dataesr/scientific-paragraphs-categorization huggingface dataset:
LC-MS/MS Analyses of o-MitoPhB(OH) 2 -derived Products-Analyses of o-MitoPhB(OH) 2 and its oxidation/nitration products were performed as described recently  (21, 32). The method was modified for newly characterized products, including cyclo-o-MitoPh, and deuterated analogs were used as internal standards for quantitative analyses. Dose-Response Analyses-For determination of the apparent IC 50 values, the dose-response fitting application was used, as implemented in OriginPro 9. 1. 0 program (OriginLab Corp. ). Equation 2 used for the fitting is as follows: y ϭ A 1 ϩ A 2 Ϫ A 1 1 ϩ 10 ͑log IC50 Ϫ log c͒ p (Eq. 2) where y is the measured quantity (proportional to Nox2 enzyme activity); A 1 and A 2 correspond to bottom and top asymptotes, p to the Hill slope, and c is the concentration of the compound.
The apparent IC 50 values for inhibition of Nox2 activity in the dHL60 model determined with a fluorescence plate reader using the CBA-based assay are shown in Table  4. Next, the effect of selected compounds on Nox2 activity was tested by HPLC-based simultaneous monitoring of O 2. and H 2 O 2 (Fig. 5 , a and b), by measuring oxygen consumption stimulated by Nox2 activation using the 96-well platebased extracellular flux analyzer (Seahorse XF96, Fig. 5, c  and d ) and by monitoring the inhibitory effect on spin-trapped superoxide adduct using DEPMPO (data not shown). Fig. 5a  shows the results of the confirmatory assays for selected compounds, sulconazole, mefloquine, cetylpyridinium cation, and DPI, on formation of 2-hydroxyethidium, the specific marker product for O 2. Similarly, Fig. 5b  shows the effect of these compounds production also compare favorably with those measured using Nox2-mediated oxygen consumption.
Electrophysiology. Acute transverse hippocampal slices (300-400 μ m) were prepared as previously described  26, 27. Slices were transferred to a submerged recording chamber mounted on an Olympus BX51WI microscope and were perfused with an artificial cerebrospinal fluid (ACSF) saturated with 95% O 2 and 5% CO 2 , containing (in mM): 119 NaCl, 2. 5 KCl, 2. 5 CaCl 2 , 1. 3 MgSO 4 , 1 NaH 2 PO 4 , 26. 2 NaHCO 3 and 11 glucose (pH 7. 4). Recordings were acquired using a Multiclamp 700B amplifier (Molecular Devices), digitized at 10-20 kHz, filtered at 2-10 kHz and analyzed using pCLAMP10 and Clampfit softwares (Molecular Devices). CA1 pyramidal cells were recorded in voltage-clamp mode, using 5-10 MΩ glass pipettes filled with (in mM): 107. 5 Cs-gluconate, 20 HEPES, 0. 2 EGTA, 8 Na-gluconate, 8 TEA-Cl, 4 Mg-ATP, 0.
3 Na3-GTP, and 5 QX314 (pH 7. 3; 280-290 mOsm). All the voltage-clamp experiments were performed in the presence of picrotoxin (100 μ M). Spontaneous miniature excitatory postsynaptic currents (mEPSCs) were recorded at -70 mV in the presence of 0. 5 μ M tetrodotoxin (TTX). Evoked excitatory postsynaptic currents (eEPSCs) were induced by stimulating Schaffer collaterals (0. 1 Hz) in CA1 stratum radiatum with ACSF filled glass pipettes. Evoked AMPAR-mediated EPSCs were measured at -70 mV, while NMDAR-mediated EPSCs were measured at + 40 mV when the AMPAR-mediated EPSC had fully decayed. Paired-pulse facilitation of AMPAR EPSCs was induced by delivery of two stimuli at 40 ms interpulse intervals. The average mEPSCs charge transfer was calculated using the Clampfit software. The coefficient of variation (CV) of AMPA eEPSC amplitudes was calculated as: standard deviation/mean.
Slices were then incubated in avidin-biotinylated horseradish peroxidase in 1% Triton X-100 followed by diaminobenzidine (DAB) peroxydase and finally transferred to slides, dehydrated in ethanol and mounted with Eukitt. Detailed shape of neurobiotin-filled CA1 pyramidal cells was imaged using a CX 9000 Olympus microscope and analyzed using the Neurolucida software (MicroBrightField). Western blot. Hippocampi were dissected and lysed as previously reported  15. 20 μ g of proteins was separated on 10% Bis-Tris polyacrylamide gels (NuPAGE, Invitrogen) and transferred to nitrocellulose (iBlot, Invitrogen). Western Blot analysis was performed using rabbit polyclonal anti-GluR1 (1 μ g/ml, ab31232, Abcam), rabbit polyclonal anti-GluR2/3 (1/1000, AB1506, Millipore) and anti-α -actin (1/1000, A2066, Sigma-Aldrich) primary antibodies.
Quantification was done using Multi Gauge densitometry software. Electron microscopy. P8 mice were anesthetized with an intraperitoneal injection of a lethal dose of sodium pentobarbital and transcardiacally perfused with 2% paraformaldehyde/1% glutaraldehyde in 0. 1 M phosphate buffer (PB), pH 7. 4. Brains were removed and postfixed in 4% paraformaldehyde. Coronal slices (45 μ m) were cut using a vibratome. Briefly, hippocampi were microdissected and postfixed in 1% osmium tetroxide, incubated in 1% uranyl acetate, dehydrated in ethanol, and embedded in Epon. Ultrathin sections (50 nm) were cut, contrasted with uranyl acetate and lead citrate, and analyzed with an electron microscope (JEOL, 1200 EX II). Density of visually identified asymmetrical synapses, length of postsynaptic density (PSD) and number of docked vesicles (within 30 nm from the synaptic membrane of the active zone) were measured using ImageJ software on acquired images (30.
Acknowledgements This study was supported by the  Agence Nationale de la Recherche  ( ANR R10193DD  and  ANR R11174DD  to S. B. ),  the program 'Investissements d'avenir'   ANR-10-IAIHU-06  (S. B. , C. A. ), the  Fondation Française pour la Recherche sur l′ Epilepsie (S. B. ) , the  Ligue Française contre l'Epilepsie  (M. B. ),  INSERM ,  CNRS  and  Collège de France  to N. R. and the  Fondation pour la Recherche Medicale  (C. Y. L. ). This work was partly carried out on the Histomics platform of the ICM and we thank all technical staff involved. The authors thank  M. Dumont  for her technical support at the ICM animal facility,  J. Garrigue  for genotyping,  M. P. Muriel  and  B. Dufresnois  for technical assistance, the teams of  J. Y. Delattre  and  J. Honnorat  for performing clinical diagnosis and for providing patient's  CSF  and  A.
Statistical Methods Continuous data were expressed as means and SD. Both bacterial strains like as L929 and SAOS-2 cells grown in 24-TCP were used as the reference (100%). For bacterial adhesion, antibacterial activity and cell viability, two-group comparisons (PLGA and each PLGA/Ag nanocomposites) were performed by Student's t-test. All analyses were performed using GraphPad Prism 4. 0 (Graph Pad Software Inc. , San Diego, CA, USA). Two-tailed p values < 0. 05 were considered statistically significant.
Acknowledgments: Livia Visai would like to acknowledge financial support from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), Progetti di ricerca di Interesse Nazionale (PRIN) 2010 project entitled "Nanomed" (protocol NO. 2010FPTBSH_009). The author Elena Fortunati is the recipient of the fellowship "L'Oreal Italia per le Donne e la Scienza 2012" for the project "Progettazione, sviluppo e caratterizzazione di biomateriali nanostrutturati capaci di modulare la risposta e il differenziamento delle cellule staminali". Carla Renata Arciola.
The data are examined in bins of N jet , N b-jet , H T , and H miss T , where N jet is the number of jets and N b-jet the number of tagged bottom quark jets (b jets). The search is performed in exclusive bins of these four observables. We consider SUSY scenarios in the context of four simplified models  [17] [18] [19] [20]  of new particle production. Diagrams for the four models are shown in Fig. 1. Simplified models contain the minimal particle content to represent a topological configuration. As SUSY production scenarios, the four simplified models can be interpreted as follows. In the first scenario, shown in Fig. 1  (upper left), gluino pair production is followed by the decay of each gluino to a bottom quark and an off-shell bottom squark. The off-shell bottom squark decays to a bottom quark and the LSP, where the LSP is assumed to be the lightest neutralino χ 0 1 and to escape detection, leading to significant H miss T.
A more detailed description of the CMS detector, together with a definition of the coordinate system and relevant kinematic variables, is given in Ref. [24]. Signal event candidates are recorded using trigger conditions based on thresholds on H T and missing transverse momentum. The trigger efficiency, which exceeds 98% following application of the event selection criteria described below, is measured in data and is accounted for in the analysis. Separate data samples requiring the presence of either charged leptons or photons are used for the determination of backgrounds from SM processes, as discussed below. Physics objects are defined using the particle-flow (PF) algorithm  [25, 26] , which reconstructs and identifies individual particles through an optimized combination of information from different detector components.
Simulation of the detector response is based on the GEANT4  [43]  package. The simulated samples are normalized using the most accurate cross section calculations currently available  [37, 41, 42, [44] [45] [46] [47] [48] [49] [50] [51] [52] , generally with NLO or next-to-NLO accuracy. Signal T1bbbb, T1tttt, T1qqqq, and T5qqqqVV events are generated for a range of gluino m g and LSP m χ 0 1 mass values, with m χ 0 1 < m g. For the T5qqqqVV model, the masses of the intermediate χ 0 2 and χ ± 1 states are taken to be the mean of m χ 0 1 and m g. The signal samples are generated with the MADGRAPH5 aMC@NLO program at leading order, with up to two partons present in addition to the gluino pair. The decays of the gluino are described with a pure phase-space matrix element  [53]. The signal production cross sections are computed  [54] [55] [56] [57] [58]  with NLO plus next-to-leading-logarithm (NLL) accuracy.
To reduce computational requirements, the detector is modeled with the CMS fast simulation program  [59, 60] , which yields consistent results compared with the GEANT4-based simulation, except that we apply a correction of 1% 4 Event simulation to account for differences in the efficiency of the jet quality requirements  [32] , and corrections of 3-10% to account for differences in the b jet tagging efficiency. The NNPDF3. 0LO  [61]  parton distribution functions (PDF) are used for the simulated samples generated at leading order, and the NNPDF3. 0NLO [61]  PDFs for the samples generated at NLO. All simulated samples use the PYTHIA 8. 2  [53]  program to describe parton showering and hadronization. To model the effects of pileup, the simulated events are generated with a nominal distribution of pp interactions per bunch crossing and then reweighted to match the corresponding distribution in data.
A correction derived from data is applied to the weights to account for the trigger efficiency, while corrections from simulation account for contamination due to nonprompt electrons, contamination due to dilepton events in which one of the leptons is lost, and the selection efficiency of the m T requirement. Corresponding efficiencies are evaluated for dileptonic events in which both leptons are lost. This latter source of background is predicted to account for <2% of the total lost-lepton background. Finally, a correction is applied to account for the selection efficiency of the isolated-track veto. The weighted distributions of the search variables, summed over the events in the CRs, define the lost-lepton background prediction. The procedure is performed separately for single-electron and single-muon events.
Summary A search is presented for an anomalously high rate of events with four or more jets, no identified isolated electron or muon or isolated charged track, large scalar sum H T of jet transverse momenta, and large missing transverse momentum, where this latter quantity is measured with the variable H miss T , the magnitude of the vector sum of jet transverse momenta. The search is based on a sample of proton-proton collision data collected at √ s = 13 TeV with the CMS detector at the CERN LHC in 2015, corresponding to an integrated luminosity of 2. 3 fb -1. The principal standard model backgrounds, from events with top quarks, W bosons and jets, Z bosons and jets, and QCD multijet production, are evaluated using control samples in the data. The study is performed in the framework of a global likelihood fit in which the observed numbers of events in 72 exclusive bins in a four-dimensional array of H miss T , the number of jets, the number of tagged bottom quark jets, and H T , are compared to the standard model predictions.
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  7 Summary 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 (Republic of Korea) ;  LAS (Lithuania) ;  MOE  and  UM (Malaysia) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  MST (Taipei) ;  ThEPCenter, IPST, STAR  and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU  and  SFFR (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
, 2015). However, in our dataset, BRCA1/2 genes show a weaker correlation with Polθ expression in lung cancer and no correlation in colorectal and breast cancer. MRE11 and NBS1, two genes coding for proteins of the MRN complex involved in primary resection, an earlystep in the HR pathway, do not instead correlate with Polθ expression. Notably, published work has repeatedly suggested that a number of proteins involved in the HR pathway play a role in the management of stalled replication fork under replicative stress  (Carr and Lambert, 2013). Moreover, RAD51 and BLM have been described to be involved in remodelling stalled replication fork in a mechanism described as 'fork reversal'  (Neelsen and Lopes, 2015). These observations prompted us to evaluate the role of Polθ in the response to chemotherapeutic agent that mediates replicative stress.
DNA combing was performed as described previously  (Fernandez-Vidal et al. , 2014). The number of bi-colour forks analysed in this experiment are 74 and 64 for siLuc and siPOLQ conditions, respectively. Fig. 5. Polθ expression positively correlates with HR but not MMEJ genes in solid tumours. (A) A Pearson's test was used to compare POLQ mRNA expression and expression of any other analysed gene within each cohort. The number of patients analysed for lung, breast and colorectal cancer was 103, 221, and 52, respectively  (Lemeé et al. , 2010; Pillaire et al. , 2010; Allera-Moreau et al. , 2012). A coefficient superior to 0. 65 was considered associated to a positive correlation. Pathway enrichment analysis was performed using the KEGG pathway database. Pie charts report the pathways detected by KEGG analysis in relation to the number of genes in each pathway.
DNA combing Cells were successively labelled for 15 min with 50 µM IdU (Sigma-Aldrich) and 100 µM CldU (ICN) and incubated 3 h with 200 mM thymidine. Genomic DNA was prepared in agarose plugs (0. 5×10 5 cells/plug), and DNA combing was performed as described previously  (Fernandez-Vidal et al. , 2014). IdU and CldU were detected with monoclonal mouse (347580, 1:20, Becton Dickinson) and rat anti-BrdU antibodies (Abc117-7513, 1:20, Seralab), respectively. Signals were captured with a CoolSNAP HQ camera (Photometrics) on a Leica DM IRB equipped with a 63×/1. 4 PL APO objective. Measurements were performed with MetaMorph (Universal Imaging Corp. ). Fork speed was calculated by dividing the median track size by the labelling time and the non-parametric test of Mann-Whitney was used to data sets from different cell lines.
Statistical and bioinformatics analysis of gene expression from tumour cohorts Written informed consent was obtained from all patients before testing. All informed consents were collected and stored in the Pathology Department. This study was approved by the Ethics of Human Research Committee at the Pathology Toulouse Hospital. The experiments conformed to the principles set out in the WMA Declaration of Helsinki. RT-qPCR data from human tumour samples were retrieved from 221 breast, 94 NSCLC and 52 colorectal cancer samples previously  (Allera-Moreau et al. , 2012; Lemée et al. , 2010; Pillaire et al. , 2010). Correlation with POLQ gene expression was assessed using Pearson test with a P=0. 65 cut-off. For each cancer type, total gene set and POLQ-correlating genes were analysed for pathway enrichment using the KEGG database  (Kanehisa et al.
Numerical solution of the problem The bubble dynamics was simulated by solving simultaneously the Eqs. (  2 ), (  3 ), (  20 ) and (  21 ) as a system of first order ODEs by means of MATLAB routine ODE113. At any time t, the solution provided the bubble radius R, bubble wall velocity U, the gas temperature inside the bubble T g and the vapor quantity inside the bubble N v. The gas pressure P g inside the bubble was then calculated by Eq. (  1 ) and the liquid temperature T i at the bubble wall by Eq. (  35 ). This last equation provided also the liquid temperature distribution all around the bubble. The liquid dynamics around the bubble was simulated by solving simultaneously the Eqs. (  13 ), (  17 ) and (  18 ) as a system of first order ODEs (MATLAB routine ODE45). The calculations were carried out along a characteristic, each characteristic originating at the bubble wall.
Supplementary simulations with our model B showed that a 30% decrease of T g corresponded to a 5% decrease in T i. So the error of calculating T i due to chemical reactions omission would be no more than 5%, which is in the range, or even below, of the error induced by the uncertainty on gas and liquid thermo-physical properties. The model B proposed in this study comprehends all the relevant thermal phenomena and at the same time it writes mathematically rather simply. The thermal model B coupled with the fluidics and thermodynamics model of cavitation proposed in this study writes as a set of ODE's and solves more conveniently (MATLAB) and quickly than a full multi-physics model based on PDE's which requires a finite element software. At the same time, this model gives realistic results, similar to those provided by complex models and sophisticated solvers.
To illustrate the results of this time-frequency analysis in a more intuitively accessible way, Fig. 3  shows the extent to which the amount of perceived mislocalization is correlated with oscillation phase, calculated for the single time-frequency point of maximum influence (electrode POz, -358 ms, 6. 6 Hz). For each subject, we normalized mislocalization data by converting to z-scores, fitted a smoothed curve (Matlab 'smooth' function using a 2 nd -degree Savitsky-Golay filter, equivalent to a weighted moving average but allowing for the irregular x-spacing of the data points; span set to include 30% of data points, or approximately a 45 ms window) to the mislocalization vs phase data, then averaged these curves across subjects. Note that this figure is intended for easier understanding only, not as any further evidence of the correlation between mislocalization and oscillation phase, because we selected these data from the most significant point in Fig.
Stimuli and procedure. Stimuli were presented on a 150 Hz cathode ray tube monitor. The experiment was run using Matlab (Mathworks) and the Psychophysics Toolbox extensions  31, 32. Stimuli were presented against a dark red background (CIE xyY coordinates, 0. 524, 0. 354, 5. 78). During each trial, several objects (black, CIE xyY: 0. 507, 0. 257, 0. 02) were continuously on-screen (Fig. 1A ): a) a fixational start point on the left hand side (random position from 9. 9° to 6. 4° left of screen centre) b) a saccade target towards the right (always 10. 6° from fixation point) c) a pair of vertical tramlines (1. 5° and 5. 3° to the right of the saccade target) to aid in perception and reporting of the mislocalization probe and d) a pair of small horizontal markers on each of these tramlines demarcating a rectangular zone from 4.
Six blocks of 60 trials were carried out by each participant. At the end of the experiment, subjects were asked to sketch their perceptual impression of the probe trajectory on a diagram (Fig. 1B ). Data Acquisition and Analysis. Eye position was continuously monitored using an IView system (SensoMotoric Instruments), to detect start point fixation and saccade timing. The system was calibrated at the start of each 60-trial block, using a 13 point calibration defined by an IviewX Matlab command. Calibration was checked at the beginning of each trial with an invisible boundary check in a 2°-side square centred on the fixation cross. Signals were digitized at 1 kHz. Simultaneously, continuous EEG was acquired with a 64-channel ActiveTwo system (Biosemi). Electrodes were placed according to the international 10-20 system, mounted in an elastic cap.
Vertical and horizontal electrooculograms were recorded using additional electrodes below the left eye and at the outer canthi of both eyes-these signals were used as an additional check to ensure good synchronization of the EEG and eyetracker signals. EEG signals were digitized at 1024 Hz, 24-bit A/D conversion. Data were analyzed using Matlab (Mathworks) and the EEGLAB toolbox  33  , with eyetracker data imported and saccadic events detected automatically using the EYE-EEG plug-in for EEGLAB  34, 35  (detects saccades using the velocity-based approach described previously  35  ). Data were converted to an average reference, downsampled offline to 256 Hz, and epoched from 1750 ms before to 1250 ms after the saccade time. Data were screened manually for unwanted eye movement and other artefacts.
We rejected any trials in which there was not an initially stable eye position followed by a single clear saccade to the target. Note that although epochs extended past the time of the saccade, in further analysis, only pre-saccadic time points were of interest: the time course for classical flashed-stimulus perisaccadic mislocalization is from around 50 ms pre-saccade up to and including the saccade itself but not after  24  and further, data after the onset of the saccade are too contaminated by muscular eye-movement artefacts to be useful. Initial time-frequency analysis was carried out using the EEGLAB toolbox (timefreq function). Parameters were set to yield an analysis over a range of 60 discrete frequencies increasing logarithmically from 2 to 100 Hz, with filter length (Morlet wavelets) varying smoothly from 2 cycles at the lowest frequency to 20 cycles at the highest.
Galindo-Albarran et al. examine the distinct pattern of gene transcription and histone modification landscape in human neonatal CD8 + T cells. Their data suggest that cells are skewed toward an innate immune response and low cytotoxic function. These properties could explain the high susceptibility of neonates to infections and inflammation. Explore the consortium data at the Cell Press IHEC webportal at www. cell. com/consortium/ IHEC.