dataesr/scientific-paragraphs-categorization huggingface dataset:
Classification and features Representative genomic 16S rRNA sequences of strains AK58 and BO21CC were compared with those present in the Ribosomal Database by using Match Sequence module of Ribosomal Database Project  [8]. Representative genomic 16S rRNA sequences of closer phylogenetic relatives of the genus Ensifer/Sinorhizobium and of Rhizobiales family (as outgroup) were then selected from IMG-ER database [Table  1 ],  [16]. All strains from the genus Ensifer/Sinorhizobium form a close cluster, including strains AK58 and BO21CC, thus confirming the affiliation of these two strains within the species. Figure  1  shows the phylogenetic neighborhood of E. meliloti AK58 and BO21CC in a 16S rRNA based tree. E. meliloti AK58 and BO21CC show different symbiotic phenotypes with respect to the host plant Medicago sativa, as well as differences in substrates utilization  [5].
Genome project history AK58 and BO21CC strains were selected for sequencing on the basis of the Community Sequencing Program 2010 of DOE Joint Genome Institute (JGI) in relation to the project entitled "Complete genome sequencing of Sinorhizobium meliloti AK58 and BO21CC strains: Improving alfalfa performances through the exploitation of Sinorhizobium genomic data". The overall rationale for their genome sequencing was related to the identification of genomic determinants of different symbiotic performances between S. meliloti strains. The genome project is deposited in the Genomes On Line Database  [21]  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE-JGI. A summary of the project information is shown in Table  2.
24 (High Performance Software, LLC). Possible misassemblies were corrected with manual editing in Consed  [29] [30] [31]. For AK58, the 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2. 6 (20110517_1502). The Newbler consensus sequences were computationally shredded into 2 kb overlapping fake reads (shreds). Illumina sequencing data was assembled with Velvet, version 1. 1. 05 [28] , and the consensus sequence was computationally shredded into 1. 5 kb overlapping fake reads (shreds). We integrated the 454 Newbler consensus shreds, the Illumina Velvet consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS -4. 24 (High Performance Software, LLC). The software Consed  [29] [30] [31]  was used in the following finishing process.
Genome annotation Genes were identified using Prodigal  [33]  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline  [34]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGRFam, 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  [16].
The tree with the highest log likelihood (-3411. 7124) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. A discrete Gamma distribution was used to model evolutionary rate differences among sites (G, parameter = 0. 3439). A total of 1,284 nt positions were present in the final dataset. Model test and Maximum Likelihood inference were conducted in MEGA5 [19]. In bold E. meliloti AK58 and BO21CC strains.
[10]sification and g eneral features of E. meliloti AK58 and BO21CC according to the MIGS recommendations[9]and the Names for Life database[10]Gap closure was accomplished using repeat resolution software (Wei Gu, unpublished), and sequencing of bridging PCR fragments with Sanger and/or PacBio (unpublished, Cliff Han) technologies. For improved high quality draft and noncontiguous finished projects, one round of manual/wet lab finishing may have been completed.
Acknowledgements We are grateful to  Dr. M. L. Roumiantseva  and  D r. B. Simarov  ( Research Insti tute for Agricultural Microbiology, St-Petersburg-Puskin, Russia ) for original isolation and the permission to use strain AK58 in this work. The work conduc ted by the  U. S. Department of Energy Joint Genome Institute  is supported by the  Office of Science of the U. S. D epartment of Energy  Under Contract No. DE-AC02-05CH11231.
Nylon membrane array hybridization and raw data production. cDNA arrays were generated by CRB GADIE (http://crb-gadie. inra. fr/) as previously described  [24]. Prehybridization of the membranes was performed at 65uC for 4 h in 5X Denhardt's, 5X SSC and 0. 5% SDS. Labelled cDNA targets were denatured at 95uC for 5 min and incubated with microarrays for 48 h at 65uC in the same buffer. The membranes were then washed three times for 1 h at 68uC in 0. 1X SSC containing 0. 2% SDS prior to a 48 hour exposure to phosphor-imaging plates. Plates were scanned using a FUJI BAS 500 and the BZscan software was used for signals acquisition  [25]. Each membrane was also hybridized with a 33 P-labelled oligonucleotide (59-TAATACGACTCACTATAGGG-39) that recognizes the vector part of every PCR product to quantify the amount of spotted cDNA.
Normalization procedure. Expression data were normalized as previously described  [26]. Briefly, raw data were corrected for the amount of spotted cDNA by dividing the sample signal (Si) of each spot by the corresponding vector signal (Vi). To avoid the bias affecting relative gene expression levels, the corrected signal of each spot was further multiplied by the median vector signal of all arrays for this same spot ((Si/Vi)6medVi). Expression values were then log2-transformed and submitted to a quantile-quantile normalization using the AMEN software (http://sourceforge. net/projects/amen/)  [27]. Raw data as well as a normalized expression file are available at the GeneOmnibus public data repository http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc = GSE46458. Statistical and cluster analyses.
Meta-analysis. Expression data obtained in a previous study  [10]  were used to investigate whether the 2 categories of Fshresponsive genes (sensitive or insensitive to trilostane), were regulated by Lh. Samples in this dataset included explants of testis in early stages of spermatogenesis which were incubated for 4 days in the absence or in the presence of either Fsh or Lh (500 ng/mL). The data were normalized to avoid bias due to the different batches of nylon membranes as well as the 2 separate hybridization experiments. For each row (i. e. each gene) the expression signals of all arrays in one experiment were median-centered then normalized by the median expression of the second experiment. Only the clones demonstrating a statistically significant response to Fsh in both experiments were considered and submitted to a non-supervised hierarchical classification.
05) was observed between groups in the ANOVA analysis. Real-time PCR oligonucleotide primers were designed using the Primer3 software (http://frodo. wi. mit. edu/primer3/) and were verified with the oligoanalyser 3. 1 web interface (http://eu. idtdna. com/analyzer/Applications/OligoAnalyzer/) to avoid self-and hetero-dimer formation as well as hairpin structures. Nucleotide sequences of the primers were also systematically matched (BLAST algorithm) against the SIGENAE trout contig collection (som. 10 version) to avoid non-specific annealing to other transcripts. PCR amplification effectiveness was verified using serial dilutions of pooled RT products. All primer sequences are provided in Table  S1.
Trilostane modified the Fsh regulation of testicular gene expression The variations of the transcriptome were analyzed at a large scale using trout cDNA microarrays. The effects of Fsh on testicular gene expression were studied after 4 days of incubation because we previously showed that Fsh and Lh modified testicular transcriptome more efficiently after a 4-day treatment compared to shorter durations. The microarray data were analyzed with AMEN software. After a double filtration on expression level and fold change, followed by a Limma analysis (FDR 1%; see M&M), 102 clones corresponding to 96 non redundant (NR) genes were found significantly differentially expressed between control and Fsh-treated conditions or between trilostane and Fsh+trilostane groups. All the information on annotation together with response to Fsh, trilostane and Lh for these 102 clones is provided in the searchable file S1.
Mann et al. (2012)  reported that correctly classifying and removing giant stars removes the correlation between cool star metallicity and planet occurrence observed by  Schlaufman & Laughlin (2011). After removing giant stars from the target list,  Mann et al. (2012)  calculated a planet occurrence rate of 0. 37 ± 0. 08 planets per cool star with radii between 2 and 32 R ⊕ and orbital periods less than 50 days. Their result is higher than the occurrence rate we report in Section 5. 3, most likely because of our revisions to the stellar radii. In this paper, we characterize the coolest Kepler target stars by revisiting the approach used to create the Kepler Input Catalog  (Brown et al. 2011 ) and tailoring that method for application to cool stars. Specifically, we extract grizJHK photometry from the KIC for the 51813 planet search target stars with KIC temperature estimates ≤ 5050K and for the 13402 planet search target stars without KIC temperature estimates and compare the observed colors to the colors of model stars from the Dartmouth Stellar Evolutionary Database  (Dotter et al.
Validating Methodology We confirm that we are able to recover accurate parameters for low mass stars from photometry by running our stellar parameter determination pipeline on a sample of stars with known distances. We obtained a list of 438 M dwarfs with measured parallaxes, JHK photometry from 2MASS, and g ′ r ′ i ′ photometry from the AAVSO Photometric All-Sky Survey 5  (APASS) from Jonathan Irwin (personal communication, January 2, 2013) and performed a series of quality cuts on the sample. We removed stars with parallax errors above 5% and and stars with fewer than two measurements in the APASS database. We then visually inspected the 2MASS photometry of the remaining 230 stars to ensure that none of them belonged to multiple systems that could have been unresolved in APASS and resolved in 2MASS.
We determine σ CDPP by fitting a curve to the observed Combined Differential Photometric Precision (CDPP;  Christiansen et al. 2012 ) measured for each star over 3hr, 6-hr, and 12-hr time periods and then interpolating to find the expected CDPP for the predicted transit duration. CDPP is available from the data search form on the Kepler MAST. 8  Although the CDPP varies on a quarter-by-quarter basis, we choose to interpolate the median CDPP value at a given time period for each star across all quarters. We also repeat our analysis using the minimum and maximum CDPP for each time interval to quantify the dependence of the planet occurrence rate on our estimate of the noise in the light curve on the timescale of a transit. We then estimate the number of transits n that would have been observed by dividing the number of days the star was observed by the orbital period of the planet.
This paper includes data collected by the Kepler mission. Funding for the Kepler mission is provided by the NASA Science Mission directorate. We thank the Kepler team for acquiring, reducing, and sharing their data. This publication makes use of data products from the Two Micron All Sky Survey, which is a joint project of the University of Massachusetts and the Infrared Processing and Analysis Note. -Table  4  is published in its entirety in the electronic edition. A portion is shown here for guidance regarding its form and content. ( R ⊕ ) F (F ⊕ ) T eff (K) R * ( R ⊙ ) a This column lists the ratio estimated from the fit to the light curve. We compute the geometric probability of transit using the semimajor axis determined from the planet orbital period and the host star mass listed in v Transits noted as "v"-shaped by  Batalha et al.
Second Attendant (singing as Head): I sing a song of Jack and Jill […] 6 In the first song, an 'I' addresses a 'you' and both interlocutors seem to be properly identified: the Queen on the one hand and the severed head on the other. What is more, the tone is one of command, thus confirming that there are two entities, one addressing the other. The scene therefore seems to be a dialogue between two perfectly distinct identities. Yeat's two games of masks, or duality, are quicky revealed as these two identities come across each other or accumulate with one another. The first layer of this game of doubles is found in the inner split occuring in both the Queen and the Swineherd, between each one's public and private (if not spectral) sides. This split stems from the association between reported speech and singing.
Excluding the last two groups, some 70% are artists and 79% writers, more if Darwin and Lamarck are counted as writers. Hazard Adams treats the same data slightly differently, and makes the point that 'Yeats sees the writers in or as their work', The Book of Yeats's Vision: Romantic Modernism and Antithetical Tradition (Ann Arbor: University of Michigan Press, 1995), 88. 25 It is one of the paradoxes of Yeats's perception that the poet of 'Song of Myself ' expresses not self but 'a product of democratic bonhomie, of schools, of colleges, of public discussion' (AVB 114; CW13 41; AVA 47). assume 'an intensity which is. always lyrical and personal, and this intensity, though always a deliberate assumption, is to others but the charm of the being' (AVB 141-42; CW13 63; AVA 76), the tension should appear effortless and the value lies in sincerity, winning the audience by the strength of the voice.
Readers who rely on the Oxford University Press Collected Letters of W. B. Yeats published only to 1907) and do not have access to the InteLex database may be astonished at WBY's first full love letters to GY: 'at first you were but a plan & a dream & then you became a real woman, & then all in a moment that real woman became very dear' (5 October  [1917] , 10). Two earlier letters of 3 and 4 October begin 'My beloved', and in the first of these there may be a hint of psychological transference when WBY writes' [I] think of the time when I shall find you, when my work is over, sitting at the gass fire or dealing firmly with Mrs Old' (8). George Hyde-Lees is now the 'beloved', replacing Maud Gonne for whom he wrote, 'When you are old and grey and full of sleep, | And nodding by the fire, take down this book, And slowly read' (VP 120).
Study participants Twenty asymptomatic patients with mild-to-severe aortic stenosis were recruited from outpatient clinics at the Edinburgh Heart Centre (see Supplementary data online). Twenty healthy volunteers were recruited from the community and the University of Edinburgh. All individuals had normal renal function and a left ventricular ejection fraction within the normal range. The exclusion criteria for patients with aortic stenosis were as follows: (i) other significant valvular heart disease (moderate to severe in nature), (ii) acquired or inherited cardiomyopathies, (iii) previous myocarditis and (iv) the presence of focal LGE. The exclusion criteria for healthy volunteers were as follows: (i) hypertension, (ii) diabetes mellitus, (iii) coronary artery disease (previous myocardial infarction, evidence of myocardial ischaemia, or.
CMR imaging CMR was performed at 3T (MAGNETOM Verio, Siemens AG, Healthcare Sector, Erlangen, Germany) according to the study protocol (Supplementary data online). Short-axis cine images were obtained using a balanced steady-state free precession sequence (8-mm parallel slices with 2-mm spacing) for the assessment of left ventricular function and volumes. T1 mapping was performed using the MOdified Look-Locker Inversion recovery (MOLLI; flip angle 358; minimum TI 100 ms; TI increment of 80 ms; time delay of 150 ms with a heart beat acquisition scheme of 3-3-5) with built-in motion correction. 27 A gradient echo field map and associated shim were performed to minimize off-frequency artefact. Short-axis T1 maps of the mid-cavity slice were acquired in diastole before and at 2, 5, 10, 15, 20, and 30 min following the administration of 0.
1 mmol/kg of gadobutrol (Gadovist/Gadavist, Bayer Pharma AG, Germany). Additional basal and apical T1 maps were obtained in diastole at 0, 15, 20, and 30 min (see Supplementary data online). The basal slice was defined as the first complete ring of myocardium below the aortic outflow tract, and the mid-cavity slice as the most basal slice to include both papillary muscles. The apical slice was selected between the apex and the mid-cavity on the image least affected by trabeculations and partial volume averaging. LGE imaging was performed between 8 and 15 min using two approaches: an inversion-recovery fast gradient-echo sequence and a phase-sensitive inversion recovery sequence, performed in two phaseencoding directions to differentiate true enhancement from artefact. 28, 29 The inversion time was optimized for each slice to achieve satisfactory nulling of the myocardium.
Reproducibility analysis (intra-, inter-observer, and scan-rescan) was performed using intra-class correlation coefficients (ICC). ICC values between 0. 50 and 0. 75 indicated moderate reliability and values. 0. 75 good reliability. For clinical measures, excellent ICCs of. 0. 90 are required to ensure sufficient reliability. 31 Fixed and proportional biases with 95% limits of agreement were assessed using Bland-Altman analyses. All statistical analyses were performed using GraphPad Prism (GraphPad Software, Inc. , San Diego, CA, USA) and SPSS version 19 (SPSS, Inc. , Chicago, IL). A two-sided P , 0. 05 was considered statistically significant.
Proportions were calculated with 95% exact confidence intervals (CI). In a primary analysis, differences between proportions were tested for significance using the Fisher exact probability test (STATA 10. 0), in order to avoid data loss and as the effect of matching, which was done for another study component, was expected to be small on RDT performance. For comparison of specificity, this primary analysis was followed by a secondary analysis using McNemar chi square, after matching controls and HAT again taking into account the PCR result. For sensitivity, the low number of PCR-matched samples precluded meaningful comparison with the McNemar test. Inter-reader reliabilities were assessed for the test results expressed as positive and negative line readings and kappa values for each pair of readers were calculated.
Discussion We demonstrated that specificity of seven out of ten malaria RDT products was significantly lower in HAT patients compared to controls. RDT products generated false positive test results in various proportions. The problem was most pronounced with pan-pLDH test lines and occurred to a lesser extent with HRP-2 test lines. The Pf-pLDH test lines were not affected. Rheumatoid factor was not associated with false positivity. Our study has some limitations. It was set up to test the specificity of the RDTs and not their sensitivity to detect clinical malaria. Furthermore, our data only apply to chronic T. b. gambiense HAT, from which we collected specimens in a single HAT focus, and not to the more acute disease form caused by T. b. rhodesiense, and did not address other diseases that might influence malaria RDT specificity.
All RDT products were stored according to the instructions of the manufacturers and were used before their expiry date. Lot to lot variation was assessed for ICT Malaria Combo Cassette Test and obtained specificities were similarly low for the second as for the first lot tested (data not shown). Cross-reactions of specific trypanosome antigens present in blood of HAT patients with the antibodies used in the malaria RDTs also seems unlikely, because of the large variation of proportions of false positive results between the different RDT products. Although malaria constitutes the main differential diagnosis of HAT  [10] , this is the first study evaluating accuracy of malaria antigen detection RDTs in HAT. Although in areas with high malaria endemicity such as Bandundu, people of 12 years or older have acquired sufficient immunity against malaria parasites, so that if they have fever or feel unwell the reason should not be automatically ascribed to malaria even if the RDT, or any other diagnostic test, is positive, mistaking HAT for malaria is probably a frequent event.
Furthermore, in HAT endemic areas, awareness among health personnel of the possibility of HAT infection, even if tests for other diseases are positive, should be increased. Rapid tests for screening on HAT specific antibodies are now available, and allow identification of HAT suspects even at the level of the health centre  [26]. We withhold from proposing a particular malaria RDT to be used in HAT and malaria co-endemic regions since actually we cannot present relevant data on sensitivity of the RDTs in clinical malaria. Parasite densities in immune patients exhibiting symptoms range from 2,500 in infants to 30,000/ml in adults  [2]. The highest parasite densities observed in our participants were 978 and 694 parasites/ml, and corresponding blood samples tested positive in all malaria RDTs (data not shown).
Using the Catalog The ALESS catalog can be found accompanying this paper or from the ALESS website 21. For a detailed description of the data columns in the catalog, see the README file accompanying the catalog. Some of the relevant columns for the MAIN and Supplementary samples are also listed in Tables  3  and 4  and described below. Note that while we list both the observed and primary beam corrected flux densities for reference, the primary beam corrected flux densities should always be used for science applications. • LESS ID: LESS source ID in order of appearance in the S/N-sorted  Weiß et al. (2009)  catalog. • ALESS ID: Official IAU short ID for ALESS SMGs (ALESS XXX. X), based on LESS ID and ranking in S/N of any subcomponents. Note that higher S/N subcomponents will not make it into the MAIN catalog if they are outside the primary beam FWHM.
Immunofluorescence Cells fixed with 2% paraformaldehyde were incubated with the following primary antibodies: rabbit polyclonal anti-FLAG (Sigma-Aldrich, 1:300) and mouse monoclonal anti-VEGFR2 (Fitzgerald, MA USA, 1:100). Then, samples were incubated with the secondary antibodies (goat anti-mouse FITC or goat anti-rabbit FITC; Jackson Immunoresearch, Suffolk, UK; 1:250), stained with TRITC-conjugated Phalloidin (Sigma-Aldrich, 1:5000) and nuclei were counterstained with DAPI. The glasses were analyzed with a Leica DMIRE2 microscope equipped with a Leica DFC 350FX camera and elaborated by Leica FW4000 deconvolution software (Leica, Solms, Germany).
RESULTS The vegfr-2 gene contains a G4 structure in the promoter and its expression is inhibited by G4 ligands VEGFR-2 is the main receptor expressed on the surface of EC regulating tumor angiogenesis. Here, based on computational analysis with the QGRS G4 structure prediction software  (33) , we identified a G-rich strand in the promoter (region from À117 to À94) of vegfr-2 gene (Figure  1A ) whose probability to form G4 structures (G-score) is similar to that of human telomeric repeats stretch (Figure  1B ). To experimentally validate the predictive analysis, we investigated the structure adopted by an oligonucleotide reproducing the putative G4-forming region of vegfr-2 promoter by CD  (34) (35) (36). The CD bands of DNA samples are generated when the bases are chirally oriented with respect to each other, i.