dataesr/scientific-paragraphs-categorization huggingface dataset:
The presence or absence of mecA, fusB, lukS/F-PV, tet(K), tet(L), tet(M), and ileS2 was examined using local BLASTN against the generated contigs from the genome data of the 97 CC80 isolates (Genomics Workbench; CLCbio). The query sequences used were mecA, fusB, lukS/F-PV (GenBank accession number NC_017351), tet(K) (GenBank accession number NC_017331), tet(L) (GenBank accession number FN390947), tet(M) (GenBank accession number AM990992), and ileS2 (GenBank accession number EU366902). Accessory genome. Protein sequences were extracted from the genome sequences using Prodigal  (100). All protein sequences were searched against the Pfam-A database (101, 102) using HMMER3  (103). The protein sequences were binned by the absence or presence of Pfam protein domains. Within each bin, all sequences were compared pairwise using BLAST 2.
Sequence data accession numbers. The accession numbers for the Illumina sequences generated from the 97 S. aureus CC80 isolates described in this study are available in the European Nucleotide Archive (ENA; http://www. ebi. ac. uk/ena) under the primary identification number PRJEB6777. Sequences can also be located in the ENA using the following study title: "Origin and Evolution of the European Community-Acquired Methicillin-Resistant Staphylococcus aureus. " The sequence of the SCCmec type IVc1 element has been deposited in GenBank under accession number KM281804; the sequences of plasmids pT45 and pT49 have been deposited in GenBank under accession numbers KM281802 and KM281803.
prior to SNP calling; type IVa, isolate JCSC1968; type IVb, isolate JCSC1978; type IVc, isolate MR108; type IVc, isolate 2314, type IVe, isolate AR43/ 3330. 1; type IVg, isolate M03-68, with GenBank accession numbers AB063172, AB063173, AB096217, AY271717, AJ810121, and DQ106887, respectively.
ACKNOWLEDGMENTS Stine-Frese Madsen ,  Alexandra Medina ,  Mille Weismann Poulsen ,  Lone Ryste Kildevang Hansen ,  Elvira Chapka , and  Julie Hindsberg Nielsen  ( Statens Serum Institut ),  Tania Contente-Cuemo  and  Katerina Soldanova  ( Translational Genomics Research Institute ), and  Michele Bes  ( CIRI, French National Reference Center for Staphylococci ) are thanked for excellent technical assistance. This work was supported by  Pfizer  (Grant Europe  ASPIRE 2010 Research Awards ) and the  Foundation pour la Recherche Médicale  (grant number  ING20111223510 ). We declare that we have no conflicts of interest.
Flow cytometric analysis of adhesion molecules and surface differentiation antigens After being cultured with different conditions, NB4 cells were harvested and re-suspended in 50 mL PBS-0. 5% BSA solution containing appropriate concentrations of the antibodies for adhesion molecules or surface differentiation markers. Corresponding isotype antibodies were used as controls. After 30 min incubation at 4uC in the dark, cells were washed twice and analyzed immediately by FACSCalibur cytometer, with data being collected by CellQuest software.
Western blot detection of signaling molecules Cells were lysed with lysing buffer, supplemented with protease inhibitor cocktail, and then protein concentrations were measured by BCA assay. Equal amounts of total protein from different samples were subjected to 10% SDS-polyacrylamide gels and then transferred to polyvinylidenedifluoride membranes, which were probed with the indicated primary antibodies. Detection was accomplished using corresponding horseradish peroxidase (HRP)conjugated secondary antibodies followed by development with ECL Plus (Beyotime Co. , Suzhou, Jiangsu Province, China). Images were captured by G: BOX iChemi XR (Syngene Inc. , UK). The intensities of the bands were analyzed by Image J2x software. Cell lysing solution, protease inhibitor cocktail, BCA protein assay kit, and chemiluminescent substrate were purchased from Thermo Scientific (Pierce, Rockford, MA, USA).
Quantitative RT-PCR of ICAM-1 mRNA Total RNA was isolated using TRIzol reagent according to the instructions of the manufacturer (Life Technologies Corporation (Invitrogen, Carlsbad, CA, USA). RNA quantity and quality were confirmed with a Drop-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA). cDNA was synthesized from 1 mg total RNA by oligo(dT)18 primers and M-MLV reverse transcriptase. Quantitative RT-PCR analysis was performed using the LightCycler (Roche China Center, Shanghai, China) and Taq DNA polymerase. Specific primers of ICAM-1 used for quantitative RT-PCR analysis assays were 59 CAC AAG CCA CGC CTC CCT GAACCT A 39 (sense) and 59 TGT GGG CCT TTG TGT TTT GAT GCT A 39 (antisense)  [8]. Data were normalized by b-actin level. Oligo(dT)18 primers, Taq DNA polymerase, and M-MLV reverse transcriptase were from Takra Biotechnology Co.
ImmunoFluorescence For staining of eIF3G protein and stress granules, HuH7 cells were grown in 24-well plates, fixed with 4% paraformaldehyde for 10 min, and permeabilized with 0. 1% Triton X-100 for 1 min at room temperature. Cells were then incubated with anti-Myc Tag and anti-TIA-1/TIAR antibodies for 1 h at room temperature followed by incubation with fluorescently labeled secondary antibodies. Protein subcellular localization was performed using an epifluorescence microscope with a Zeiss 63 1. 4 oil immersion objective, recorded with a digital camera, and analyzed with Northern Eclipse software (Emprix Imaging, Mississauga, Ontario, Canada). The percentage of stress granules per cells was performed as described previously  [62]. In non-treated conditions (left panel-A), HIF-1a translation is controlled by HDAC9 and then HIF-1a mRNA is translated in protein.
Acknowledgments We thank  Dr. E. Chevet  ( INSERM U1053, Universitede Bordeaux, Bordeaux, France ) for his gift of HuH7 and Hep3B cells and plasmids and his helpful discussions. We are grateful to  Dr. B. Drogat  ( UniversiteLibre de Bruxelles, IRIBHM, Brussels B-1070, Belgium ) for his help and fruitful discussions.
HST AND THE LENSING MODEL Although the main motivation for our study comes from the new submm data, it makes the most scientific sense to first describe the optical data. We retrieved previously unpublished observations using WFC3 on HST from the Canadian Astronomical Data Centre (program 11591). The observations were taken at 1. 1 and 1. 6 µm with 2400 and 2600 second exposures, respectively. A small pointing shift in the data, with respect to HST data published by  Borys et al. (2004)  and Berciano  Alba et al. (2010) , was corrected by aligning to the older HST data in this field. These observations reveal a host of new red objects in the region of the submm arc (Fig. 1 ). Using Lenstool  (Kneib et al. 1996; Jullo et al. 2007; Jullo & Kneib 2009)  and a new lensing model for the cluster, we were able to identify four new multiply-imaged galaxies within the HST images in the region of the submm arc.
2 arcseconds, calculated by bootstrapping the 24 µm source list. Two PACS  (Poglitsch et al. 2010 ) observations taken as part of the PACS Evolutionary Probe key program  (Lutz et al. 2011 ) are also available and were processed using the "multiple obsid scanMapDeepSurvey" pipeline within HIPE 10 (Ott 2010). The default units were converted from Jy pixel -1 to Jy beam -1 by multiplying by the beam area and dividing by the pixel area. The beam area for the 160 µm point spread function (PSF) was found to be 180 arcsec 2 and was computed by integrating over the beam profile provided by the NASA Herschel Science Center. The FWHM at 160 µm is 11. 6 arcseconds. For galaxies at z ∼ 3, 70 µm PACS data are expected to be dominated by warm dust, which is not well reproduced by the simple SED model adopted in § 4, and are therefore not used in this study.
Model fitting The model is fit to the data using an MCMC Metropolis-Hastings algorithm  (Metropolis et al. 1953; Hastings 1970)  with Gibbs sampling  (Geman & Geman 1993). Since the SCUBA-2 450 and 850 µm and PACS 160 µm data are limited by instrumental noise, the log likelihood functions for these data are calculated as follows: -log L b = X b + k (D b (x k ) -M b (x k )/c b ) 2 2σ 2 b,k , (5) where subscript b denotes the band, D b (x k ) are the data, x k denotes the position of pixel k in the image, σ 2 b,k is the instrumental noise for pixel k, c b is the instrument calibration factor (with a mean value of unity), and X b is a constant. The log likelihood function for the Herschel SPIRE data is more complicated, since we are limited by extragalactic confusion noise as opposed to instrumental noise.
The confusion limit in each channel is 5. 8, 6. 3 and 6. 8 mJy at 250, 350 and 500 µm, respectively  (Nguyen et al. 2010). This means that the residuals after subtracting the model will be: (i) much larger than instrumental noise; (ii) correlated spatially with the beam; and (iii) correlated across wavelengths. This is because confusion noise is real signal generated from many faint sources that are all blending together to produce an unknown and correlated variable background. Taking confusion into account, the log likelihood function for the Herschel SPIRE data is therefore -log LSPIRE = XSPIRE + 1 2 R T C -1 R, (6) where R is a one-dimensional list of the residuals, and contains all three channels of SPIRE data (R = {D250(x k ) -M250(x k )/c250, D350(x k ) - M350(x k )/c350, D500(x k ) -M500(x k )/c500} ), and C -1 is the inverse covariance matrix for the residuals.
ACKNOWLEDGEMENTS This research has been supported by the  Natural Sciences and Engineering Research Council of Canada. IRS acknowledges support from  STFC  ( ST/I001573/1 ), a  Leverhulme Fellowship , the  ERC   Advanced Investigator program  DUSTYGAL and a  Royal Society/Wolfson  merit award. The James Clerk Maxwell Telescope is operated by the  Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the United Kingdom , the  National Research Council of Canada , and (until 31 March 2013) the  Netherlands Organisation for Scientific Research. Additional funds for the construction of SCUBA-2 were provided by the  Canada Foundation for Innovation. SPIRE has been developed by a consortium of institutes led by  Cardiff University (UK)  and including  Univ. Lethbridge (Canada) ;  NAOC (China) ;  CEA ,  LAM (France) ;  IFSI ,  Univ.
This research has made use of data from the  HerMES  project (http://hermes. sussex. ac. uk/), a  Herschel Key Programme utilising Guaranteed Time  from the  SPIRE  instrument team, ESAC scientists and a mission scientist. The HerMES data were accessed through the HeDaM database (http://hedam. oamp. fr)operated by CeSAM and hosted by the  Laboratoire d'Astrophysique de Marseille. This research used the facilities of the  Canadian Astronomy Data Centre  operated by the  National Research Council of Canada  with the support of the  Canadian Space Agency. Based on observations made with the  NASA/ESA Hubble Space Telescope , obtained from the data archive at the  Space Telescope Institute. STScI is operated by the association of  Universities for Research in Astronomy, Inc. under the  NASA  contract  NAS 5-26555.
Status of advanced LIGO (Presenter: L. Barsotti on behalf of the LIGO Scientific Collaboration) Two 4 km-long Advanced LIGO detectors are currently in their installation phase in United States, one in Hanford (WA) and one in Livingston (LA). The Livingston idetector, L1, is currently commissioning the central part of the interferometer, with all the main components integrated and tested, except the kilometric arms. A complementary strategy has been carried out on the Hanford interferometer, H1, where one of the two 4 km arms has been fully commissioned. Both interferometers are on target to complete the installation and to be operational in 2014, and to start collecting observational data in 2015. Compared to initisal LIGO, the high frequency performance (above a few hundred hertz) will be improved by increasing the amount of laser light power circulating inside the interferometers, the mid-band through reduction of thermal noise, while the low frequency part of the spectrum will approach the design target by reducing the impact of technical noises, such as seismic, and length and angular control noises.
GEO-HF commissioning update (Presenter: K. Dooley) The German-British laser interferometer gravitational-wave detector, GEO 600 is located near Hannover, Germany. It has served as the sole interferometric gravitationalwave detector in operation since September 2011. While other observatories worldwide are being upgraded and constructed, GEO 600 has been collecting science quality data with a duty cycle of approximately 2/3. The data will be searched for gravitational waves in the event of an external trigger indicating, for example, a supernova in our Galaxy. Data quality tools aid our monitoring of the detector  [13]. GEO 600 is expected to run together with early Advanced detectors, as they come online over the next few years. Above about 1 kHz, the potential target sensitivity of GEO 600 is similar to that of the early Virgo detector (in Virgo's foreseen first phase without Signal recycling mirror).
Mode healing in GW interferometers (Presenter: C. Bond) For the commissioning of advanced detectors it is crucial to understand the behaviour of the interferometers in the presence of deviation of the mirror surfaces from an ideal sphere. This can result in distorted beams at the interferometer output. The presence of a signal recycling mirror (SRM), intended to enhance gravitational wave sidebands in the detector, has the additional benefit of healing the distorted beam. Observed in GEO600, it results from the effective cavity formed between the two interferometer arms and the SRM, in which the TEM 00 mode is enhanced and higher-order spatial modes are suppressed. Using the simulation program FINESSE  [3]  an initial investigation of this phenomenon was carried out for Advanced LIGO in the presence of unbalanced thermal distortions.
31 Temperature effects on the optical properties of highly uniform, porous, amorphous Ta 2 O 5 coatings on silica (Presenter: G. Gemme) We present spectroscopic ellipsometry results (0. 755 eV range) obtained on Ta 2 O 5 coatings deposited on silica substrates by ion sputtering. Two sets of samples of different thickness were considered: a sub-set was treated with post-growth annealing, in different conditions. Absorption losses data were obtained with photothermal common-path interferometry at 1,064 nm. The best simulation of data was obtained using the CodyLorentz approach on a three-phase model (substrate/film/surface) and a quasi-uniform density (∼7 %) of empty spherical pores inside the coating. The analysis of samples annealed to increasingly higher temperatures showed a slight blue-shift of the energy gap, an increase in the pore volume fraction, an increase (∼1 %) in the coating thickness, a small (<1 %) reduction in the index of refraction in the transparency region and a limited increase in absorption losses.
Histogram equalization can reduce these visibility errors. This method is described in detail in  Kreplin et al. (2012). We were able to extract H and K band visibilities (cf. Fig. 2 ). Within the error bars, the obtained closure phase is zero for all nights (Fig. 3 ), which is consistent with a centro-symmetric brightness distribution. We also used archival low-resolution data obtained with the MIR two-beam combiner MIDI  (Leinert et al. 2003; Schegerer et al. 2013). The data (see Table  2 ) were reduced using our own IDL codes (see Appendix A of  Kishimoto et al. 2011  for details), which utilize a part of the standard software EWS 2 and also implement an average over a relatively large number of frames to determine the group-delay and phase-offset tracks with a good signal-to-noise ratio.
3. 1). The errors of the radii include the distance error (116 ± 30 pc). We simultaneously fit all visibilities with a two-dimensional visibility model. The model curves are plotted for all position angles for which visibilities were measured. The color sequence (blue to red) describes the decreasing difference between the PA of the measurement and the disk's fitted semi-major axis ϑ. sition angle ϑ of the semi-major axis of the disk. A more detailed description of our modeling of temperature-gradient disks can be found, for example, in  Vural et al. (2012)  or  Kreplin et al. (2012). We computed models for all mathematical combinations of the parameter values listed in Table  4. We chose the model with the lowest χ 2 red value as the best-fit model. The given error bars are 3σ errors. We first attempted to fit the data with a model consisting of a stellar point source (distance, L * , and T * from Table  1 ) and a temperature-gradient disk (model A in Table  4 ).
Then, the 32 optical passes are simulated and the TASD is computed separately for each pass. For a misaligned laser beam, we must then numerically compute the geometrical factor of the TASD, more precisely the luminosity geometrical factor, which consists of a quadruple integral describing the space-time overlap between electron bunches and laser pulses  [38]  (Table  I  provides the beams parameters). Thus, the CODE V optical simulations must be complemented by another software, e. g. , MATLAB, to perform the geometrical luminosity calculations. However, with 128 reflective surfaces to simulate, such a procedure turns out to consume an unrealistic amount of computing time. One way to circumvent this problem is to use a fast simulation based on an estimator correlated to TASD losses for a given optical misaligned configuration.
More precisely, for a given recirculator misalignment, the optimum space-time overlap of the electrons and laser beam will occur when the laser pulse will be synchronized to the electron bunch at the SDBA. To demonstrate the correlation between the TASD and the SDBA, we again use the recirculator parameters of Table  II , taking Δε ¼ 3. 8 μrad for the sequences of misaligned MPS and choosing the injection and parabolic mirrors perfectly aligned. An ensemble of misaligned MPS configurations is then simulated using CODE V and TASD are finally computed using the MATLAB software  [39]. Figure  11 (a) shows TASD as a function of the SDBA. This plot contains all optical recirculations of 400 randomly misaligned recirculator simulations (i. e. , there are 32 entries for each recirculator configuration).
A Gaussian fit is also shown on Fig. 11(a ) which perfectly matches the data points. Notice that in all following figures the laser pulses are synchronized with the electron bunches at the SDBA position. As indicated in Sec. II, this is done by rotating the MPS (by at most 12 mrad for the data of Fig. 11 ). SDBA is nearly perfect as the average difference between the fit and the data is equal to -3 × 10 -4 and the standard deviation is equal to 5 × 10 -4. Thus, we are allowed to circumvent the CODE V simulation by using a simple ray tracing algorithm for the laser beam propagation and the Gaussian function to derive the corresponding TASD. Finally, our simulations of the recirculator misalignments are then done solely with a simple and thus fast MATLAB code.
VII. CONCLUSION In this article, we have described a new kind of optical multipass device. It is dedicated to γ-ray production by Compton scattering between multibunch electron beams and of a high power laser for ELI-NP-GBS at the ELI-NP facility under development in Romania. A general method to design the recirculator's geometry and optical surfaces was developed for optimizing the γ-ray beam properties. Detailed numerical simulations were carried out within the framework of the specifications of the ELI-NP-GBS project. Owing to the optical properties of the laser beam propagation inside the recirculator, we could set up a fast simulation code and thereafter show that the performance required by ELI-NP-GBS is achievable. Moreover, considering all the losses (due to synchronization, alignment, and mirror reflections) equal to 6%, the recirculator has an enhancement factor of about 30 with respect to the TASD of a single pass.
After fixation, cells were suspended in 100 ml phosphatecitrate buffer (0. 19 mol l À 1 Na 2 HPO 4 and 4 mmol l À 1 citric acid (both from Sigma)) and incubated for 30 min at room temperature. Cells were then resuspended in 1 ml PBS (Lonza, Verviers, Belgium) containing 10 mg ml À 1 propidium iodide (Sigma) and 10 mg ml À 1 RNase A (Sigma). The propidium iodide-stained cell samples were analysed with a flow cytometer (FACSCalibur, Becton Dickinson, Oxford, UK) at 620 nm. Further DNA analysis was performed using MultiCycle AV software (Innovative Cell Technologies, San Diego, CA, USA). Apoptosis analysis. Cells were seeded and treated as described for the cell cycle analysis. Cells and washings were pelleted by centrifugation at 600 g, washed twice with PBS and resuspended in 600 ml Annexin V-binding buffer (10 mM HEPES pH 7.
s u m m a r y Objective: The aim of this study was to compare the responsiveness of various patient-reported outcome measures (PROMs) and clinician-reported outcomes following total knee arthroplasty (TKA) over a 2year period. Methods: Data were collected in a prospective cohort study of primary TKA. Patients who had completed Forgotten Joint Score-12 (FJS-12), Western Ontario and McMaster Universities (WOMAC) osteoarthritis (OA) index, EQ-5D, Knee Society Score and range of movement (ROM) assessment were included. Five time points were assessed: pre-operative, 2 months, 6 months, 1 year and 2 years post-operative. Results: Data from 98 TKAs were available for analysis. Largest effect sizes (ES) for change from preoperative to 2-month follow-up were observed for the Knee Society Score (KSS) Knee score (1.
Sample population Data were collected in a prospective cohort study of primary TKA between 2007 and 2009 at Kantonsspital St. Gallen, Switzerland. This was a pragmatic study that reflected local surgical practice at the time using both, mobile and fixed bearing designs. Informed consent was obtained from the participants and ethical approval was granted by the local ethics committee. Patients who had completed FJS-12, WOMAC score, EQ-5D and Knee Society Score (KSS) were included. Participants were assessed at five different time points: pre-operatively, and at 2, 6, 12 and 24 months postoperatively. Socio-demographic and clinical data included gender, Body Mass Index (BMI), age at time of surgery and side of implant.
Responsiveness over time To highlight how the different measures perform over different time-intervals following surgery we analysed data by investigating responsiveness compared to baseline and also to the previous follow-up assessment. Presenting responsiveness indices this way allows to demonstrate more clearly at which time point after surgery the various measures are able to capture change. Baseline comparisons are also detailed in the Tables  III  and IV. Pre-operative to 2-month follow-up Largest ES for change from pre-operative to 2-month follow-up were observed for the KSS knee score (1. 70), WOMAC-pain (À1. 52) and WOMAC total (À1. 50). In contrast, range of motion only changed little with an ES of À0. 19. SRM was biggest for WOMAC pain (À1. 18) and WOMAC function (À0. 91) and smallest for ROM (À0.
There is scant data on PROM responsiveness for 2-year follow-up periods and longer. Whereas Browne et al. 28  suggested to follow-up patients until 1 year postoperatively, our data demonstrate the need of longer follow-up periods. We captured change between 12 and 24 months using responsive measures. The need for follow-up beyond one year has been recognised and is also reflected by journal author guidelines  29. It is of note that orthopaedic journal author guidelines started to require 2-year outcome data for clinical studies involving new implants despite the fact that the ability of various PROMs to capture change over this time frame still needs further investigation. The sex ratio we report in this study was unexpectedly equal, however, this reflects the patient throughput in our clinics on the 2 days/week the study nurse was present to recruit.