dataesr/scientific-paragraphs-categorization huggingface dataset:
The final galaxy group and group galaxy samples The aim of our analysis is to study how the star formation activity in group-sized halos depends on the global properties of the systems. In order to do that, we would need to sample the complete group galaxy population in stellar mass and SFR. However, since the group members are spectroscopically selected, we need to consider how the spectroscopic selection function drives our galaxy selection and, thus, how it can affect our results. We point out that we can not define a galaxy sample which is, at the same time, complete in stellar mass and SFR. For this purpose, we check how the spectroscopic completeness in the IRAC band translates into a completeness in mass and SFR. For ECDFS and CFDN this is already done in  Ziparo et al. (2013). For the new datasets of AEGIS and COSMOS we follow the same approach of the mentioned work.
2010 ). We stress here that this does not produce a problem for our approach. Indeed, we aim to understand the bias induced by selection function like the spectroscopic selection function of our dataset by using the Millennium galaxy mock catalogues. In other words, we only need to extract mock catalogues randomly to reproduce the same bias in selecting, on average, the same percentage of most starforming and most massive galaxies of the parent sample. By comparing the results obtained in the biased randomly extracted mock catalogues and the unbiased parent catalogue, we estimate the bias of our analysis. Since in both biased and unbiased mock catalogues the underestimation of the SFR or the stellar mass of high redshift galaxies exists, it does not affect the result of this comparative analysis.
(2006). We assume that the group galaxy members identified by the FoF algorithm, which takes into account also the real 3D spatial distribution of galaxies, are the correct ("true") group members. The "true" velocity dispersion, ΣSFR, ΣM * and N are, thus, the one based on this membership. We apply, then, our method for calculating the membership, the velocity dispersion, total M * , total SFR and halo occupation distribution on the "incomplete" mock catalogs described in Section 2. 6, which include also the effect of the different spectroscopic selection functions. For each group we assume the coordinates of the central galaxy (the identification of central and satellite galaxies is provided in the mock catalog) as group center coordinates. These estimates are based on the 2D projected galaxy distribution and redshift information as in the real dataset.
We estimate the "observed" velocity dispersion on the basis of this membership to take into account the effect of spectroscopic incompleteness. We measure the "observed" σ as in the real dataset. In other words, we base the velocity dispersion estimate on M200 and the relation between σ and r200 as in  Carlberg, Yee & Ellingson (1997)  for groups with less than 10 members and on the dynamical analysis for groups with more than 10 galaxies. We consider also that our first guess for the velocity dispersion is affected by the uncertainty in the M200 in the observed dataset, which is retrieved via LX -M200 correlation. To take this into account we add a random error to the M200 of the group provided by the mock catalog. The scatter of the LX-M200 relation is quoted about 20% in the group mass region based on the estimation via stacking analysis  (Leauthaud et al.
Comparison with the mock catalog To compare our results with theory, we look at the results based on the mock catalog of the Millennium Simulation as described in Sect. 2. 6. We analyse the same relations studied in our work by extracting from the mock catalog a sample of groups in the same mass range and redshift range adopted in our study. The quantities Σ M * , Σ SFR and number of galaxies per halo mass are calculated by following the same criteria used for the real dataset. In addition, we also estimate the properties of the groups at 1<z<2 to completely follow the evolutionary trends of galaxies up to z ∼ 2. As already known, the semi-analytical models of the Millennium simulation underpredict the level of star formation activity of the galaxy population and, in particular, of the group and cluster galaxies.
(2013)  based on a similar dataset. -The analysis of the evolution of the fraction of SF galaxies as a function of halo mass or velocity dispersion shows that high mass systems seem to be already evolved at z∼1 by showing a fraction of star-forming galaxies consistent with the low redshift counterparts at z < 0. 085. Given the almost linear relation between the ΣSFR and M200 in the high-z sample, this implies that most of the contribution to the total SFR of the most massive systems (M200 ∼ 10 14 M⊙) is given by few highly star-forming galaxies, while in lower mass systems (M200 ∼ 10 13 M⊙) is given by many galaxies of average activity. This would be an additional sign of a faster evolution in the more massive systems in terms of star formation activity with respect to lower mass groups. Thus, it would confirm the "halo downsizing" effect.
2012). There is also evidence that at z∼1 there is a flattening of the SFR-density relation  (Elbaz et al. 2007; Popesso et al. 2011; Cooper et al. 2008; Ziparo et al. 2014)  with respect to the local anti-correlation. Ziparo et al. (2014)  find on the very same dataset that the differential evolution of the groups galaxies with respect to field is due to the fact that starforming group galaxies are perfectly on the Main Sequence at z∼1 whereas at lower redshift they are quenched, thus, dropping off the MS quicker than field galaxies towards the region of SF quiescence. What is causing this differential evolution as a function of the halo mass? According to  Peng et al. (2010)  massive galaxies, as the ones considered in our sample, evolve mostly because of an internally driven process, called 'mass 20 Erfanianfar dvi.
Figure7. Distribution of the residuals of the logarithm of the "true" and "observed" velocity dispersion. The blue histogram shows the distribution of the residuals obtained from the original mock catalogs. The red histogram shows the distribution obtained if we take into account the error on M 200 derived from L X as done in the real dataset. The green histogram show the same diagram but with the "observed" velocity dispersion estimated on the basis of the "incomplete" mock catalog.
ACKNOWLEDGEMENTS GE acknowledges the support from and participation in the  International Max-Planck Research School on Astrophysics at the Ludwig-Maximilians University. MLB acknowledges financial support from an  NSERC   Discovery Grant , and from  NWO  and  NOVA  grants that supported his sabbatical at the  University of Leiden , where this work was completed. PACS has been developed by a consortium of institutes led by  MPE (Germany)  and including  UVIE (Austria) ;  KUL, CSL, IMEC (Belgium) ;  CEA, OAMP (France) ;  MPIA (Germany) ;  IFSI, OAP/AOT ,  OAA/CAISMI, LENS, SISSA (Italy) ;  IAC (Spain). This development has been supported by the funding agencies  BMVIT (Austria) ,  ESA-PRODEX (Belgium) ,  CEA/CNES (France) ,  DLR (Germany) ,  ASI (Italy) , and  CICYT/MCYT (Spain). This research has made use of  NASA 's Astrophysics Data System, of  NED , which is operated by  JPL/Caltech , under contract with  NASA , and of  SDSS , which has been funded by the  Sloan Foundation ,  NSF , the  US Department of Energy, NASA , the  Japanese Monbukagakusho , the  Max Planck Society , and the  Higher Education Funding Coun-cil of England.
difficile. Using the xFiToM software  [24] , we screened genomes of thirty C. difficile strains (Additional file 1: Table  S1 ) for the C. acetobutylicum and C. perfringens consensus operator sequence of LexA  [15, 16] , allowing for two mismatches in one of the two half sites positioned within 350 bp upstream to 35 bp downstream of a protein coding sequence. Among the thirty genomes, the search yielded at least one putative operator sequence upstream of more than 30 genes involved in a variety of biological processes e. g. DNA repair, transport, virulence and antibiotic resistance (Table  1 ). Subsequently, we purified C. difficile LexA and RecA proteins with an N-terminal hexa-histidine tag (Additional file 2: Figure  S1 ) as described for E. coli orthologs  [25]. SPR analysis was performed to validate the in silico data and determine the LexA-operator interactions in vitro in real time.
Variability of lexA gene Variability of lexA in C. difficile was compared by analysis of alignment and phylogenetic trees of nucleotides and amino acid sequences performed with Vector NTI (Invitrogen) and with the interactive viewer for phylogenetic trees: Dendroscope  [32]. Sixty three sequences were analysed in total (NCBI -9 strains, MicroScope -44 strains, PCR product of in-house strains -10). Strains CD196, R20291 and 630 were obtained from both databases. List of strains used for lexA gene variability can be found in Additional file 1: Table  S1.
In silico determination of the C. difficile SOS regulon The search for LexA binding sites was performed for 30 genomes (Additional file 1: Table  S1 ). The number of strains covering ribotypes was as follows: ribotype 027eight strains; ribotypes: 078, 001, 005 and 012 -three strains from each; ribotypes 075 and 126 two strains from each and one genome from each ribotypes 017, 087, 014, 053. The analysis was performed with xFiToM software  [24]. The searched motifs, based on C. acetobutylicum and C. perfringens consensus, were as follows: GAAC nnnnGTTT, GAACnnnnGTTC, GAACnnnnnTTT, GA ACnnnnnTTC. The default options were used with the limitation to 350 base pairs upstream to 35 bp downstream of a protein coding sequence. An exception was the promoter region of the putative endonuclease/exonuclease/ phosphatase (MicroScope: CDR20291_2056) where we found 2 operators positioned approximately 460 upstream of the coding sequence and hence, we included the targets in the analysis.
(In this Letter mention of a particular decay implies the use of the charge-conjugate decay as well. ) One third of the data was recorded at 7 TeV center-of-mass energy, and the remainder at 8 TeV. The search strategy is based on our previous analysis  [2] , but extends the sensitivity to neutrino lifetimes, τ N , from the picosecond range up to about 1000 ps. The selection is aimed at maximizing the efficiency squared divided by the background yield. For lifetimes 1 ps, the π + µ -decay products can appear as significantly detached from the B -decay vertex. Therefore, we use two distinct strategies, one for short τ N (S) and another for τ N up to 1000 ps (L). The LHCb detector is a single-arm forward spectrometer covering the pseudorapidity range 2 < η < 5, designed for the study of particles containing b or c quarks  [5].
We acknowledge support from CERN and from the national agencies: CAPES, CNPq, FAPERJ and FINEP (Brazil); NSFC (China); CNRS/IN2P3 and Region Auvergne (France); BMBF, DFG, HGF and MPG (Germany); SFI (Ireland); INFN (Italy); FOM and NWO (The Netherlands); SCSR (Poland); MEN/IFA (Romania); MinES, Rosatom, RFBR and NRC "Kurchatov Institute" (Russia); MinECo, XuntaGal and GENCAT (Spain); SNSF and SER (Switzerland); NAS Ukraine (Ukraine); STFC (United Kingdom); NSF (USA). We also acknowledge the support received from the ERC under FP7. The Tier1 computing centres are supported by IN2P3 (France), KIT and BMBF (Germany), INFN (Italy), NWO and SURF (The Netherlands), PIC (Spain), GridPP (United Kingdom). We are indebted to the communities behind the multiple open source software packages we depend on.
The number of eggs and hatch rates were recorded en masse. Statistical Analysis. Egg hatch rate data were arcsine-transformed to achieve normal distribution and compared between treatment using analysis of vari-ance (ANOVA) and TukeyÕs post hoc tests. Radiationinduced sterility values were corrected for the mean natural sterility of the controls. KaplanÐMeier survival analyses were conducted to determine differences between groups in terms of adult survivorship; survival curves were compared using the survdiff function of the R Survival package, Peto & Peto modiÞcation of the GehanÐWilcoxon test was used to give a greater weight to the early or late deaths. ANOVA, log-rank, and Wilcoxon tests were performed to compare mean longevity of the different groups. For all tests, the alpha level was P Ͻ 0.
Acknowledgments We appreciate the donation of the Rimini strain by the  Centro Agricultura Ambiente, Crevalcore, Italy. H. Y. greatly appreciates the Þnancial support and exceptional employment provided by the  U. S. State Department. C. F. O. is supported by a grant from the  European Social Funds  and the  Reunion Region. We greatly appreciate the valuable comments on the manuscript by  Marc J. B. Vreysen.
The angle h corresponds to a rotation around the vertical Y-axis. The spatial resolution of the THz scanner is limited to a few millimeters owing to the long wavelength of the emitting source. Symmetrically, the focal volume is imaged using a similar arrangement on a commercial pyroelectric sensor (Spectrum Detector Inc. ). For final data acquisition, the THz beam is modulated at 20 Hz by an optical chopper and the amplitude of the transmitted THz is acquired with a lock-in amplifier. A 2D transmission image of the sample is obtained by moving the object in the X and Y directions with a scan step of 1 mm in both directions. With a scan speed of 5 pixels/sec, the acquisition time for a 100 9 100 pixels 2D image size is about 30 min. For 3D reconstruction, the sample is rotated in order to provide a different visualization of the object.
The custom optics projects a 48. 6 9 48. 6 mm 2 area onto the 13 9 13 mm 2 sensitive surface of the CCD chip. The resolution of the imaging system falls between 220 and 500 lm, depending on the sample's distance to the neutron sensitive screen. The imaging acquisition software Andor SOLIS was applied to record images in external triggering mode. The radiographic projections (601 images) were taken with the full neutron beam, at every 0. 3°increment through a 180°r otation. The radiography images were corrected for the spatial inhomogeneity of the beam and the thermal noise of the camera. For tomographic imaging, the reconstruction code OCTOPUS 8. 6 was used, that relies on the inverse Radon transformation and filtered back-projection algorithms  [21]. The visualization of the dataset in 3D space (volume rendering) was carried out using VGStudio 2.
Acknowledgments The authors gratefully acknowledge Francois Hubert, director of the  Museum of Aquitaine, and the city of Bor deaux  for the authorization to perform the measurements at the museum. They also thank  R. Trouette ,  M. Montaudon  and  J. B. Boutolleau  from the radiotherapy centre at the  Haut Leveque Hospital (Bordeaux)  for X ray measurements,  P. Decout  and  T. Solaire  from  General Electric Healthcare  for the X ray data reconstruction. This project has been supported by the  CHARISMA  project (Contract  228330 ) and the  Action Interdisciplinaire de Recherche 'Arch eometrie'  ( TeraScan  project, CNRS, France).
Statistical analysis The quality indicators reporting the appropriateness or inappropriateness of caesareans were presented as percentages. Continuous variables were compared by Student's t test. Crude odds ratios (OR) of inappropriate caesareans were calculated according to maternity unit level, with their 95% confidence intervals (95%CI). Significance was set at 0. 05. Data collection and analysis were performed with SAS software (version 9, SAS Institute, Cary, NC, 2002-2010).
Conclusions Our study revealed that the French healthcare providers do not always follow French guidelines about indications for caesareans. This conclusion had already been suggested by an earlier French study from the Audipog database about the impact of clinical practice guidelines in France  [53]. Such an appropriateness review of caesareans, conducted within a perinatal health network, is feasible and would, more than a feedback of quantitative indicators to obstetricians, make it possible to quantify the rate of inappropriate caesareans, regardless of their cause. This type of medical qualitative assessment appeared to have some effect on medical practices in the short run, as this rate decreased in our perinatal network and in 8 of 10 maternity units, although the difference was significant in only two maternity units.
Blood was sent immediately to the hemostasis laboratory to determine the VASP phosphorylation state of whole blood. We used a standardized flow cytometric assay [Platelet VASP®; Diagnostica Stago (Biocytex), Asnières, France], which is an adaptation of the method of Schwarz et al. previously described  [16]. PRI VASP was calculated from the median fluorescence intensity (MFI) of samples incubated with PGE1 or PGE1 and ADP according to the formula: PRI VASP = [MFI (PGE1) -MFI (PGE1 + ADP) / MFI PGE1 ] × 100. The platelets were stimulated with ADP (10 μmol/L), and aggregation was assessed with a PAP4 aggregometer (Biodata, Wellcome, Paris, France). Aggregation is expressed as the percentage of change in light transmittance from baseline, with platelet-poor plasma as the reference. In the present study, we report the data on the maximum intensity of 10 μM/L ADP-induced platelet aggregation.
In an attempt to clarify this question we performed experiments where cells were pre-treated with sera containing MBL with subsequent washing and incubation with shed GP. As demonstrated in Figures  2C  and S3C , shed GP binding to the cells was also blocked under these conditions, in this case most likely via interaction of TLR4 with MBL. In agreement, pre-incubation of cells with MBL deficient sera did not affect shed GP binding. Thus far data obtained clearly indicate an interaction between shed GP and DCs and Mø. This is contrary to a previous publication in which no evidence of an interaction was found between shed GP and immune cells  [32]. In this regard, the cells were transfected with plasmids expressing GP-WT (WT), GP-HS (HS), GP-LS (LS), sGP and GFP and 36 h post-transfection cells and culture supernatants were collected and analyzed by Western Blot using anti-GP 1 and anti-GP 2 antibodies.
Estimation of shed GP amounts in the sera of animals in comparison with shed GP from GP-HS expressing cells was performed using ImageQuantTL software (GE Lifesciences). Sera of animals contained approximately 85 times higher amounts of shed GP than those used in experiments with immune cells. (D). Samples of sera collected at different intervals post infection from Mock (day 3 p. i. ) -and EBOV-infected guinea pigs  (animal numbers 192, 193, 195 & 196)  as indicated, were analyzed by Western blot using anti-GP2 antibodies. The release of shed GP dramatically increased during the course of infection. Sera of infected animals contains both virion GP and shed GP as demonstrated by the presence of full-length virion-associated GP 2 and truncated GP 2 (GP 2D ). doi:10. 1371/journal. ppat. 1004509.
Data shown are representative of three independent experiments with at least three different donors. For quantitative data and statistics see figure  S3. doi:10. 1371/journal. ppat. 1004509. g002 Figure  3. Shed GP induces transcriptional activation of cytokines in DCs and MØ. DCs and MØ (5610 5 cells) were incubated with concentrated culture supernatants as above (as Figure  2 ) and with LPS (500 pg/ml). Cells were collected at 4, 8, 12 and 24 h post-incubation as indicated. Expression levels of mRNA encoding TNF-a, IL-6, IL-10 IL-12p40, and GAPDH were measured by RT-Q-PCR in DCs (A) and MØ (B). Relative levels of the cytokines were obtained by normalization to GAPDH and Mock as indicated. (C) DCs and MØ as above were treated with concentrated immune cells could induce the expression of these surface molecules.
5 ng/ml) before addition to DCs or MØ. An MBL-deficient serum (MBL 2 ) was used as a negative control. Cells were collected 8 hours post treatment and analyzed by RT-Q-PCR as above. Human sera did not itself activate DCs or MØ. (A, B, C and D) The data shown are representative of three independent experiments using three blood donors and presented as mean 6 sd of triplicates. Statistical significance (paired-sample t test) compared to GP-HS is shown as follows: * -p,0. 05 and ** -p,0. 01; n. s. -not significant. doi:10. 1371/journal. ppat. 1004509. g003 Taken together the data obtained support a role for EBOV shed GP in the creation of excessive and dysregulated host inflammatory responses and an increased vascular permeability. Based on the results presented here we postulate that once released from the surface of infected cells shed GP could be responsible for the induction and release from non-infected macrophages and DCs of a battery of pro-and anti-inflammatory cytokines.
(B) 5610 5 of DCs (in white) and MØ (in gray) were incubated for 24 h with concentrated culture supernatants as above and, in addition, the cells were pre-incubated with an anti-TLR4 antibody (Ab + ) followed by treatment with HS or LPS. (C) Shed GP induces secretion of cytokines from DCs and MØ in a dose-dependent manner. 5610 5 of DCs (in white) and MØ (in gray) were incubated for 24 h with concentrated culture supernatants, or LPS as above. Decreasing quantities of shed GP (HS) ranging from 0. 4 mg to 0. 1 mg were tested as indicated. (A, B and C) The concentration of each cytokine in duplicate was measured using Multiplex cytometric bead array (Bio-Rad) in Luminex MAGPIX. The data shown are representative of three independent experiments with three blood donors and presented as mean 6 sd of triplicates.
In addition the cells were incubated with *HS following LPS treatment (*HS+LPS). The concentration of TNFa in duplicate was measured using Multiplex cytometric bead array (Bio-Rad) in Luminex MAGPIX. The data shown are representative of three independent experiments with three blood donors and presented as mean 6 sd of triplicates. Statistical significance (paired-sample t test) compared to GP-HS is shown as follows: * -p,0. 05. doi:10. 1371/journal. ppat. 1004509. g006 Figure  7. EBOV Shed GP increases cell permeability of HUVEC in vitro. HUVEC cells were seeded onto the culture inserts of permeability assay chambers and incubated for 22 h with concentrated culture supernatants from 293T cells expressing GFP (Mock), sGP, GP-LS (LS), GP-HS (HS) and LPS (10 ng/ml). Cells were also incubated with human sera containing MBL (MBL + ), MBL-deficient sera (MBL 2 ), a mixture of HS/MBL-containing sera (HS+MBL + ) and HS/MBL-deficient sera (HS+MBL 2 ).
The culture medium was removed and replaced by medium containing EBOV GPs (in VP-SFM medium, Gibco). Cells were incubated for 1 hour at 4uC, washed twice with ice-cold phosphate-buffered saline (PBS) and then incubated in FACS buffer (PBS containing 2% FBS, 2% normal rat serum, 2% normal hamster serum, 2% normal mouse serum and 2% human FcR blocking solution, Milteny Biotec) at 4uC for 30 min. Cells were then incubated with mouse anti-GP1 antibody for 1 hour at 4uC, washed twice with PBS and incubated with anti-mouse IgG1 coupled to Alexa 488 for DCs and Mø or to Allophycocyanin (APC) for lymphocytes for 30 min at 4uC. All mAbs were purchased from BD Pharmingen except those indicated otherwise. After incubation with antibodies, cells were washed and fixed with 1% PFA solution. Cells were analyzed using a Becton Dickinson LSRII flow cytometer (BD) and FlowJo software.
In some experiments samples of GP were incubated with human sera containing MBL (150 ng/ml) or MBL-deficient sera (Statens Serum Institute, Denmark) for 1 hour at 4uC prior to addition to immune cells. In TLR4-related experiments, cells were incubated for 10 min at room temperature with 30 mg/ml of anti-TLR4 antibodies (HTA125) or unspecific isotype antibody prior to addition of EBOV GPs. The statistical significance of the differences in median fluorescence intensity (MFI) values for each donor were evaluated by paired-sample t test and GraphPad Prism 6 software (GraphPad Software, La Jolla California, USA).