling pathways that influence the expression of these genes, promoter sequences were scanned for conserved cis-acting elements using the PLACE database  (Higo et al. , 1999). Of the eight promoters of photosynthesis genes induced at the end of dormancy, only one (12.
Validation of microarray results highlights participation of flowering time, the circadian clock, and hormone signalling pathways Gene selection for microarray validation gave priority to predicted genes that fitted in one or more of the following criteria: (i) DE in more than one comparison; (ii) located inside the LG9-QTL; and (iii) functions in dormancy and/or flowering time regulation, according to current models  (Horvath et al. , 2003; Amasino and Michaels, 2010; Rinne et al. , 2011). Confirmation of differential expression was accomplished by RT-qPCR employing the same RNA samples isolated for the hybridizations. Microarray and RT-qPCR results for selected predicted transcripts are shown in Fig. 4. For the sake of clarity, the names of the best matches to Arabidopsis and/or NCBI databases are used to refer to the selected transcripts, except for genes already characterized for apple (AFL1, MdFT, and MdDHN2).
On the other hand, MDP0000207984 was confirmed as being strongly upregulated in RfRcD and RfRfD (Fig. 4 ). BLAST searches in the Arabidopsis genome revealed no significant similarity between these genes and FLC, and returned other MADS-box domain-containing proteins as more similar. MDP0000126259 resembled Arabidopsis APETALA1, while MDP0000207984 returned MADS AFFECTING FLOWERING2 (MAF2) as the best hit, although both results yielded a relatively high expect value (0. 0005 and 0. 0004, respectively). MAF2 is an FLC paralogue with a role in avoiding premature flowering after short cold periods  (Ratcliffe et al. , 2003). In addition to having no bona fide homologues in the Arabidopsis genome, BlastX searches in the NCBI non-redundant database using either gene as a query returned few significant matches (data not shown).
Hence, MDP0000126259 will be referred to as FLC-like and MDP0000207984 as MAF2-like. A contig assembled from apple EST databases and very similar to FLC-like can be found at the Rosaceae genome database (http://www. rosaceae. org, Malus_v4_Contig6253). An alignment of FLC-like, MAF2-like, and the contig is shown in Fig. 5. Both transcripts were predicted from genomic sequences anchored to apple chromosome 9 and were distanced by approximately 23 million base pairs. FLClike was located approximately 700 000 bp from the start of chromosome 9, therefore lying inside the LG9-QTL.
Green and red colour intensity refer to down-and upregulation, respectively, as indicated by the bar on the top of the figure. The image was generated by MeV  (Saeed et al. , 2003). at Empresa Brasileira de Pesquisa AgropecuÃ¯Â¿Â½ria on March 6, 2015 http://jxb. oxfordjournals. org/ Downloaded from A series of hybridizations was performed comparing RNA isolated from field-harvested buds and buds chilled under controlled conditions. The dormancy status from all materials was monitored by forcing, and an attempt was made to identify transcripts associated with changes in dormancy status. Transcript profiling studies of bud dormancy usually involve comparison of samples either harvested in the field, with CR being fulfilled under field conditions  (Horvath et al. , 2008; Liu et al. , 2012)  or forced to release dormancy by chilling or chemical treatments  (Mazzitelli et al.
Acknowledgements This work was supported by  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brazil) ,  Financiadora de Estudos e Projetos (FINEP, Brazil) ,  Fundação de Amparo à Pesquisa do Rio grande do Sul (FAPERGS, Brazil) , and  Empresa Brasileira de Pesquisa Agropecuária -Embrapa. We thank  Décio Amorim  for the availability of apple orchards,  M. Sc. Diana Muratt  for technical assistance, and  Dr François Laurens  for very helpful discussions. We also thank the  ANAN Platform of the SFR QuaSaV  for microarray facilities.
GSK proprietary AS15 immunostimulant is composed of 3-O-desacyl-4′-monophosphoryl lipid A (monophosphoryl lipid A; MPL), QS-21 (extract from the soap bark tree [Quillaja saponaria]) and a synthetic oligodeoxynucleotide containing unmethylated CG dinucleotides (CpG ODNs 7909), in a liposomal formulation. Combination of the MAGE-A3 tumor antigen with AS15 induced cellular and humoral responses that were more robust and a higher clinical activity compared to MAGE-A3 combined with the AS02B immunostimulant in a phase II clinical trial in patients with melanoma  (Kruit et al. , 2013). Therefore, AS15 was chosen for further clinical development in phase III trials for the treatment of non-small cell lung cancer (NSCLC) (NCT00480025) and melanoma (NCT00796445). The Wilms' tumor gene (WT1) was originally identified as the gene responsible for the childhood kidney cancer, Wilms' tumor  (Call et al.
, 1990; Gessler et al. , 1990; Lee and Haber, 2001). WT1 is highly expressed in a number of hematopoietic (such as acute myelocytic, acute lymphocytic, chronic myelocytic leukemia) and solid (including NSCLC and breast cancer) cancers  (Nasomyon et al. , 2014; Oka et al. , 2002; Xu et al. , 2013). A breast cancer candidate vaccine combining the WT1 recombinant antigen with the AS15 immunostimulant (WT1 + AS15) is currently in phase I/II clinical development in patients with WT1-positive breast cancer (NCT01220128). The p501 antigen (known also as prostein) is uniquely and widely expressed in both normal and cancerous prostate tissues, and can serve as a marker for metastases of prostatic origin  (Sheridan et al. , 2007). It was also detected in adenocarcinomas of the bladder  (Lane et al. , 2008).
Another vaccine candidate, containing the p501 recombinant antigen combined with the AS15 immunostimulant (p501 + AS15), was evaluated in a phase I/II clinical trial in patients with hormone-sensitive prostate cancer and rising prostate-specific antigen (PSA) (NCT00148928). The human epidermal growth factor receptor 2 (HER2) is overexpressed in 20-30% of breast cancers  (Slamon et al. , 1987). A candidate cancer vaccine consisting of a truncated recombinant HER2 protein (dHER2) combined with the AS15 immunostimulant (dHER2 + AS15) has been evaluated in a phase I trial in patients with high-risk breast cancer overexpressing HER2 (NCT00058526), in a phase I/II clinical trial in patients with metastatic breast cancer overexpressing HER2 (NCT00140738), and in a phase I/II clinical trial in patients with metastatic breast cancer overexpressing HER2 and resistant to trastuzumab (NCT00952692)  (Hamilton et al.
, 2012). The PReferentially expressed Antigen of MElanoma (PRAME) was isolated from several types of cancer and may be directly involved in oncogenesis  (Epping and Bernards, 2006; Epping et al. , 2005). The recombinant PRAME antigen combined with AS15 (recPRAME + AS15) is currently in clinical development for the treatment of NSCLC (NCT01159964; phase I) and melanoma (NCT01149343; phase I/II). In these studies, recPRAME + AS15 was immunogenic and had a clinically acceptable safety profile  (Gutzmer et al. , 2012; Pujol et al. , 2012). The non-clinical safety studies presented here assessed the potential in vivo toxicity of the full human doses of the cancer vaccine candidates containing the WT1, p501, dHER2 or recPRAME tumor antigens combined with the AS15 immunostimulant in animal models.