dataesr/scientific-paragraphs-categorization huggingface dataset:
Chromatin immunoprecipitation (ChIP) assay ChIP was performed using transiently transfected Drosophila S2 cells  [52]. 10610 6 cells were seeded in 10 cm cell culture dish, and transfected one day later with either 5 mg pUASt-Abd-B-HA and 5 mg pAC-GAL4 plasmids or 5 mg empty pUASt and 5 mg pAC-GAL4 plasmids. 1/10 of cells were collected to monitor the protein expression by Western blot. The remaining cells were cross-linked, lysed and sheared to 350-1000 bp as described in  [53]. Six microliters of anti-HA antibody (Abcam) was used per 100 mg sheared chromatin, and the immunoprecipitation was performed according to  [54]. qRT-PCR was done using primers emsQPCR2for and emsQPCR2rev (Table  S1 ) amplifying inside the ems0. 35 enhancer sequence. The data are represented as recovered percentage from the input in AbdB-HA-transfected cells against GAL4-transfected cells.
Therefore, the time required to reach equilibrium was determined by luminescence spectroscopy, monitoring both the ligand fluorescence (Zn II -HL 6 and Gd III -HL 6 systems) and the phosphorescence of the Eu III ion (Eu III -HL 6 and Eu III -Zn II -HL 6 systems). In the case of the lanthanide solutions with 1:3 and 2:3 Ln:HL 6 ratios, steady states were reached within times not exceeding 1 h at room temperature. On the other hand, equilibrium times could be estimated at about 5-6 days at 313 K for heterometallic solutions. Consequently, solutions were carefully equilibrated before recording spectra, taking these data into consideration: 2 h at room temperature for homometallic solutions and 7 days at 313 K for heterometallic mixtures. These observations are interesting because in previous works, the kinetics of formation of homodinuclear 4f-4f helicates with a ligand similar to HL C1 but with carboxylic acid groups replaced with diethylamide groups  (Hamacek et al.
5/49. 5/1) or MeOH; the capillary temperature was set to 180 • C and the ion spray voltage to 3. 5 kV. The instrument was calibrated using horse myoglobin and the analyses were conducted in positive mode. Phosphoric acid was used for mass calibration in the range 500-2000 m/z. Data were acquired and processed with Masslynx version 4. 0. Electrospray conditions were as follows: capillary voltage, 3 kV; source temperature, 80 • C; cone voltage, 35 V; source block temperature, 150 • C. The ESI nebulization and drying gas was nitrogen. The sample was introduced through a syringe pump operating at 20 μL•min -1. Simulation of spectra was achieved with Molecular Weight Calculator 6. 42®. UV/Vis absorption spectra were measured in 1. 0 cm quartz Suprasil® cells on a Perkin-Elmer Lambda 900 spectrometer.
Stability constants were determined by spectrophotometric titration of (L 4,5 ) -by Eu III or Eu III /Zn II (1:1) in Tris-HCl 0. 1 M (pH 7. 4) under N 2 atmosphere. All titrations were performed batch wise in thermostated (25. 0 ± 0. 1 • C) 1-cm quartz cuvettes. Factor analysis  (Malinowski and Howery, 1991)  and mathematical treatment of the spectrophotometric data were performed with the Specfit® software  (Gampp et al. , 1986). Luminescence spectra and lifetimes were collected either on a Horiba-Jobin Yvon FL 3-22 fluorometer or on a home-made high-resolution set-up, according to procedures published previously  (Rodriguez-Cortinas et al. , 2002). Quantum yields were measured by an absolute method using a specially designed integration sphere  (Aebischer et al. , 2009).
Background model and signal extraction The dominant background comes from Quantum Chromodynamics (QCD) multijet production with two or more jets containing b hadrons, and can neither be fully reduced by kinematic selection, nor reliably predicted by Monte Carlo (MC) simulation. For this reason, a method based on control data samples, similar to the one used in Ref. [29]  is applied. The background model is constructed from templates that are derived from the double-b-tag sample. We divide the events in the double-b-tag sample into the following categories: bbx, bxb, and xbb, depending on the rank, sorted by p T , of the untagged jet, which is represented by the lower-case letter x. The ranking in descending p T of the three jets is incorporated in the nomenclature adopted here, e. g. bbx means a sample of events where the two leading jets are b tagged and the third jet is the untagged jet.
Trigger and event selection The data used in the semileptonic analysis were collected using different trigger selections, to cope with the increasing luminosity. All the triggers required a muon with a p T > 12 GeV threshold and the presence of one or two central jets (|η| < 2. 6) with transverse momentum above a given threshold (20 or 30 GeV, depending on the data-taking period). Furthermore, one or two b-tagged jets are required online. Initially the track with the second-most significant impact parameter was used. Later, when a second online b-tag was introduced, the selection was on the first track, in order to retain enough signal efficiency even with this tighter selection. An integrated luminosity of 4. 8 fb -1 has been analyzed, and about 1. 67 × 10 7 events were collected. The offline analysis requires a muon with p T > 15 GeV, at least three jets with |η| < 2.
Summary and conclusions We searched for a Higgs boson decaying into a pair of b quarks, produced in association with one or more additional b-quark jets. We used data samples corresponding to an integrated luminosity of 2. 7-4. 8 fb -1 collected in 2011 in proton-proton collisions at a center-of-mass energy of 7 TeV at the LHC. The data were collected with dedicated multijet triggers including b-tag selection, utilizing both all-hadronic and semileptonic event signatures. The search was performed on a triple-b-tag sample, using the invariant mass of two leading jets as a discriminating variable, with a prediction of the multijet background using control data samples. The all-hadronic analysis makes use of a second discriminating variable, X 123 , that reflects the heavy flavor content of the event.
Acknowledgements 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:  BMWF  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MEYS (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES (Croatia) ;  RPF (Cyprus) ;  MoER ,  SF0690030s09  and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NKTH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  NRF  and  WCU (Republic of Korea) ;  LAS (Lithuania) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MSI (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MSTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies.
To test the specificity of the S. aureus effect, some cell cultures received 2-mm latex beads instead (25 beads/cell). The effect of live S. aureus bacteria was also compared to that of heat-killed bacteria used at the same concentrations. Cell morphology was examined by phase-contrast microscopy. The nuclei were stained with DAPI. To evaluate the cell size, the cell area was measured using the merged images of phase contrast and DAPI-stained cells with ImageJ software. A region was drawn around each cell to be measured. An area of at least 500 cells was measured for each condition. The results were presented using the arbitrary unit of the area. All the experiments were performed at least three times.
5% NP-40 and Hoescht 33258 in PBS  [37]. Nuclei were visualized by fluorescent microscopy. There was no significant difference between these two methods (data not shown). The method of mitotic index evaluation using the cells grown on the cover slips was chosen for the study. To stain phosphorylated H3 histone (p-Ser10 Histone H3), synchronized HeLa cells were exposed to the MW2 strain (MOI 20:1) and immunofluorescence was performed as described  [38]. After 4% PFA fixation, cells were permeabilized with 0. 3% Triton X-100/PBS solution and then incubated in 10% goat serum (Sigma) for 1 h at room temperature. Cells were then incubated overnight with rabbit anti-p-Ser10 Histone H3 antibody (Millipore, Molsheim, France) (1:1000 in 3% BSA/PBS), followed by incubation with goat anti-rabbit FITC-labeled antibody (Sigma) at a dilution of 1:2000 for 2 h at room temperature.
After washing, the cover slips were mounted on slides with ProLong antifade Vectashield medium containing DAPI, as described above. Samples were viewed with a Nikon fluorescence microscope (using 640 and 6400 magnifications) coupled with a camera. Cells incubated only with secondary antibody as a negative control showed no reactivity. The images were captured with strictly identical acquisition settings for every sample. Fifty mitotic cells in infected vs. non-infected culture were analyzed. The relative level of fluorescence (corrected total cell fluorescence (CTCF) arbitrary unit) of p-Ser10 Histone H3-positive mitotic nuclei was measured using ImageJ software, as previously described  [39]. A region was drawn around each cell to be measured. The same region in an area without fluorescent cells was used for background subtraction.
To carry out a relative quantification of samples, densitometric analysis of Western blots (a method for measuring the intensity of a band in a gray-scale image) was performed using Gene Tools software (Syngene). Band intensities in the linear range of the signal were measured using underexposed membranes. Two different concentrations of each sample were tested during the same Western blot analysis, making it possible to verify the proportionality of the band intensities. The samples with lower concentrations were used for densitometric analysis. One of the samples was used in all experiments as a reference for densitometric analysis. Data are presented as mean 6 SD from three densitometry scans, adjusted with total histone H3, and expressed as fold changes over the appropriate control, as previously described  [17].
Exposure of cells to S. aureus results in the accumulation of phosphorylated Cdk1 and unphosphorylated histone H3 Flow cytometry data clearly showed an accumulation of S. aureus-infected cells in the G2/M phase. It was therefore important to determine whether S. aureus-infected cells were delayed in the G2 phase and failed to enter mitosis or, instead, were blocked in the M phase and failed to complete mitosis. Cycline-dependent kinase Cdk1 is one of the key players of the G2-M transition  [49]. Dephosphorylation of the Thr14 and Tyr15 residues of Cdk1 at the end of the G2 phase is essential for triggering mitotic entry. In order to analyze S. aureus-induced G2 delay, the phosphorylated status of Cdk1 was assessed by Western blot analysis using antiphospho-Cdk1 antibody 20 h after elimination of the extracellular bacteria.
The optical density after 24 hours of growth reached 0. 6 at 600 nm, corresponding to approximately 10 8 CFU/ml for all bacterial samples. HeLa cells were pre-incubated for 3 h before infection and then throughout infection until analysis in the inhibitor-containing medium to arrest the cells in the G 1 or G 2 phase, as described in the Materials and Methods section. The CFU value and HeLa cell cycle at 0 h, 2 h, 4 h and 20 h from the beginning of incubation in cDMEM-Gent100 were determined. There were no significant differences in the number of CFUs between the cells treated with inhibitors and those without inhibitors 2 h post-infection (T0, the beginning of the gentamicin treatment) (data not shown). At that time, the CFU value corresponds to both adherent and internalized bacteria. Analysis of the cell cycle distribution at T0 did not reveal any significant difference between the cells treated or not with the inhibitors.
The S. aureus induced a G2/M phase transition delay. HeLa cells were synchronized by DTB and were exposed to live or heat-killed bacteria (MW2) at MOI 20:1, to the latex beads or to the media alone for 2 h, followed by incubation in cDMEM-Gent100 for 2 h, and further incubated for 24 h. Some cells were exposed to etoposide for the same length of time as the exposure to bacteria. Detached cells were then combined with adherent cells and stained with PI. Cell cycle phases of PI-stained cells were monitored by FACS. The data were collected from 20,000 cells and analysis was performed with Cell Quest software. The average percentage of cell cycle phase 6 SD is indicated. Each experiment was performed at least five times. Exposure of the cells to live S. aureus bacteria induced an increase in the number of cells in the G2/M phase, (*) p,0.
2-fold and 1. 4-fold higher than the value at T2. These results indicate the bacterial replication 20 h post-infection. An even greater difference was observed for the CFU value in the G2 phase-enriched cells. The CFU value in the G2 phase-enriched Figure  6. S. aureus induced dose-dependent G2/M phase transition delay in the subsequent G2/M phase. A. HeLa cells were synchronized by DTB and were exposed to S. aureus bacteria (MW2) at MOI 20:1 or to the media alone for 2 h, followed by incubation in cDMEM-Gent100 for 2 h, and subsequently incubated for an additional 12 h, 14 h, 18 h, 20 h and 24 h. Detached cells were then combined with adherent cells and stained with PI. Cell cycle phases of PI-stained cells were monitored by FACS. The data were collected from 20,000 cells and analysis was performed with Cell Quest software.
Each experiment was performed four times. The number of cells in different phases is presented on the histograms. The values shown are those of a representative assay out of the four assays performed. Exposure of the cells to S. aureus bacteria induced a G2/M phase transition delay in a time-dependent manner. B. HeLa cells were synchronized by DTB and were exposed to S. aureus bacteria (MW2) at different MOIs ranging from 5:1 to 20:1, followed by incubation in cDMEM-Gent100 for 2 h, and further incubated for an additional 20 h. Detached cells were then combined with adherent cells and stained with PI. Cell cycle phases of PI-stained cells were monitored by FACS. The data were collected from 20,000 cells and analysis was performed with Cell Quest software. The percentage of cells is presented on the graph as a function of bacterial concentration.
Blocking HeLa cells in the G2 phase results in an increased internalization and in an increased intracellular replication of S. aureus. HeLa cells were treated with either 10 mM CDK4/6 inhibitor IV (enrichment in the G1 phase) or 9 mM of RO-3306 (enrichment in the G2 phase) 3 h before the addition of S. aureus at MOI 10:1 and 50:1 for 2 h (T0). The cells then were incubated in cDMEM-Gent100 for an additional 2 h, 4 h (T4) or 20 h (T20). The proportions of cells in the different cell cycle stages at T2, T4 and T20 were determined by FACS (A). The CFU of intracellular S. aureus at T2, T4 and T20 was determined by plate count. CFU values were normalized to 10 5 HeLa cells (B). Experiments were performed in triplicate. The data are presented as mean +/2 SD. Tukey's Honestly Significant Difference test was applied for comparison of means between the groups.
Acknowledgments We would like to thank  Fabien Cousin ,  Caroline Le Mare  ´chal ( UMR STLO), Claire Piquet-Pellorce and Remy Le Guevel (Biosit, Rennes ) for their invaluable assistance with some of the experiments. We are grateful to  Christian Jaulin  and  Laura Magnaghi-Jaulin  for their helpful discussions and constructive suggestions (CNRS-UMR 6290, BIOSIT), as well as to  Sylvie Lortal  ( UMR STLO ) and  Anne-Yvonne Cozic  ( Rennes Metropole ) for their help in the organization of this work. We thank  Gail Wagman  for revising the English.
Tensile and 3 Points Bending Tests Tensile and 3 point bending tests were conducted according to ISO 527-2  [34]  and ISO 178  [35]  using a H5KT Universal testing machine (Tinius Olsen, Horsham, PA, USA) at 1mm/min speed. These standards are related to the evaluation of mechanical properties of plastics. From these tests, four variables were collected: Young's Modulus, Tensile Strength at break, Bending Modulus and Bending Strength at break. Significance of difference between means of the 4 variables was analyzed with ANOVA and Scheffé's contrasts test (multiple comparison of means) using Matlab (Mathworks, Natick, MA, USA). Every statistical analysis was performed with 95% confidence. The tests were performed within each series of experiment, and not on the whole set of experimental results.
Acknowledgments The authors would like to thank  Christèle COMBES  from  CIRIMAT (INP-ENSIACET, Toulouse ) for performing the SEM observations, the  French National Research Agency (ANR)  and the  Competitive Cluster for the Agriculture and Food Industries in South-West of France  for their financial support through their implication in the project  HYPMOBB (High Pressure Molding of Biopolymers and Biocomposites ).
Among the eligible patients, if they were visiting the centre for the first time and starting a new treatment regimen (i. e. , starting a new drug or a new dosage), these patients were classified as "naïve". Patients were not eligible if they had concomitant diseases for which there was life expectancy of less than 52 weeks, if at the time of enrolment they were hospitalized or staying in Residential Care Units, if they were attending a specialist centre for the care and treatment of people addicted to drugs or alcohol, or if they were pregnant or breast-feeding. At the enrolment examination, patients' data attributable to the previous 90 days were collected (retrospective period) and they were then targeted to be followed up for up to 12 months (prospective period). During the prospective follow-up, data collection occurred at 12 ± 2 (follow-up examination 1), 36 ± 2 (follow-up examination 2), 52 ± 2 (follow-up examination 3) weeks: a 2-week time variation per examination was allowed in order to make the occurrence of examinations coincident with those established according to clinical practice.
Assessments In order to achieve good quality of the data collected and a good level of inter-rater reliability, the centres participated in two kick-off meetings before the study started, within a 3-years long educational program in which the raters (clinical investigators) who collected the data and assisted the patients during data collection were trained for the completion of all the instruments used in the project. Data on socio-demographic characteristics, clinical status, HRQoL, drug treatment, compliance and attitude toward antipsychotic treatment, use of health care resources, and loss of productivity were collected by means of case report forms, scales/questionnaires completed by the physician (socio-demographic and clinical data, costs, opinion on patients' compliance) or by the patient (HRQoL and attitude toward antipsychotic treatment).
Socio-demographic data included patients' gender and age, education, family and working status, and receipt of economic support for their condition. Clinical data were based on diagnosis (schizophrenia vs. schizophreniform disorder), disease severity, type of schizophrenia, duration of disease, age at onset of symptoms, first treatment, first hospitalization, psychiatric symptoms. Functioning and disease severity were assessed using the Positive And Negative Syndrome Scale (PANSS), the Clinical Global Impression -Severity (CGI-S) and the Global Assessment of Functioning (GAF) scales. PANSS is a 30-item scale measuring the presence of positive and negative syndromes in schizophrenia patients and the severity of psychopathology in the week before the day of assessment. Higher scores indicate more severe psychopathology  [31, 32].
SF-36 assesses HRQoL in eight dimensions related to the physical and mental components of health. It is possible to synthesize the information obtained with the eight domains into two summary scores, one specific for physical health (Physical Summary Score -PCS)and the other for mental health (Mental Summary Score -MCS): the higher the score, the better the component of HRQoL measured  [37, 43]. For this study, PCS and MCS results will be shown. Data on both antipsychotic and concomitant drug treatments were taken, recording information on type of drug, dosing, duration of treatment and details on switches or interruptions. Compliance and attitude toward antipsychotic treatment at the time of each examination were assessed with the 30-item version of Drug Attitude Inventory (DAI-30)  [44] , a scale self-completed by the patients to measure their subjective response to medication as well as their attitude towards pharmacological treatment, illness and health.
NM_007100. 2) and 59-GTC AAT AGT GCT CAG ACT G-39 (nucleotides 446 to 464 of ATP5L; accession number NM_006476). To control the potential side effects of transducing cells with lentiviral particles, a control experiment was systematically run in parallel with lentiviral particles where a sequence (59-ACT ACC GTT GTT ATA GGT G-39) that does not target any protein encoding mRNA of the cell is encapsulated. This control is referred to as Scramble. HeLa cells were transduced by incubating growing cultures with the lentiviral particles for 72 hours (MOI = 3 and MOI = 4 for ShATP5I and ShATP5L lentiviral particles respectively).
6 mM). Each measurement was performed three times in 5 minutes. Data are the mean of 4 experiments and are expressed as picomole of O 2 per minute per 10 6 cells (black bar: Scramble; gray bar: ShATP5I; error bar: standard deviation; *: P,0. 002). (C) Mitochondrial proteins (50 mg) were separated by Trisglycine SDS-PAGE. Subunits representative for each respiratory complex were revealed by western blot using the appropriate antibodies (Sc: Scramble; Sh; ShATP5I). This figure is representative of three independent experiments. doi:10. 1371/journal. pone. 0075429. g006.
Hybridization Arrays and Microarray Data Analysis RNA quality control was performed on an Agilent 2100 Bioanalyzer (Massy, France) with 6000 Nano Chips, according to the manufacturer's instructions. For human adipocytes and 3T3-L1 cells, six independent cultures were grown in quadruplicate (i. e. 24 controls and 24 TNF-a treated). RNAs were hybridized to Agilent Whole Human Genome (4644 k; Massy, France). All labeling, hybridization, washing and scanning were performed as described in the manufacturer's protocol and as previously described  [22]. Arrays were scanned with an Agilent Scanner (Massy, France). Data were extracted with Agilent Feature Extraction v10. 5. 1. 1 and analyzed with Agilent GeneSpring GX v11. 0. 2 (Massy, France). Data were normalized according to the locally weighted scatterplot smoothing (LOWESS) method, and multiple correction test false discovery rate was applied.
RNA Isolation and qPCR Total cellular RNAs were extracted using TRIzol reagent according to the manufacturer's instructions. cDNAs were synthesized from 1 mg of total RNA using random primers and Moloney murine leukemia virus reverse transcriptase. Real-time quantitative RT-PCR analyses were performed using the Mx3005P Real-Time PCR System (Stratagene, La Jolla, CA) as previously described  [23]. For each condition, expression was quantified in duplicate and 18S rRNA was used as the endogenous control in the comparative cycle threshold (C T ) method. Data were expressed as relative expression ratio. The sequences of the primers and Taqman gene expression assays (Applied Biosystems) used for qPCR determination of gene expression are displayed in Table  S1.