dataesr/scientific-paragraphs-categorization huggingface dataset:
In contrast to the IS26 examples identified here, we found several copies of these family members flanked by direct repeats of the expected lengths, suggesting intermolecular transposition followed by resolution. While Tn3 family members such as Tn4401 often encode their own resolvase (64), IS903B and ISKpn14 do not (see the ISfinder database). Perhaps resolution of cointegrates generated by these elements relies on RecA-mediated homologous recombination, as suggested for IS26, or these IS elements may be able to transpose by simple insertion  (65, 66). Results of our analysis suggest that IS26 prefers to transpose within plasmids rather than into the chromosome. This is not a general feature of ISs, as there are many other ISs present at very high copy number in the chromosomes analyzed here.
For example, up to 17 copies of ISKpn26 were observed in certain chromosomes (e. g. , KONIH1 [data not shown]). As the chromosomal IS copies tend to have conserved flanking TSDs more frequently than those in the plasmids, it seems that most chromosomal transposition events employ simple transposition mechanisms, such as cutand-paste or copy out-and-paste  (26) , which might be better tolerated, as they cause less overall disruption than replicative transposition. Although there are several chromosomal IS26 copies within the nine analyzed NIHCC strains, these are exclusively located in a prophage-carrying region and may have transposed into the phage genome before its integration into the host chromosome. We also believe that selection bias might be involved, which would constrain the IS26 copy number in the chromosome so as to avoid potentially harmful deletions.
However, we cannot exclude the possibility of replicative transposition within chromosomes: IS903B may have deleted a 15-kb region from the KPNIH1 chromosome (region 2716602 to 2731997 in CP008827) that is rich in transporter genes and whose loss results in the absence of this region in NJST258_1 (data not shown). This is consistent with the reported intramolecular replicative transposition activity of IS903B  (63). The availability of whole-genome sequencing carried out with new tools, such as Pacific Biosciences RS II SMRT technology, makes possible the unambiguous identification of mobile elements, and we expect many more clinical isolates to be sequenced. Combining these sequence data with IS annotation tools like ISsaga provides robust and reliable data from which to derive mechanistic information about the activity of mobile elements in their native hosts and therefore to understand the evolution of their host genomes.
MATERIALS AND METHODS Genomic sequences of the nine NIHCC isolates as well as other clinical isolates analyzed in this paper are from the NCBI public database (see Table  S2  in the supplemental material for a list of the analyzed genomes). IS annotation for these genomes was carried out with the ISsaga program (insertion sequence semi-automatic genome annotation; at http://issaga-. biotoul. fr/ISsaga/issaga_index. php)  (33). SnapGene 2. 5 was used to visualize the annotation results. Mauve 2. 3. 1 was used to perform comparative genome alignments.
ACKNOWLEDGMENTS This work was partially supported by the  Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases (S. H. , A. B. H. , and F. D. ) and the  NIH Clinical Center  (J. P. D. ). S. H. , A. B. H. , M. C. , J. P. D. , and F. D. contributed to project design and cowrote the paper. S. H. carried out genome IS annotations and data analysis. P. S. performed the IS annotations of the  NJST258_1  and  NJST258_2  genomes. A. M. V. adapted the ISsaga annotation tool to allow batch genome analysis. We declare no competing financial interests.
Processing of the experimental plan was performed using the JMP software (SAS Institute publisher, Cary, NC, USA). The test results are shown in Table  2. It is important to note that the experimental plans do nothing to explain the physical mechanisms brought into play during milling. In the present study, they are used to highlight the various determinant machining parameters for surface integrity and generate different surface conditions for fatigue testing. Face milling was performed on a 3-axis milling machine of the HURCO brand (Indianapolis, IN, USA) with a power of 10 kW. The cutting tools used were of the ISCAR brand (Tefen, Israel) references ADKT 150524R-HM IC928 and ADKT 150540R-HM IC928, named respectively T1 and T2. These cutters are carbide grade IC928 with a PVD TiAlN coating as recommended for the machining of titanium alloys.
This bulge interacts with the exit base of the CD (Fig. 1a ). Overall, the topology and strand-connectivity of PPAD IgSF is strongly reminiscent of that of Kgp and RgpB  [22] [23] [24]  , but while the width (~25 Å) and depth (~20 Å) of the domains are similar, the length-along the strands of the sheets-is much greater in PPAD than in gingipains (~50 Å vs. ~35 Å). Active site of PPAD. The propeller shaft in PPAD is rather solid, with a shallow cavity on its entry base coinciding with the tooth cusp that contains the active site (Fig. 1a, b ). The latter is mainly a narrow funnel-like hole, which accommodates an arginine side chain of a peptidic or protein substrate. It is    1  in  55. c  For definitions, see  56,57. d  According to the XDS program  40. Average intensity is < I/σ (I)> of unique reflections after merging.
ADIs, in turn, citrullinate standalone arginine and protect cells from acidic environments. They are found in plants and microorganisms but are likewise absent from animals  27. Both families do not have extra domains further to the catalytic α /β -propeller. To date, only the structures of human PAD2 and PAD4 have been determined among PADs  8, 28  , and they comprise a ~375-residue calcium-dependent α /β -propeller domain preceded by two IgG domains (see Fig. 1  in 8 and  28  ), which are unrelated to PPAD IgSF further to being all-β protein domains. Among AgDIs, structures have been reported from Enterococcus faecalis (Ef; Protein Data Bank (PDB) access code 2JER  26  ) and Helicobacter pylori (Hp; PDB 3HVM  29  ), and other potential relatives have been deposited with the PDB but not functionally analyzed or published (PDB 2EWO, 1XKN, 1ZBR, 2CMU, 3H7C and 1VKP).
Finally, ADI structures have been reported from Streptococcus pyogenes (Sp; PDB 4BOF  30  ), Pseudomonas aeruginosa (Pa; PDB 1RXX  31  ), and Mycoplasma arginini (Ma; PDB 1S9R  32  ). Among all these, closest structural similarity of PPAD is found with AgDIs (Z-score of 35 according to program DALI  33  ; see Fig. 5c ), followed by PADs (Z = 18-21; Fig. 5a, b ) and ADIs (Z = 18-19). Superposition of the PPAD α /β -propeller on that of human PAD4 (Fig. 5a, b ), EfAgDI (Fig. 5c ), and PaADI, SpADI and MaADI (data not shown) reveals good overall conservation of the five-blade architectures, although several decorations in the distinct blades of each family account for large differences, especially in the loops surrounding the active-site cleft. In particular, PADs evince a large partially helical insertion between β 14 and α 6 of PPAD blade IV and lack α 2 of blade I (Fig.
Methods Protein production, purification, and characterization. P. gingivalis PPAD (UniProt database [UP] access code Q9RQJ2 or GenBank entry WP_005873463. 1 for NCBI gene tag PG_1424) was obtained through small-scale homologous overexpression as a secreted protein from plasmid-transformed P. gingivalis W83 PPAD-deletion mutant strain Δppad. Briefly, plasmid pT-COW, which confers resistance against tetracycline  36  , was used as expression vector, and plasmid derivatives encoding the wild type (wt) and a total of 18 PPAD point mutants (W 127 A, D 130 A, D 130 N, R 152 A, R 154 A, R 154 E, T 180 A, G 182 A, H 236 A, H 236 N, D 238 A, D 238 N, C 239 A, C 239 E, C 239 S, N 297 A, C 351 S, and C 351 A; see Table  1 ) were generated. For this, the wt gene sequence plus 1081 upstream base pairs and 267 downstream base pairs was amplified from P.
Crystallization and diffraction data collection. Prior to crystallization, DTDP-treated anduntreated wt PPAD and DTDP-untreated PPAD-C 351 A were dialyzed overnight against buffer A (20 mM Tris-HCl, 20 mM sodium chloride, pH 7. 5) and further purified by ionic-exchange chromatography on a TSKgel DEAE-2SW column (TOSOH Bioscience) equilibrated with buffer A. A gradient of 4-60% buffer B (20 mM Tris-HCl, 500 mM sodium chloride, pH 7. 5) was applied over 30 ml and samples were collected and pooled. Finally, each pool was concentrated by ultrafiltration and subjected to size-exclusion chromatography on a Superdex 75, 10/300 column (GE Healthcare Life Sciences) equilibrated with buffer C (20 mM Tris-HCl, 150 mM sodium chloride, pH 7. 5). Crystallization assays were performed by the sitting-drop vapor diffusion method.
Complete diffraction datasets were collected at 100 K from liquid-N 2 flash cryo-cooled crystals (Oxford Cryosystems 700 series cryostream) on a Pilatus 6 M pixel detector (from Dectris) at beam line XALOC of ALBA synchrotron (Barcelona, Spain  39  ). Further data were collected on the same detector type at beam line ID23-1 of ESRF synchrotron (Grenoble, France) within the Block Allocation Group "BAG Barcelona. " Diffraction data were integrated, scaled, merged, and reduced with program XDS  40. PPAD-TP, PPAD-C 351 A+ M-R, and PPAD+ D-Q crystals all contained one protein molecule per asymmetric unit (solvent content, respectively, 41%, 44% and 48%), had the symmetry of the space groups P2 1 2 1 2 1 , C2, and P2 1 2 1 2 1 , respectively, and had different cell constants (see Table  2  for data processing statistics).
Structure solution and refinement. A similarity search with programs PSI-BLAST and HHPRED identified only low homology models (PDB 3HVM, 1ZBR, 1XKN, 2JER, 3H7C, and 2EWO), which failed to render a solution by conventional molecular replacement and Patterson-search methods. At this point, wt PPAD-TP crystal diffraction data were used for structure solution with ARCIMBOLDO  [41] [42] [43]. Therefore, 16 datasets with resolutions ranging from 3. 0 Å to 1. 5 Å from different native protein crystals or heavy-ion soaks with similar cell dimensions were merged with program XPREP. A collection of structure fragments was generated from the six aforementioned distant structural relatives, and ARCIMBOLDO runs were set up in parallel with these fragments and libraries  41, 42. These calculations eventually enabled structure solution (see  44, 45  for details), and the resulting phase set was subjected to density modification and autotracing with SHELXE  46  , which yielded an improved set of phases and a partial model.
These phases and the resulting Fourier map enabled subsequent manual model building with the COOT program  47  , which alternated with crystallographic refinement with PHENIX  48  and BUSTER/TNT  49  under inclusion of TLS refinement, until the final refined model of PPAD-TP was obtained. This consisted of residues A  44  -N 464 , one structural sodium ion, seven glycerols, 460 solvent molecules, and 4-thiopyridine moieties respectively attached to the Sγ atoms of C 351 , C 462 , and C 239. The final Fourier map indicated that the side chain of the latter residue was present in two alternate conformations, one bound to thiopyridine and the other with the sulfur as sulfoxide. See Table  2  for final refinement and model quality statistics. The structure of PPAD-C 351 A+ M-R was solved with PHASER within the PHENIX 50 package using the refined coordinates of PPAD-TP.
Acknowledgments We are grateful to  Joan Pous  and  Xandra Kreplin  from the joint IBMB/ IRB Automated Crystallography Platform  for assistance during crystallization experiments and to  Robin Rycroft  for very helpful contributions to the manuscript. We further acknowledge the help provided by local contacts at the  ESRF  and ALBA synchrotrons. We are also grateful to  Adam Lesner  from the  University of Gdansk  and  Oliwia Bochenska  from the  Małopolska Center of Biotechnology  for peptide synthesis and mass spectrometry analysis. This study was financially supported in part by grants from  European, US American ,  Polish ,  Spanish , and Catalan agencies ( UMO-2012/04/A/NZ1/00051 ,  UMO-2012/05/B/ NZ6/00581 ,  UMO-2013/08/W/NZ1/00696 ,  2137/7. PR-EU/2011/2 ,  2975/7. PR/13/2014/2 ,  NIH   NIDCR DE09761 ;  FP7-PEOPLE-2011-ITN-290246 "RAPID"; FP7-HEALTH-2012-306029-2 "TRIGGER"; FP7-HEALTH-2010-261460  "Gums&Joints";  BFU2012-32862 ;  BFU2012-33516 ;  BFU2012-35367 ;  BIO2013-49320-EXP; MDM-2014-0435 ;  2014SGR9  and  2014SGR997 ).
Dataset PPAD-TP (substrate free) PPAD(C 351 A)+M-R (substrate complex) PPAD+D-Q (substrate-mimic complex) Space group P2 1 2 1 2 1 C2 P2 1 2 1 2 1 Cell constants (a, b, c, in Å; β in °) 58. 56, 60. 30, 113. 68, 90. 00 105. 36, 59. 32, 84. 61, 126. 60 60. 53, 71. 31, 105. 66, 90. 00 Wavelength (Å) 0. 9786 0. 9795 0. 9795 No. of measurements/unique reflections 288,438/64,233 254,674/38,882 1,133,182/90,283 Resolution range (Å) (outermost shell) a 42. 0-1. 50 (1. 59 -1. 50) 67. 9 -1. 80 (1. 90 -1. 80) 46. 1 -1. 40 (1. 48 -1. 40) Completeness (%) 98. 5 (95. 7) 99. 3 (98. 9) 99. 6 (97. 5) R merge b 0. 041 (0. 190) 0. 062 (0. 529) 0. 042 (0. 305) R r. i. m. [= R meas ] c / CC( 1 / 2 ) c 0. 047 (0. 217)/0. 998 (0. 973) 0. 067 (0. 584)/0. 999 (0. 927) 0. 043 (0. 321)/1. 000 (0. 973) Average intensity d 21.
We present a kinematical study of 29 spiral galaxies included in the Spitzer Survey of Stellar Structure in Galaxies, using Hα Fabry-Perot data obtained with the Galaxy Hα Fabry-Perot System instrument at the William Herschel Telescope in La Palma, complemented with images in the R band and in Hα. The primary goal is to study the evolution and properties of the main structural components of galaxies through the kinematical analysis of the FP data, complemented with studies of morphology, star formation and mass distribution. In this paper we describe how the FP data have been obtained, processed and analysed. We present the resulting moment maps, rotation curves, velocity model maps and residual maps. Images are available in FITS format through the NASA/IPAC Extragalactic Database and the Centre de Données Stellaires.
TARGET SELECTION The galaxies in our survey satisfy the following requirements: first of all, the declination should be higher than -10 • so that the altitude in the sky could be enough at the time of the observation in La Palma, and only galaxies with inclinations between 0 • and 70 • were selected. According to the instrument specifications, the galaxy should fit well in the GHαFaS FOV of 3. 4 × 3. 4 arcmin. Therefore, galaxies with diameters between 2 and 3. 4 arcmin were selected. Secondly, the range in velocity of the galaxy should not be higher than the free spectral range (FSR) of the instrument (see Sect. 3 for details), although we did not have this ancillary information for all the galaxies. Furthermore, the data reduction processes require that the galaxy should have at least three bright point sources in the field, i.
e. three stars or two stars and the nucleus. The observed sample was selected at the time of the observations, looking at the visibility on the sky, but also requiring a spread in morphological type, bar presence and finally, the availability of ancillary data (interferometric CO, Hi, ultraviolet or Spitzer mid-IR). The final sample consists of 29 galaxies. For the morphological classification, we have followed the up-to-date Mid-IR Classifications for S 4 G Galaxies in the Comprehensive  de Vaucouleurs revised Hubble-Sandage System (CVRHS, Buta et al. 2015). The morphological classification also includes bar presence (9 SA galaxies, 12 SAB galaxies and 7 SB galaxies). In Fig. 1 , we present the morphological classification as a histogram. The general properties of the galaxies in the sample are presented in Table  1.
We used four different Hα filters depending on the galaxy's redshift (6577/23, 6589/24, 6613/24 and 6631/17; central wavelength/FHWM, in Å). The exposure times per galaxy were 3×20 seconds for the R-band images and 3×100 seconds for the Hα images. The typical seeing was around 1 arcsec, ranging from 0. 6 to 1. 6. Table  1. General properties of the galaxies in the sample. Notes. (1) Updated morphological classifications from the CVRHS, where "double stage" galaxies are allowed (i. e. , large-scale S0 or S0/a galaxies with smaller-scale inner spirals) (2) Adopted values of the distances, calculated after applying the Virgo, GA and Shapley corrections, with H 0 = 73 ± 5 km s -1 Mpc -1 , from the NASA/IPAC Extragalactic Database (NED). The uncertainties in the distance measurements have been adopted as per cent of the value.
De-rotation, phase-correction, combination and wavelength calibration There is no suitable de-rotator at the Nasmyth focus of the WHT. Therefore, the first step is to de-rotate the data cubes. To do this, we followed  Blasco-Herrera et al. (2010). At least two point sources in all the planes are selected (ideally stars), and selected throughout the cubes. After that, each plane of the subsequent cubes is de-rotated to the same position. Due to the nature of the FP data, any 2D spatial transformation (rotation or translation) has to be done also in the third dimension (the spectral dimension), and therefore de-rotation must be done simultaneously with the phase calibration. The wavelength calibration is also performed at this point. Lamp exposures were taken between galaxy observations and are used to calibrate in wavelength (see  Carignan et al.
Continuum subtraction The resulting de-rotated, phase-corrected and wavelengthcalibrated data cube is then imported into gipsy (Groningen Image Processing System; van der  Hulst et al. 1992 ). The continuum was subtracted using conrem of gipsy, which estimates the continuum level from line-free frames. To determine the channels free of line emission, we visually check the images and also the spectra, after additional smoothing. For NGC 2748, NGC 5678 and NGC 6070, the velocity amplitude is equal or larger than the FSR and there are no channels free of line emission. The Hα line falls into the next interference order and reappears in the first or last channels (what we call "peak intrusion"). Those channels containing emission from a peak intrusion are copied after or before the first or last channel, where they should really be, increasing the number of channels per cube.
The velocity dispersion maps will be used in Paper III, and they will be corrected for instrumental, thermal and natural line broadening. The natural width has a value of 3 km s -1 (O'dell & Townsley 1988). The thermal width corresponds to 9. 1 km s -1 , assuming a temperature of 10 4 K  (Osterbrock & Ferland 2006). The instrumental width for each galaxy was obtained from the data cube taken with the calibration lamp, following the procedures in ?, and is 8. 3 km s -1. After creating the moment maps, the stars and central regions may leave a residual (i. e. , the continuum may not be properly determined and removed), and therefore the outputs from moments need to be masked. Specifically, for the AGN hosts NGC 4151 and NGC 4639, the central emission saturated the detector and in consequence the continuum subtraction could not be removed properly, leaving a residual that had to be masked out.
As for the inclination, the largest discrepancies occur in NGC 4151 (already discussed), and in NGC 2748 and NGC 3504, where the inclinations as derived from the kinematic data are substantially higher than those derived from the surface photometry. This can be due to the non-uniform distribution of the Hii regions as compared to the distribution of the stars and dust as seen in the S 4 G 3. 6 µm images. NGC 2748 shows a bulge at faint light levels, hence the discrepancy in inclination. NGC 3504 has a low inclination, seen in the S4G image. Also, NGC 2748 and NGC 3504 host an outer ring (R' and R'1, respectively), not seen in Hα.
11 and 12 (a,d,g), we conclude that Q b does not correlate with the amplitude of the non-circular motions. Also, the middle plots of  Figs. 11 and 12 (b, e, f)  show no correlation between the amplitude of the non-circular motions and the presence of a bulge. Although the few cases with a significant bulge (B/T > 0. 1), show that the residual velocities in the bar decrease as B/T increases, more data would be needed to prove whether the bulge is constraining the velocities to remain circular. We have measured the luminosities from the three regions identified previously in the galaxies of the sample (bar, SAR and spiral arms), and derived the SFRs in those regions using the equations presented in Sect. 5. 4. In panels Fig. 11c  and Fig. 12c , we see a slight tendency that the higher noncircular motions correspond to star forming bars, or to bars that show more Hα emission (note that the scale in SFR is logarithmic).
ACKNOWLEDGMENTS We acknowledge financial support to the DAGAL network from the  People Programme  ( Marie Curie Actions ) of the European Union's  Seventh Framework Programme FP7 /2007-2013/ under REA grant agreement number  PITN-GA-2011-289313 , and from the  Spanish MINECO  under grant number  AYA2013-41243-P. This work was cofunded under the  Marie Curie Actions  of the  European Commission  ( FP7-COFUND ). We also gratefully acknowledge support from  NASA JPL/Spitzer  grant  RSA 1374189  provided for the S 4 G project. E. A. and A. B. thank the  CNES  for support. KS, JCMM, and TK acknowledge support from  The National Radio Astronomy Observatory , which is a facility of the National Science Foundation operated under cooperative agreement by  Associated Universities, Inc. This research has been supported by the  MINECO  under the grant  AYA2007-67625-CO2-O2 , and is based on observations made with the WHT operated on the island of  La Palma  by the  Isaac Newton Group of Telescopes , in the  Spanish Observatorio del Roque de Los Muchachos  of the  Instituto de Astrofísica de Canarias.
1  B-C ). To rule out the MOs off-target effects mediated through p53 activation  14  , SUMOs or Ubc9 MO was injected with p53 MO or into p53 null mutants, respectively. Similar phenotypes were observed in the co-injected embryos or p53 null mutants (Fig. 1 J-O  and Supplementary Fig. 1D ). Collectively, these data indicate that impairment of sumoylation leads to depletion of HSPCs during definitive hematopoiesis. To further confirm that HSPCs were depleted in SUMO-deficient embryos, lineage-specific markers related to definitive hematopoiesis were examined. Expression of the myeloid lineage marker lysozyme C and erythroid lineage marker hbae1 were drastically decreased in both SUMOs and Ubc9 morphants (Fig. 2 A-F ). Expression of the lymphoid lineage marker rag1 was absent in the developing thymus compared with control siblings (Fig.
2 G-I ). Thus, these results demonstrate that the three major definitive hematopoitic lineages are all compromised in SUMO-deficient embryos. The defects of definitive hematopoiesis are due to reduced HSPC generation and proliferation. HSPCs arise directly from the aortic endothelium during embryogenesis  [15] [16] [17]. To assess whether the depletion of HSPCs in SUMO-deficient embryos was caused by improper vascular morphogenesis, the expression of flk1, a marker of endothelial cells, was examined. No overt differences were observed between control siblings and SUMOs or Ubc9 morphants (Fig. 3 A-C ), suggesting that the vascular system remains intact. Accordingly, a similar phenotype was also detected in the Tg (flk1-EGFP) transgenic line (data not shown). Next, we investigated whether the HSPC budding process was affected in SUMOdeficient embryos by confocal time-lapse imaging experiments.