dataesr/scientific-paragraphs-categorization huggingface dataset:
S5 , the integrated fluorescence intensity of GFP::CycBNt::Bub3 was measured from a sum projection (5. 5 µm) at the kinetochore and tether (signal above the maximum pixel intensity in the cytoplasm) and normalized to the fluorescence intensity at the kinetochore and tether at metaphase (1 min before anaphase onset). Data points were fit to a sigmoid curve (Y = 1/{1 + 10^[(LogEC-X)*Hill slope]}) using Prism software (GraphPad). The Hill slope (h) was used to compare the kinetics of GFP::CycBNt::Bub3 signal disappearance between the WT without I-CreI expression (WT no HS; Fig. S5, C  and D ), the WT after I-CreI expression (WT), and bubR1-KEN mutant cells after I-CreI expression (bubR1-KEN). In Fig. S5  B, the average fluorescence intensity of GFP::Cyclin B signal in the whole cell was measured over time from a sum projection (5.
Acknowledgments We thank  Zohra Rahmani ,  Roger Karess ,  Christian Lehner ,  Claudio Sunkel , and  Jordan Raff  for sharing reagents. We thank all laboratory members for technical help and fruitful discussion. N. Derive was supported by the  University of Bordeaux. C. Landmann  and  E. Montembault  were supported by grant  ANR-12-PDOC-0020-01/ ARC2-ChromSCeD. E. Montembault was also supported by  Centre National de la Recherche Scientifique (CNRS). M. -C. Claverie  was supported by the  University of Bordeaux. N. Founounou was supported by grant  ATIP-AVE NIR/INCa 2010-291  and  Conseil Régional d'Aquitaine  (grant  20111301010 ). D. Goutte-Gattat  and P. Pierre-Elies were supported by grant  ERC-STG-2012 GA311358-NoAneuploidy. D. McCusker  was supported by grant  ANR-13-BSV2-0015-01-POL ARFLUX  and  CNRS.
Dataset The genome assemblies of eight Wolbachia strains belonging to A-D and F supergroups (wMel, wRi, wPipPel, wDi, wOo, wBm, wLs and wCle) and of seven other Alphaproteobacteria (Caulobacter crescentus strain CB15, Cre; Anaplasma centrale strain Israel, Ace; Anaplasma phagocytophilum strain HZ, Aph; Ehrlichia chaffeensis strain Arkansas, Ech; Ehrlichia ruminantium strain Gardel, Eru; Neorickettsia risticii strain Illinois, Nri; Neorickettsia sennetsu strain Miyayama, Nse) were retrieved from public database (for more information about genome features, see table  1 ). Caulobacter crescentus was chosen because it is a complete genome of an alphaproteobacterium for which origin and terminus of replication were experimentally determined  [29]. The genome assemblies included in the study are all complete or almost complete, with the exception of the genome of wLs, which is divided into 10 contigs.
GC skew The cumulative GC skew curve was calculated for each of the ORI-starting Wolbachia genome assemblies. It was calculated applying the formula SG 2 C/G þ C, with a window size of rsob. royalsocietypublishing. org Open Biol. 5: 150099 1000 nt and step size of 100 nt (analyses were performed with an in-house PERL script). For each of the Wolbachia strains in the dataset, with the exception of wLs (fragmented in 10 contigs), the potential effect of genomic rearrangements on the current GC skew curve was evaluated. The following procedure was used: (i) the ORI-starting genome was aligned against the ORI-starting wDi genome with PROGRESSIVEMAUVE; (ii) the detected syntenic blocks were sorted and oriented according to the ORI-starting wDi order; (iii) the cumulative GC skew curves were calculated for both the obtained reoriented genome and relative aligned wDi genome; and (iv) the mean absolute difference between the two curves was calculated.
Mutational bias The effect of mutational bias on the guanine and cytosine distribution along the genomes of Wolbachia strains C and F (wDi, wOo-C supergroup; wCle-F supergroup) was evaluated using Wolbachia strains A, B and D (wMel, wRi-A supergroup; wPipPel-B supergroup; wLs and wBm-D supergroup) as outgroups. A dataset of single-copy orthologous genes, shared among all the eight Wolbachia strains included in the study, was obtained with ORTHOMCL  [35]  and in-house PERL scripts. Nucleotide gene sequences were aligned on the corresponding amino acid alignments, using MUSCLE  [36]  and in-house PERL scripts. For each gene, the number of mutations towards G and towards C for third position residues was evaluated for each pair of Wolbachia strains, using a custom PERL script. The mutational biases along wDi, wOo and wCle genomes were evaluated comparing each of them against all the other seven Wolbachia strains included in the study.
Gene loss and gain Events of gene loss/gain that occurred in the genome of the ancestor of Wolbachia supergroup C were inferred on the basis of the pattern of gene presence/absence in the present strains. This presence/absence pattern was reconstructed, annotating the genomes of the eight Wolbachia strains included in the study and of six Anaplasmataceae outgroups, against the clusters of orthologous groups (COGs) database by PSI-BLAST with a p-value cut-off of 10 -5. The loss and gain events occurred in the genome of the ancestor of Wolbachia supergroup C were inferred using the GLOOME tool  [37] , mapping the pattern of Table  1. List of the genomes included in this study. For each genome, information about the strain, the corresponding host and the genome are reported. rsob. royalsocietypublishing.
GC skew and mutational bias Another feature described as characteristic of arthropod Wolbachia genomes is the absence of strong GC skew  [39] , in contrast with the pattern commonly observed in most freeliving bacteria and in endosymbiotic bacteria such as Buchnera aphidicola  [44, 45]. The cumulative GC skew curve of the seven completely sequenced Wolbachia genomes included in the study (wMel, wRi, wPipPel, wDi, wOo, wBm and wCle) and of the Alphaproteobacterium outgroup, C. crescentus, were calculated (figure  2 ). In agreement with previous analyses on a smaller dataset  [39] , most Wolbachia genomes do not present any genome-wide pattern of GC skew (figure  3 ). However, the wDi genome has a strong pattern of GC skew (figure  3 ), which, among endosymbionts, is typically observed in bacteria with extremely reduced genomes.
C Image analysis Vesicles were imaged using a phase contrast microscope (Ellipse, Nikon) and recorded using a digital camera (AVT Marlin F-146B, First Sight Vision, UK). Vesicle pictures were analyzed with a custom-written Labview program. Basically, the analysis program detects the edges of the vesicle and then performs a Fourier decomposition of this 2D cross-section of the spheroidal vesicle contour. An ellipse is fitted to the Fourier contour in order to find the semi-major axis, M and the semi-minor axis m of the fitted ellipse as defined in Fig. 1c. The major axis strain (respectively minor axis strain) is defined by DM/R = (M R)/R (respectively Dm/R = (m R)/R), where R is the mean radius of the vesicle in the undeformed state.
Acknowledgements The authors deeply thank  Jacques Prost  and  Jean-François Joanny  for fruitful discussions. U. D. acknowledges financial support from  Pierre-Gilles De Gennes  foundation and J. G. acknowledges financial support from the  Alexander von Humboldt Foundation  ( AvH Professorship ) the  ERC (Starting grant ''LightTouch'')  and the  HFSP  (research grant).
The CMS and ATLAS Collaborations have performed many searches for physics beyond the SM. Thus far, no significant evidence for new physics has been obtained. The search for supersymmetry is particularly interesting phenomenologically because of the large number of new particles expected. The LHC SUSY search program consists therefore of a wide array of searches  [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22]. Any particular manifestation of SUSY in nature would likely result in topologies that are detectable in a variety of final-states. Individual searches can therefore be combined to provide complementarity and enhanced sensitivity in the global search for new physics. Naturalness arguments suggest that the supersymmetric partners of the gluon (gluino, g) and third-generation quarks (the top and bottom squarks, t and b) should not be too heavy  [23] [24] [25] [26].
The total visible jet activity H T is defined as the scalar sum of the jet p T in the event, and H miss T as the p T imbalance of the reconstructed jets, where the p T and η requirements for accepted jets are specified for the individual searches in Section 4. The identification of b jets is performed using the combined secondary vertex algorithm at the medium working point  [40] , which has a b-jet tagging efficiency of 70% and a light-flavor jet misidentification rate below 2% for jets with p T values in the range of interest for this analysis. The missing transverse momentum vector p miss T is defined as the projection on the plane perpendicular to the beam axis of the negative vector sum of the momenta of all reconstructed particles. Its magnitude is referred to as E miss T. The data sample used for the fully hadronic analysis was recorded with trigger algorithms that required events to have H T > 350 GeV and E miss T > 100 GeV.
The events are examined in exclusive regions of H T and E miss T for 2 ≤ N jets ≤ 3 and N jets ≥ 4, all for N bjets = 0, 1, and ≥2. There are three main sources of SM background in this analysis: non-prompt leptons, rare SM processes, and electrons with wrong charge assignments. The main sources of non-prompt leptons are leptons from bottom-and charm-quark decays, misidentified hadrons, muons from light-meson decays in flight, and electrons from unidentified photon conversions. The background from non-prompt leptons is evaluated from data control regions. Diboson, ttW, and ttZ production are the most important rare SM background sources. Their contributions are estimated from MC simulation. Opposite-sign dileptons can also contribute to the background when the charge of an electron is misidentified because of bremsstrahlung emitted in the tracker material.
Individual data points are shown as white dots on top of the corresponding bars. **P < 0. 05, ***P < 0. 01, n. s. , not significant (Student's t-test, assuming normal distribution of the data points). (D) Likewise, the role of syndecans was investigated by treating MCF-7 cells with RNAi targeting syndecan-1 and -4 (KD). Non-targeting RNAi (NT) was used as a control. Cells were treated with increasing concentrations of proheparanase (0 to 25 nM) and both the lysates and exosomal fractions were analyzed. Western blots are representative of three independent experiments. Note that lysate and exosome samples derived from NT-and KD-treated cells, separated by a blank space in Figure  2D , were run in the same gel, but not side by side, and that the band intensities in each row are directly comparable.
Western blot To allow detection of full-length syndecan core proteins, the samples were digested with (0. 006 U/ml) heparitinase (Amsbio) and (0. 166 U/ml) chondroitinase ABC (Amsbio) for 3 h at 37 °C in heparitinase buffer (0. 1% Triton, 0. 1 M NaCl, 1 mM CaCl2 , 50 mM 6-aminohexanoic acid and 50 mM HEPES, at pH 7). Samples were fractionated in 4%-12% gradient gels (NuPAGE Novex Bis-Tris gels, Invitrogen), electro-transferred to Hybond-C extra 0. 45μm nitrocellulose membrane (GE Healthcare Life Sciences) and incubated with the indicated antibodies. Signals were visualized with enhanced chemiluminescence detection reagent (GE Healthcare Life Sciences) and were quantified by densitometric scanning using ImageJ Software (National Institutes of Health).
(E) Quantification of intraluminal budding of mCherry-syntenin-1 and syndecan-1 cytoplasmic domain, as in C and (F) quantitation of intraluminal budding of mCherry-syntenin-1, as in D, measuring the mean fluorescence intensity of mCherry-syntenin-1 and syndecan-1 in the lumen of RAB5 Q79L -positive endosomes (mean gray value per pixel). Bar heights represent mean values calculated from three independent experiments, scoring at least 30 cells per experiment. Individual data points are shown as white dots on top of the corresponding bars. **P < 0. 05, ***P < 0. 01 (Student's t-test, assuming normal distribution of the data points).
Acknowledgments We thank  Dr Baietti MF  for her feedback on this study and for critical comments during the redaction of this manuscript,  Dr Granjeaud S  for advice on statistical analysis and the  Imaging Core Facility of the KU Leuven  for access to confocal microscopes. This work was supported by the  Fund for Scientific Research-Flanders  ( FWO, G. 0683. 09N ), the  Concerted Actions Program of the KU Leuven  ( GOA/12/016  and  GOA/2006/13 ), the  VIB , the  Belgian Federation against Cancer (Stichting tegen Kanker ,  SCIE2006-36  and  214-2008 ) and the  Interuniversity Attraction Poles of the Prime Ministers Services (IUAP). The  TRC 1/1. 5 human and mouse shRNA libraries of BCCM/LMBP ( Ghent University, Belgium ) were obtained through structural funding for medium-scale research infrastructure (HERCULES,  AUGE/09/040 ).
We present a measurement of the Z boson differential cross section in rapidity and transverse momentum using a data sample of pp collision events at a centre-of-mass energy √ s = 8 TeV, corresponding to an integrated luminosity of 19. 7 fb -1. The Z boson is identified via its decay to a pair of muons. The measurement provides a precision test of quantum chromodynamics over a large region of phase space. In addition, due to the small experimental uncertainties in the measurement the data has the potential to constrain the gluon parton distribution function in the kinematic regime important for Higgs boson production via gluon fusion. The results agree with the next-to-next-to-leading-order predictions computed with the FEWZ program. The results are also compared to the commonly used leading-order MADGRAPH and next-to-leading-order POWHEG generators.
Differential measurements of Z boson production at the LHC have already been performed  [1] [2] [3] [4] [5] [6] [7] [8]. In this Letter we present the first measurement of the DY cross section at a centre-of-mass energy of 8 TeV for dimuon pairs in the vicinity of the Z boson peak, doubly differential in the transverse momentum q T and in the rapidity y of the Z boson. The analysis uses the data sample of pp collisions collected with the CMS detector at the LHC in 2012, corresponding to an integrated luminosity of 19. 7 fb -1. We present the absolute fiducial cross section and the fiducial cross section normalised to the inclusive fiducial cross section. The measurement probes the production of Z bosons up to high transverse momenta, q T ∼ 100 GeV, a kinematic regime where the production is dominated by gluon-quark fusion.
The energy of muons is obtained from the corresponding track momentum. The energy of charged hadrons is determined from a combination of the track momentum and the corresponding ECAL and HCAL energies, corrected for zero-suppression effects, and calibrated for the nonlinear response of the calorimeters. Finally, the energy of neutral hadrons is obtained from the corresponding calibrated ECAL and HCAL energies. The first level of the CMS trigger system, composed of custom hardware processors, uses information from the calorimeters and muon detectors to select the most interesting events in a fixed time interval of less than 4 µs. The high-level trigger processor farm further decreases the event rate from around 100 kHz to around 400 Hz before data storage.
Measured observables and granularity The reconstructed and background-corrected double differential distribution in q T and |y| is unfolded to pre-final-state radiation (FSR) lepton kinematics. The unfolding is performed to the kinematic region 81 ≤ M(µµ) < 101 GeV and within the kinematic selection of the leading (second) muon, p T > 25  (10)  GeV and |η| < 2. 1 (2. 4). The unfolding is done using an iterative unfolding technique  [35]  implemented in the RooUnfold package  [36]. The bins in q T are [0,20],  [20, 40] ,  [40, 60]  MADGRAPH is used as simulation input to the unfolding. The unfolding is validated by treating the simulated POWHEG signal sample as data. The unfolded POWHEG distribution is found to be compatible with the distribution at the generator level within unfolding uncertainty.
• Muon momentum resolution: The muon momentum resolution is measured in data and simulation, and corresponding corrections are applied. The covariance accounting for the statistical uncertainty of the muon momentum correction measurements is calculated via pseudoexperiments. In addition, an uncertainty is assigned to take into account possible correlated offsets. • Z boson polarisation: The lepton angular distribution of the Drell-Yan process can be described at LO through the coefficients, A 0 -A 4  [41]. However, inaccuracies in the way this is modelled in the simulation can affect the result of the unfolding. The angular coefficients A 0 -A 4 are inferred in bins of q T and |y| in  [42]  for both data and simulation we use. For each parameter A i the simulation is independently reweighted to correspond to the data as measured in  [42].
While the scale uncertainties are smaller at low q T , the shape is not expected to match the data well since multiple soft gluon emissions are not modelled. At very high q T QED corrections could reach a few percent  [45, 46]. The PDF uncertainties in the region q T > 20 GeV range between +1% and -4%. The uncertainty is asymmetric because the inclusive cross section computed using the NNLO CT10 PDF set is about 2. 5% larger than the one obtained using the NNLO NNPDF23 PDF set. The NNLO FEWZ computation predicts the shape correctly, within scale uncertainties of order 6-12%, where the default scale has the general feature of underestimating the relative abundance of high-q T (>20 GeV) events at the 7% level. The shape in |y| is well described by FEWZ. The absolute double differential cross section is presented in Table  2.
The comparison with the NNLO computation of the FEWZ program is shown in Fig. 4. The scale uncertainties range from 10-16% for q T > 20 GeV. The PDF uncertainties are of the order of 3% in the central rapidity region and decrease to about 1% in the forward region. The absolute cross section predicted by the NNLO program FEWZ agrees within the uncertainties with the measurement. A comparison of the measurements with the MADGRAPH and the POWHEG generators is shown in Fig. 5. The statistical uncertainties are smaller than the symbol size. The hatched bands represent the systematic uncertainties of the measurement only. The two generators show opposite trends in q T. The MADGRAPH generator overestimates the data in the highest q T bins, whereas the POWHEG generator underestimates the data up to 20% in this region.
Summary For Z bosons decaying to muons the double differential Z boson fiducial cross section in q T and |y| has been measured in pp collisions at 8 TeV. The results are compared to the next-tonext-to-leading-order predictions computed with the FEWZ program and they agree within the scale uncertainties. Deviations from the data of up to 20% at high transverse momentum are  The measured fiducial Z boson differential cross section, normalised to the inclusive fiducial cross section compared to the NNLO prediction of FEWZ. The first five plots show the q T dependence in the five bins of |y| and the last plot shows the q T dependence integrated over |y|. The NNLO NNPDF23 PDF set with radiative corrections is used for the generation. We include data in q T up to 1 TeV, but have shortened the bin for presentation purposes.
The first five plots show the q T dependence in the five bins of |y| and the last plot shows the q T dependence integrated over |y|. We include data in q T up to 1 TeV, but have shortened the bin for presentation purposes. observed in the MADGRAPH and POWHEG generators. The results are presented along with the full covariance matrix in order to enable their use in future fits of the PDF. The experimental uncertainties are significantly smaller than the current theoretical and PDF uncertainties.
Figure3: The measured fiducial Z boson differential cross section, normalised to the inclusive fiducial cross section compared to the NNLO prediction of FEWZ. The first five plots show the q T dependence in the five bins of |y| and the last plot shows the q T dependence integrated over |y|. The NNLO NNPDF23 PDF set with radiative corrections is used for the generation. We include data in q T up to 1 TeV, but have shortened the bin for presentation purposes.
Acknowledgments We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centers and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MOST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES  and  CSF (Croatia) ;  RPF (Cyprus) ;  MoER ,  ERC IUT  and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NIH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  MSIP  and  NRF (Re-.
Stimuli Greyscale luminance-defined sinusoidal Gabor grating stimuli and Gaussian noise patches were generated using MATLAB (The Math-Works) and the Psychophysics Toolbox  (Brainard, 1997). In the behavioral session, stimuli were presented on a Samsung Syncmaster 940BF screen (1024 ϫ 786 resolution, 60 Hz refresh rate). In the fMRI session, they were displayed on a rear-projection screen using a luminancecalibrated Sony VPL FX40 projector (1024 ϫ 768 resolution, 60 Hz). The stimuli consisted of a set of 60 Gaussian noise patches presented successively in a random sequence, each displayed for 16. 7 ms (total stimulus duration: 1. 0 s) to which a Gabor pattern was added in 20% of the trials. They were displayed in an annulus (outer diameter: 20°of visual angle, inner diameter: 4°) surrounding a central fixation point.
fMRI acquisition. fMRIs were acquired using a 3T Skyra MRI system (Siemens) with a T2*-weighted gradient-echo EPI sequence (TR/TE ϭ 2000/30 ms, 29 transversal slices, voxel size 2 ϫ 2 ϫ 2 mm, 80°flip angle). Anatomical images were acquired with a T1-weighted MP-RAGE sequence (TR/TE ϭ 2300/3. 03 ms, voxel size 1 ϫ 1 ϫ 1 mm, 8°flip angle). Preprocessing. SPM8 (http://www. fil. ion. ucl. ac. uk/spm, Wellcome Trust Centre for Neuroimaging, London, UK) was used for image preprocessing. The first six volumes of each block were discarded to allow T1 equilibration. All functional images were spatially realigned to the mean image, yielding six head movement parameters, and the structural image was coregistered with the functional volumes. Using custom MATLAB code, the data were high-pass filtered (cutoff 128 s) to remove lowfrequency signal drifts and the time series of each voxel was z-scored.
Consistently with previous work reporting a link between perception and prestimulus activity in sensory circuits  (Hesselmann et al. , 2008a) , we restricted our analyses to the two prestimulus scans, t ϭ Ϫ2 s and t ϭ 0 s, corresponding to the functional volumes acquired between Ϫ2 and 0 s and between 0 and 2 s, respectively. We considered the hemodynamic signal in these volumes to reflect prestimulus activity in view of the sluggishness of the hemodynamic response. Statistical significance testing was performed using R statistical software (R 3. 0. 3, GUI Rstudio 0. 98. 501); statistical tests were two-tailed. To investigate whether spontaneous fluctuations in V1 biased perception in the absence of a stimulus, we focused our analyses on CRs and FAs. We also report the data for hits, whereas misses were not analyzed due to their low number (see "Behavioral results").