dataesr/scientific-paragraphs-categorization huggingface dataset:
MV1c efficiency Fraction of events 2 -  A binned likelihood function is constructed as the product of Poisson probability terms over all bins considered in the analysis. This likelihood depends on the signal-strength parameters, which are independent multiplicative factors of the MC predictions for ttb, ttc and ttl production cross-sections, henceforth referred to as µ ttb , µ ttc and µ ttl. The nominal prediction (µ = 1) for each analysis is obtained from the PowhegBox t t sample. No constraints are applied to the values of these parameters. Nuisance parameters (denoted θ) are used to encode the effect of the various sources of systematic uncertainty on the signal and background expectations; these are implemented in the likelihood function with multiplicative Gaussian or log-normal priors.
5% between two bins. This simplification changes the final result or uncertainty by less than 1% and significantly reduces the execution time. The shape variations for the PDF uncertainties on t t in the lepton-plus-jets analysis are found to be negligible, therefore only the largest variation in acceptance is considered. In the ttb eµ analysis, the PDF uncertainty is evaluated outside of the profile likelihood fit. For each eigenvector of each PDF set, new nominal templates are obtained for each of the components and a statistics-only fit to the Asimov dataset  [97]  obtained using the central value of the MC@NLO prediction is done. The relative difference between the fitted cross-section and the one obtained from the nominal MC@NLO is considered as the PDF uncertainty of that eigenvector.
The envelope of all eigenvectors is then considered as the PDF uncertainty and added in quadrature to the total uncertainty obtained from the full profile likelihood fit. Figure  5  shows the MV1c distribution used to fit the ttb signal strength in the lepton-plus-jets analysis (top) and ttb eµ analysis (bottom). The left figure shows the predictions from simulation and the uncertainty band from the sum in quadrature of the impact of each source of uncertainty. The right plot shows the fitted results and the final uncertainty on the total prediction, which is largely driven by the size of the available MC samples. Table  10  shows the fitted values of the parameters of interest. The Asimov dataset is used to provide expected results. The total uncertainty on the measurement is found to be similar to the expected one in both analyses and the fitted ttb signal strength in both analyses is higher than one, but still compatible with unity within uncertainties.
Both the results from the Asimov dataset and the values obtained from the fits to data are shown. The uncertainties quoted are from the total statistical and systematic uncertainties. Table  11 : Effect of the various sources of uncertainty on the ttb and ttbb cross-section measurements in the lepton-plus-jets and dilepton channels. The uncertainties on the R ttbb ratio measurement in the dilepton fit analysis are also shown. Asymmetric uncertainties are shown when relevant. For the fit-based measurements, the individual and total uncertainties are evaluated from the fit to the data.
t t bb cross-section from cut-based analysis This ttbb measurement uses an event counting method in the dilepton channel to extract the crosssection. Events with at least four identified b-jets are considered. The estimate of the number of signal events is obtained from the total number of observed events passing the final selection (N data ) and the estimate of the number of background events. A distinction is made between background processes which contain two top and two bottom quarks, but do not pass the fiducial selection (referred to as non-fiducial background), and backgrounds from all other processes (referred to as non-ttbb). In order to avoid making any assumptions about the cross-section for ttbb processes, the prediction for the non-fiducial background is not taken directly from simulation; instead, simulation is used to determine the fractions of ttbb events that are signal and non-fiducial background.
The effect due to limited number of MC events in the templates is obtained from the mean of 5000 pseudo-datasets obtained from simulation, where the variance of each bin depends on the total MC statistical uncertainty of that bin. The second to last column of Table  11  shows the effect on the final ttbb cross-section measurement in this analysis whereas the rightmost column shows the uncertainties on the R ttbb measurement. The total cross-section uncertainty of each process and on the R ttbb ratio are shown in Table  14  along with the statistical and total systematic uncertainties. The uncertainties on the ttbX and ttcX processes are large and do not allow the cross-sections of these processes to be constrained significantly. The signal strength µ ttbb has a correlation of 0. 4 with µ ttbX , -0.
Conclusions Measurements in the fiducial phase space of the detector of the cross-sections for the production of t t events with one or two additional b-jets are performed in proton-proton collisions at a centre-of-mass energy of 8 TeV at the LHC. The results are based on a dataset corresponding to an integrated luminosity of 20. 3 fb -1 , collected with the ATLAS detector. The cross-section times branching ratio for top pair events with at least one additional b-jet is measured to be 950 ± 70 (stat. ) +240  -190 (syst. ) fb in the lepton-plus-jets channel and 50 ± 10 (stat. ) +15  -10 (syst. ) fb in the eµ channel. The cross-section times branching ratio with at least two additional b-jets is measured to be 19. 3 ± 3. 5 (stat. ) ± 5. 7 (syst. ) fb in the dilepton channel (eµ, µµ, and ee) using a method based on tight selection criteria, and 13.
In addition, individual groups and members have received support from  BCKDF , the  Canada Council, CANARIE ,  CRC ,  Compute Canada, FQRNT , and the  Ontario Innovation Trust ,  Canada ;  EPLANET ,  ERC ,  FP7 ,  Horizon 2020  and  Marie Skłodowska-Curie Actions ,  European Union ;  Investissements d'Avenir Labex and Idex ,  ANR ,  Region Auvergne  and  Fondation Partager le Savoir, France ;  DFG and AvH Foundation ,  Germany; Herakleitos ,  Thales  and  Aristeia  programmes co-financed by  EU-ESF  and the  Greek NSRF; BSF, GIF  and Minerva, Israel; BRF, Norway; the  Royal Society and Leverhulme Trust ,  United Kingdom. The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from  CERN  and the ATLAS Tier-1 facilities at  TRIUMF (Canada) ,  NDGF (Denmark, Norway ,.
Because of its sensitivity to unfavorable weather patterns, air pollution is sensitive to climate change so that, in the future, a climate penalty could jeopardize the expected efficiency of air pollution mitigation measures. A common method to assess the impact of climate on air quality consists in implementing chemistry-transport models forced by climate projections. However, the computing cost of such methods requires optimizing ensemble exploration techniques. By using a training data set from a deterministic projection of climate and air quality over Europe, we identified the main meteorological drivers of air quality for eight regions in Europe and developed statistical models that could be used to predict air pollutant concentrations. The evolution of the key climate variables driving either particulate or gaseous pollution allows selecting the members of the EuroCordex ensemble of regional climate projections that should be used in priority for future air quality projections (CanESM2/RCA4; CNRM-CM5-LR/RCA4 and CSIRO-Mk3-6-0/RCA4 and MPI-ESM-LR/CCLM following the EuroCordex terminology).
It had been shown previously that the remaining binding pocket (i. e. the other amino acids surrounding the retinal chromophore apart from E123 and D253) is responsible only for a minor hypsochromic (i. e. blue) shi when studying color tuning, and the inuence of the rest of the protein is very minor. 9 Therefore, the region outside the active site can be safely treated by classical force elds. Two different strategies were applied in order to evaluate the absorption spectrum properties. (i) First, 50 geometries randomly selected from the QM/MM trajectories of ChR2-WT were optimized at the DFTB3/ Charmm36 level of theory with the CHARMM37b1 suite of programs  55  to ensure that harmonic uctuations of the structures around the energy minima are avoided. For each minimized structure, a single-point calculation of the electronic excitation energy was performed with the SORCI (Spectroscopy-Oriented multireference Conguration Interaction) method,  56  as implemented in the ORCA program package.
Statistical analysis. The statistical analysis was performed using SAS software, version 9. 3 (SAS Institute, Cary, NC, USA). The baseline characteristics were summarized using descriptive statistics: Median and range for continuous variables, and number and percentage for categorical variables. OS was calculated from the date of chemotherapy initiation (cycle 1-day 1) to the date of death. PFS was calculated from the date of chemotherapy initiation (cycle 1-day 1) to the date of disease progression or death from any cause. The time-to-treatment failure (TTF) is defined as the duration between the first day of treatment and the development of toxicity or tumor progression, leading to the use of another therapeutic option. Patients without any event of interest were censored at the date of the last contact.
At an inlet pressure of 60 kPa the calculated dilution correction, compared to that of 100 kPa, increased by 5. 7 %. The CPC undercounted by approximately 10 %, giving a correction factor of 1. 15 to the detected concentration at 60 kPa. Almost no correction was needed at pressures of 80 kPa or higher. Figure  5. The detection efficiency of the nCNC measured at different pressures for 50 nm ammonium sulfate particles. The blue circles are the uncorrected data, the red data were corrected with the calculated dilution correction, the black data were corrected for the CPC under-counting and the green data were corrected for both effects. Curves have been normalized to unity at normal pressure to separate the two corrections. Green data points can only be reached by correcting the measured data with these two corrections.
Acknowledgements. This work was partly funded by the  European Research Council  (ATMNUCLE,  227463 ), the  Academy of Finland  ( Center of Excellence Program  projects  1118615  and  139656 ), the  Nordic Center for Excellence (CRAICC) , the  European Commission Seventh Framework program  (ACTRIS, contract no. 262254 ; PEGASOS, contract no. 265148 ), the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie  (grant no. 656994 ), the  Office of Science (BER)  and the  US Department of Energy  (The  Biogenic Aerosols -Effects of Clouds and Climate, BAECC ). Edited by:  J. -P. Putaud.
Injection volume was 10 µL into mobile phase Milli-Q Water plus 0. 1% formic acid (A) and acetonitrile plus 0. 1 % formic acid (B), at 0. 5 ml min -1. Separation was achieved using a gradient increasing from 40% B to 70% B over 3 min, followed by a 90% B wash step and re-equilibration. Molecules were fragmented using ion electrospray with 10 ml/min gasflow at 300° C and 50 psi nebulizer with 4000 V capillary energy, 3 V collision energy, 100 V fragmentation energy. Data were acquired in negative mode, with 131 as production ion from 207 as the precursor ion. LOD of MMPB was 1. 56 ng mL -1. The method used here was developed by  Neffling et al (2010)  and  Lance et al (2010a)  for which the sample oxidation recovery (i. e. , the measure of the proportion of MCs in a tissue recovered as the oxidation product MMPB), the MMPB extraction efficiency and the matrix effects were elaborated and optimized by spiking of control samples.
(2010a). Samples were analysed using a Waters Acquity Ultra-High Performance Liquid Chromatography coupled to a Xevo quadrupole time of flight mass spectrometer. Extracts were separated on a BEH C18 column (100 x 2. 1 mm; 1. 7 µm particle size) which was maintained at 40°C. Mobile phase was Milli-Q Water plus 0. 1% formic acid (A) and acetonitrile plus 0. 1 % formic acid (B). Separation was achieved using a gradient increasing from 20% B to 70% B over 10 min, followed by a 100% B wash step and re-equilibration. Autosampler was maintained at 6°C at all times. Data were acquired in positive ion electrospray scanning from m/z 50 to 2000 with a scan time of 2 s and inter-scan delay of 0. 1 s. Ion source parameters, i. e. , capillary and sampling cone, were 2. 9 V and 25 V respectively; desolvation temperature, 300ºC; and source temperature, 80ºC.
Cone gas and desolvation gas flows were 50 L h -1 and 400 L h - 1 , respectively. Sodium iodide (2 µg µL -1 in 50/50 Propan-2-ol/H2O) was used as the calibrant with Leucine-enkephalin (0. 5 mg mL -1 in 50/50 methanol/Milli-Q) as the lockspray. Instrument control, data acquisition (centroid) and processing were achieved using MassLynx v4. 1. LOQ of MCs was a minimum 10 ng mL -1 depending on the particular MC variant (MC-LR, dmMC-RR, MC-RR, MC-YR). The characterization of the analytical method was done using freeze-dried control tissues of gastropods spiked with pure standard of MC-LR before and after extraction and treated in the same way as the sample. The average recovery for the extraction was 49. 07%. The matrix effect, corresponding to differences in results between spiked matrix and 100% methanol spiked with the same amount of standard, was 239% due to signal enhancement caused by the matrix.
1  In that study, bone marrow (BM) grafts from a human leucocyte antigen (HLA)-matched sibling donor (MSD) resulted in the best GRFS (51%) as compared with peripheral blood stem cell (PBSC) from MSD (25%), BM from matched unrelated donors (URD) (32%), or umbilical cord blood (UCB) transplants (31%). However, there were limited numbers of adult patients (age >21) who received BM from MSD, and thus specific conclusions regarding the impact of graft source in adults could not be drawn. To address that question in a larger dataset, we now report the outcomes of 1,901 patients pooled from the UMN and the Hôpital Saint-Louis in Paris (Saint-Louis). Moreover, in our previous study, pediatric recipients of BM from MSD served as the reference group to which all other groups (including adult patients) were compared.
Statistical methods Data were analyzed independently for pediatric patients (age <21 years) and adults (age>21 years). The Wilcoxon signed-rank test was used to compare characteristics across centers for continuous factors and the Chi-square test was used for categorical variables. Kaplan-Meier curves were used to estimate the probability of GFRS at 1-and 2-years post-HCT. 3 The log-rank test was used to complete the comparisons. Direct adjusted survival curves were also calculated based on a stratified Cox model. 4 The Cox regression model was used to examine the independent effect of factors on GFRS. 5  Proportional hazards were checked using martingale residuals. 6 Transplant centers violated the proportional hazards assumption, and therefore models were stratified by center. Other factors which were examined included year of HCT (2000-2007 versus 2008-2013, based on natural cut-off point), age, gender (male versus female), diagnosis, recipient cytomegalovirus (CMV) serostatus, type of conditioning (myeloablative versus reduced intensity conditioning (RIC), with or without anti-thymocyte globulin (ATG)), GVHD prophylaxis, donor type (MSD versus other related donor versus matched URD versus mismatched URD versus UCB), graft type (BM versus PBSC versus UCB) and disease risk (standard versus high-risk).
Our study also does not address the importance of GRFS in "alternative donor" settings such as haploidentical HCT compared with UCB and mismatched HCT, which should be assessed in future studies. It is critical to consider GRFS when deciding about a donor/graft source, in addition to independent outcomes of GVHD, disease-free survival and overall survival, because GRFS potentially represents a surrogate endpoint for quality-of-life. In our study, although 64% of all patients were alive and 56% were disease-free at 1-year, only 38% were free of any GRFS defining event at that time. Analysis of GRFS outcomes in the BMT CTN 0201 trial or in larger datasets, such as those available through the Center for International Blood and Marrow Transplant Research, will shed even more light on this crucial question.
e. GES-1) possess cysteines at positions 69 and 238 without having significant carbapenemase activities, acting as extended-spectrum cephalosporinases instead  [121]. However, these enzymes may become true carbapenemases by single amino-acid changes at position 170. A number of 22 crystal structures are currently available in the Protein Data Bank (PDB)  [122]  (Table  7 ). The superposition of all these structures (Fig. 4 ) shows that they share the same fold, with very well conserved structural features. There are, however, 5 regions (A-E) presenting significant differences in the backbone conformation. These regions, which are situated relatively far from the active site and more likely do not influence directly the activity and the selectivity of class A carbapenemases, will be analyzed in more detail below (see Fig.
Study outline Eligible patients will be recruited at the outpatient department of each participating centre. Patient enrolment will be agreed after the treatment decision is made. Patients will be treated according to routine clinical practice and budesonide MMX will be prescribed in accordance with the terms of the country marketing authorisation. The recommended dose of budesonide MMX for induction of remission is one 9 mg tablet daily in the morning, for up to 8 weeks. 16 The clinician will decide if and how the dose should be reduced, and the duration of the tapering-off period, if required. These data will be collected throughout the tapering-off period until treatment has been discontinued or after a 6-month tapering-off period (whichever occurs earlier).
Data collection and monitoring Eligible patients will be seen at the outpatient department of each participating centre at baseline (Day 1), at the end of induction treatment (daily), and at follow-up ≥2 weeks after the end of the last treatment dose (table  1 ). On Day 1, data, as recommended by current ECCO guidelines, 2 will be collected by the investigator or from the patient's medical record. Patients will be given the option to fill in the questionnaires (SIBDQ, WPAI) on Day 1 and at the end of the induction treatment (daily) visit (SIBDQ, WPAI, treatment satisfaction scale), approximately 4-8 weeks after the investigator has decided to treat the patient with budesonide MMX to induce remission. An electronic case report form (eCRF) will be used to capture data. During these contacts, the clinician will also evaluate the information reported in the patient's weekly diary (if any), and will capture the data on the appropriate eCRF.
Statistical analysis Sample size was calculated on the percentage of patients with clinical improvement ≥3 points in the clinical subscores of UCDAI score at the end of the induction treatment (once daily budesonide MMX9 mg tablet). A sample size of 300 evaluable patients will allow estimation of the two-sided 95% CI with a width equal to 11. 0% of the clinical benefit when the expected percentage is equal to 38% based on the Phase III trials data. The Clopper-Pearson's formula was used for the computation. Descriptive analyses will be carried out using the tools available within standard spreadsheet and database packages. Continuous variables will be summarised using the number of patients, mean, SD, minimum, first quartile, median, third quartile and maximum. For categorical variables, data will be summarised by the number and percentage of patients in each category.
Incidence percentages will be calculated. When summarising categorical variables, if there are any missing responses, these will be shown as a separate category. When summarising continuous variables, the number of non-missing observations will be displayed. All withdrawals after enrolment will be summarised by time of, and reason for, discontinuation. Statistical analyses will be performed using the SAS System V. 9. 4. A two-tailed p<0. 05 will be considered statistically significant. Analyses will be presented with 95% CIs. Association between the response and clinical variables (with variables with a p<0. 20 in univariate analysis) will also be tested using logistic regression analysis. Odds ratios with 95% CIs will be derived from the logistic model. To evaluate effectiveness, the primary outcome (improvement ≥3 point in the clinical subscores of the UCDAI score at the end of treatment) will be compared in patients who will receive budesonide MMX added to mesalazine at least 14 days (>2 weeks) after increased/ optimised mesalazine dose for the treatment of flare (late add-on) (Cohort 1) (figure  2 ); patients who will receive budesonide MMX added to mesalazine within 14 days (≤2 weeks) since mesalazine increased/optimised for the treatment of flare, or without mesalazine dose modification (early add-on) (Cohort 2) (figure  2 ); and patients who will receive budesonide MMX as monotherapy for the treatment of flare (mono) (Cohort 3) (figure  3 ).
Dissemination plan At the end of the study, one or more manuscripts on the full results would be published in peer-reviewed journal(s). Data from individual countries may also be published separately. All study data will be stored on a fully validated, eCRF system held by an independent third-party contract x *Visits will be made in accordance with routine clinical practice, and budesonide MMX treatment must be prescribed in the usual manner in accordance with the terms of the marketing authorisation of each participating country. †Written informed consent must be obtained prior to any study-related data collection. ‡Depending on country regulations for non-interventional study and on local clinical practice. §The investigator will also offer the patient a weekly diary. If she/ he wishes to complete this, the diary will be provided at inclusion, and the patient will be requested to return the diary to the physician at the end of daily treatment visit, whenever this occurs.
26  PROs can evaluate symptoms, signs, functional status, perceptions, or other aspects, such as tolerability, from the patient's perspective, and complement clinicianreported measures. 36 In our study, PRO data will be  collected via the SIBDQ, WPAI and treatment satisfaction scale questionnaires, as well as from the patient's weekly diary. To address the potential bias due to PROs, patient weekly diaries and questionnaires will be completed by the patient alone, without any involvement of the investigator. The information provided is in line with current thinking from the FDA on the importance of PROs in assessing disease activity in IBD  25 26  and will help inform clinical care and decision-making. The results of our study are expected to provide information in the field of UC and further evidence on effectiveness to support clinicians in their daily practice and inform therapeutic guidelines.
Acknowledgements  Maciej Jesionowski ,  Agnes Ograbek ,  Henri Veerman ,  Marije van Weelden ,  Birgitta Reimers ,  Philippe Niez ,  Ferring Pharmaceuticals. Strategen Limited  provided editorial support to the authors funded by  Ferring Pharmaceuticals. Contributors SD, LP-B, LDA are involved in clinical study design, critical review of the manuscript and final approval of the manuscript; CI is responsible for clinical study design and final approval of the manuscript; GDH, AD, ID, AH, EL, GR are involved in final approval of the manuscript.