dataesr/scientific-paragraphs-categorization huggingface dataset:
Numerical results One can improve upon the analytic calculation described above by performing a numerical calculation that also takes into account the thermal evolution of the Universe. The results presented in this subsection rely on MadDM version 2. 0. 6. The MadDM package considers all tree-level 2 → 2 interactions between DM and SM particles. The processes are thermally averaged and the resulting relic density is computed. Since MadDM does not yet automatically calculate the mediator width from the model parameters, the DMsimp model was modified to use the mediator width formulae presented for instance in  [1, 7]. The DM density calculations provided in the previous LHC DM WG recommendations  [7]  used an earlier version of MadDM which did not include t-channel annihilation to pairs of mediators.
Acknowledgements The work of CD is supported by the  European Research Council  under the European Union's  Horizon 2020 research and innovation programme  ( ERC  grant agreement No. 679305  DARKJETS). MF and PT are funded by the  European Research Council  under the European Union's  Horizon 2020 program  ( ERC  grant agreement No. 648680 DARKHORIZONS). UH acknowledges the hospitality and support of the CERN theory division. The work of GL and AB is partially supported by the  Department of Energy  Award  DE-SC0010010  and  DE-SC0011726. AR is supported by the  Swiss National Science Foundation (SNSF) , project title: '' Investigating the Nature of Dark Matter '', project number:  200020-159223. The work of TMPT is supported in part by  National Science Foundation (NSF)  grants  PHY-1316792  and  PHY-1620638.
The numerical impact of the changes in the β-function for the fermion mass terms is illustrated using a toy model with a heavy vector-like fermion pair coupled to a scalar gauge singlet. Unsurprisingly, the correction to the running of the fermion mass becomes sizeable for large Yukawa couplings of the order of O(1). Furthermore, we demonstrate the importance of the correction to the β-functions of the scalar quartic couplings using a general type-III Two-Higgs-Doublet-Model. All the corrected expressions have been implemented in updated versions of the Mathematica package SARAH and the Python package PyR@TE.
Since a supersymmetric extension of the SM yields many couplings which are generically all of the same form, we opt for a more compact theory. We consider a toy model with one vector superfield B and three chiral superfields Ĥd : Q = - 1 2 , (6. 1) Ĥu : Q = 1 2 , (6. 2) Ŝ : Q = 0 , (6. 3) where Q denotes the electric charge. The superpotential consists of two terms 2  W = λ Ĥu Ĥd Ŝ + µ Ĥu Ĥd (6. 4) and the soft-breaking terms are -L SB = B µ H d H u + T λ H d H u S + 1 2 M B B2 + h. c. + m 2 H d |H d | 2 + m 2 Hu |H u | 2 + m 2 S |S| 2. (6. 5) This model contains all of the relevant generic structure we need to test. Making use of the results of Ref. [8] , which are also implemented in the package SARAH, we find the following expressions for the one-and two-loop RGEs for the different parts of the model: 1.
Thus it is crucial to use the corrected RGEs if one wants to study for instance grand unified theories which predict additional vector-like fermions with large Yukawa couplings to a gauge singlet. In addition, we have demonstrated the importance of the correction to the β-functions of the scalar quartic couplings using a general type-III Two-Higgs-Doublet-Model. As can be seen in Fig. 3  the corrections to the running couplings are non-negligible and can become very large in certain regions of the parameter space. All the corrected expressions have been implemented in updated versions of the Mathematica package SARAH and the Python package PyR@TE. We hope that this paper will be a useful resource in which all the relevant information on the two-loop β-functions is at hand in one place. Y bc 2 (S)Y b Y †a Y c Y bc 2 (S)Y b m † f Y c (A.
Data collection Data were collected in cross-sectional surveys from July to September 2011. A total of 231 participants from permanent resident populations were included in our study. Participants were included after they signed consent forms. As main inclusion criteria participant should be at least 3 years old, with no clinically chronic disease, no immune deficiency or history of blood transfusion in the last three months. A blood sample (6 ml in EDTA tube) was collected from each participant by venipuncture. Interviewing participants, we also collected the socio demographic data of each participant.
Statistical methods All data were entered and analyzed in SPSS software version 16. The phenotype frequencies were calculated for all study participants while allele frequencies were determined only in unrelated participants. Determination of alleles frequencies. For ABO, Kidd, Duffy, MNSs and Kell systems, the Bernstein formula was used to estimate the frequencies of the alleles, with the assumption that the study population was in Hardy-Weinberg equilibrium. Determination of the haplotypes frequencies in RH system. The algorithm EM (Expectation-Maximization) based on the maximum likelihood principle, and GENE [RATE] program were used to determine the genotypes of RH system.
Introduction Percutaneous interventional procedures need accurate device positioning, using imaging guidance such as ultrasound (US), Computed Tomography (CT), fluoroscopy or Magnetic Resonance Imaging (MRI). Fusion imaging guidance systems (FIGS) may be an interesting solution when the interventional radiologist needs a combination of information provided by two or more imaging modalities. This can be the case for the positioning of the needle (biopsy) or for the evaluation of the ablative margins, for instance in radiofrequency ablation (RFA) for malignant hepatic tumors  [1] [2] [3] [4]. Virtual navigation systems in preoperative 3D MRI or CT datasets bring the possibility of improving real-time tumor targeting. These systems can be used alone with optical or electromagnetic tracking platforms or associated with US guidance  [5].
1 ). The aim was to evaluate the accuracy of the system using a very fine needle that would not injure the organs, as opposed to the larger final needle used for RFA (Cool-tip™ RFA system, Medtronic, Minneapolis, USA). The pathway of this spinal needle was later used for the insertion of the radiofrequency needle, but this step does not concern the evaluation. The system evaluated in our study uses electromagnetic tracking and is composed of a tracking workstation and a magnetic field generator. Multimodality image fusion is possible with that system but in this study, only a CT-scan performed on the operative table, was employed for fusion. In brief, a magnetic position sensor was attached to the ultrasound transducer shaft. A CT-scan (16-detector row scanner, Somatom; Siemens, Healthcare GmbH, Forchheim, Germany) was performed just before the procedure and 3D Digital imaging and Communications in Medicine (DICOM) datasets were used for fusion.
Statistical analysis The aim of the study was to estimate a distance within its interval of credibility. To determine the sample size, a mean error µ = 5 mm of accuracy for each axis, was considered with a standard deviation σ = 2. 5 mm. A Bayesian analysis of the data (software R, OpenBUGS) was performed to know the probability of the error (difference between real and virtual coordinates). The estimation determined a minimal sample size of 20 patients, which was increased to 25 in this study. No interim analysis was scheduled. After the inclusion of the last patient, the Bayesian analysis was performed for µ=5 and µ=7 mm. The differences were compared to 7 mm by using gamma distributions and Bayesian methods. The relationship between the quality of the fusion, the depth of the lesion, and the global mean error was studied using Spearman's correlation coefficient.
Results Mean tumor's diameter was 22. 6±8. 6 mm for a mean depth (skin-tumor distance) of 90. 1±30. 8 mm (Table  2 ). Mean differences of (A) coordinates were 1. 8±1. 8mm, 2. 1±2. 0mm No correlation was observed between the depth of the tumor and the global mean error for point P and D (ρ = -0. 07). The mean duration of the procedure was 14. 7+/-10 min. The use of the fusion system increased the duration of the procedure for cases 6 and 8. In these cases, fusion procedure took more time as orientation in space (cranio-caudal inversion) was not correct. This required restarting the initial step of fusion which delayed the procedure. Rigid coregistration was performed using one to five (mean 2. 2 ± 1. 2) internal anatomic landmarks (portal vein, celiac artery, hepatic veins) to spatially match the two imaging datasets to each other.
Discussion The accuracy of a fusion imaging guidance system for the insertion of a 22-gauge needle in the liver was evaluated. The FIGS evaluated allows navigation in both ultrasound and preoperatively acquired CT volumes with a mean difference in Euclidian coordinates of 8. 5±4. 7 mm and 10. 5±5. 3 mm for the tip of the needle and a needle point located 3 cm proximally, respectively. The error measured corresponds firstly to the registration error, secondly to the error due to the localized deformation of the organ and thirdly to liver motion during breathing (even if precautions have been taken to register the data in expiration). Moreover, an operator error may be added, as the needle is not seen on the virtual CT-scan: the operator extrapolates the localization of the needle seen with US on the CT-scan picture.
J/ψ coming from b hadron decays are identified with the measurement of a secondary μ + μ -vertex displaced from the primary collision vertex. The displacement can be resolved using the pseudo-proper decay length J/ψ  [8]. To measure the fraction of nonprompt J/ψ, the invariant mass spectrum of μ + μ -pairs and their J/ψ distribution are fitted using a two-dimensional (2D) extended unbinned maximum-likelihood fit  [9]  in the different z bins after applying corrections for the acceptance and efficiency of the CMS detector. After the yield extractions, the migration across z bins, due to the finite jet p T resolution, is corrected for with an unfolding procedure with D'Agostini's iterative method  [10] , as encoded in the RooUnfold software package  [11]. The unfolding is carried out in two dimensions, z and jet p T , using the detector response derived from Monte Carlo simulations.
The V3 and V4 (319F-806R) regions of the 16S rRNA gene were PCR-amplified following a previously described protocol  (Kembel et al. , 2014) , and amplicons were purified with a bead-based clean-up using Mag-Bind RxnPure Plus (Omega Bio-tek, Norcross, GA, USA). Cleaned DNA was quantified using Quant-iT dsDNA assay kit, and pooled with equal concentrations of amplicons for Illumina Miseq ver. 4 paired-end sequencing using a 250-cycle kit at the University of Oregon Genomics Core (Eugene, OR, USA). Raw data are available through the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject accession PRJNA541585. Sequence data were processed using the DADA2 pipeline  (Callahan, McMurdie & Holmes; Callahan et al. , 2016)  in R statistical program (R Core Team, 2018).
During filtering, sequences were trimmed by 10 bases at the start position, and 10 and 20 bases from the end position for forward and reverse reads, respectively. No ambiguous bases were permitted, and the maximum expected errors were two and three for forward and reverse, respectively. NA matching the phiX sequencing controls was removed. Error rates were learned on 1 × 10 6 randomly-selected dereplicated reads, and used to identify Full-size  DOI: 10. 7717/peerj. 8147/fig-  1  sequence variants (SVs), after which forward and reverse reads were merged into contiguous sequences. Bimeras (two-parent chimeras) were identified and removed, and taxonomy assigned using the Silva NR ver 132 database  (Yilmaz et al. , 2014). Laboratory negative controls were used to remove identical SVs from experimental samples, using adapted code  (Ishaq, 2017).
For calculation of doubling times, cells were grown without drugs for 0, 24, 48, and 72 h following attachment. After treatment, cells were incubated with medium containing 0. 75 mg/mL of 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide (MTT) for 1-2 h at 37 °C, medium was removed and formazan crystals dissolved in 100 µL DMSO. Cell numbers were estimated by measuring the absorbance at 495 nm, using an Anthos 2020 microplate reader (Biochrom Ltd, Cambridge, UK). Data were derived from at least three independent experiments. In some experiments, direct counting in a hemocytometer after trypan blue staining was additionally used. For cell cycle analyses, cells were plated in T-25 flasks, allowed to attach, treated with drugs in   overnight. Cover slips were then removed, washed with PBS, fixed with 4% paraformaldehyde for 15 min and treated with cold methanol.
The antibodies used in this study are presented in the Supplementary Table  4. Histological images were obtained using a ×20 objective, unless otherwise indicated. Cell death and senescence assays. For cell death analyses, the Annexin-V-FLUOS (An) staining kit (Roche Diagnostics) was employed, according to the manufacturer's instructions. Stained cells were analyzed with a FACSCanto II cytometer (BD Biosciences, Franklin Lakes, NJ) using the FACSDiva software version 6. 1. 2. The combination of Annexin V and PI was used to differentiate four cell populations; namely, viable cells (An-/PI-), early apoptotic (An+/PI-), necrotic (An-/PI+), and later apoptotic/necrotic (An+/PI+). For the initial senescence studies, cells were treated for 2 h to 8 days in 6-well plates, and the Senescence Beta-galactosidase Staining kit (Cell Signaling) was be used to evaluate the presence of senescent cells by direct observation under the microscope.
The panel targets 549 variant positions in 17 selected genes frequently altered in lung tumors (AKT1, ALK, BRAF, DDR2, EGFR, ERBB2/HER2, ESR1, KIT, KRAS, MAP2K1, MET, NRAS, NTRK1, PDGFRA, PIK3CA, PTEN, ROS1) and detects copy number variations (CNV) in five genes (EGFR, FGFR1, ERBB2/HER2, MET, RICTOR). RNA was isolated by standard procedures  25. Primer and probe sets (Supplementary Table  5 ) were designed using Primer Express 3. 0 Software (Applied Biosystems) according to their reference sequences (http://www. ncbi. nlm. nih. gov/LocusLink). Quantification of gene expression was performed using the ABI Prism 7900HT Sequence Detection System (Applied Biosystems). Expression levels were calculated using to the comparative ΔΔCt method  25. Commercial RNA controls were used as calibrators (Liver and Lung; Agilent Technologies, Santa Clara, CA, USA).
Data availability The NGS data generated in this study have been deposited in the in the Sequence Read Archive (SAR) of the National Center for Biotechnology Information (NCBI), under the accession codes PRJNA524804 (project) and SAMN11035311-SAMN11035324 (individual samples). The source data underlying Figs. 1e, 2a, 2g, 3c, 3e-g, 4a, 4b, 4e, 4f, 4h, 5c-e, 6a, 6c and Supplementary Figs. 1b, 2 , 3c, 3d, 4a, 4b, 5b, 5c, 6a, 6c, 7b, 7c, 9a, 9b, 10b, 10c are provided as a source data file. The file contains uncropped and unprocessed scans of the western blots presented in Figs. 1b, 2c , 2d and 3a. The source data file has also been deposited in the Open Science Framework (OSF) repository under the unique identifier DOI 10. 17605/OSF. IO/JW4C7. The authors declare that all other data supporting the findings of this study are available within the main article and its Supplementary Information file or from corresponding authors upon reasonable request.
Results Physical performance is lower in SCA. Results indicated a significant difference in VT 1 between AA and SCA (P = 0. 03; Fig. 1a ), as well as lower time to reach VT 1 (P = 0. 02; Fig. 1b ) and lower power at VT 1 (P = 0. 02; Fig. 1c ) in SCA. Lactate concentration measured at VT 1 was 2. 5 mmol for SCA and 3. 1 mmol for AA (P = 0. 17). Exercise does not affect blood count and plasma free haemoglobin concentration in SCA. Data presented in Table  1  revealed significant difference in blood count between AA and SCA but no effect of exercise was observed in the two groups. Plasma free haemoglobin concentration was significantly higher in SCA compared to AA (P = 0. 02 at rest and P = 0. 04 at VT1) but was not significantly affected by the intervention (Fig. 2 ). RBC deformability is lower in SCA but is not affected by exercise.
Methods Study protocol. The protocols used in this study were reviewed and approved by the ethics committee of the German Sport University Cologne (date of approval 16. 07. 2014). The protocols are in line with the Declaration of Helsinki and all participants or legal guardians of the participants gave written informed consent to participate in this study. A total of 16 adolescents were included in this study of which n = 8 were patients with SCA (HbF = 13. 4 ± 7. 9%, HbS = 84. 1 ± 7. 2%) and n = 8 were healthy controls (AA). Anthropometric data are shown in Table  2. SCA diagnosis was made by haemoglobin electrophoresis and confirmed by genetic studies in case of unclear electrophoresis results. Patients were at steady-state (i. e. , without any acute vaso-occlusions or hospitalized complications and no blood transfusion in the last three months prior to intervention).
RBC Nitrite/RSNO/Fe-NO concentrations were measured according to published protocols  48, 49. Briefly, thawed RBC samples were mixed with ice-cold methanol (VWR International, Germany), centrifuged and the Nitrite/RSNO/Fe-NO levels of the supernatant were measured as described earlier  50. Samples were injected into an acidified tri-iodide solution that reduces nitrite but also iron-nitrosylheme, and S-nitrosothiols to NO gas which was analysed by chemiluminescent reaction with ozone using a chemiluminescence NO detector (CLD 88e, EcoPhysics, Switzerland). All samples were measured in triplicate. The Chart FIA software (Ecophysics, Switzerland) was used to integrate the area under the curve and the sample Nitrite/RSNO/Fe-NO concentration was calculated by the use of standard solutions. RBC Nitrite/RSNO/Fe-NO concentration of the samples was corrected for Nitrite/RSNO/Fe-NO concentrations of methanol and preservation solution, respectively.
Slides were washed with TBS, treated with 3% normal goat serum (Dako, Denmark) and incubated with a secondary goat anti-rabbit antibody (dilution: 1:400, Dako, Denmark). 3,3-diaminobenzidine-tetrahydrochloride (DAB) solution (Sigma, USA) in TBS was added to the slides and staining was stopped by adding TBS to the DAB solution. Slides were then dehydrated by exposure to alcohol solutions of increasing concentration and sealed using Entellan ® (Merck, Darmstadt, Germany). Images were taken from the stained slides using a Zeiss microscope coupled to a CCD-camera (DXC-1850P, Sony, Germany). The semi-quantitative analysis of the grey values was conducted using the 'Image J' software (National Institutes of Health, USA). Grey values of a total of 50 RBC from at least four images were determined in the test area and subtracted from the background value, which was measured in a cell-free area of the slide in order to obtain staining intensity caused by the binding of the antibodies.
EDDf was commenced at the discretion of the clinician and did not uniformly correspond with the timing of ticarcillin dosing. EDDf was performed in all patients using a 5008s online haemodiafiltration machine (Fresenius Medical Care, Bad Homburg, Germany) with Fresenius polysulfone AV600S 1. 4 m 2 high-flux haemodiafilters (Fresenius Medical Care). The standardised EDDf prescription included a blood flow rate ( Q b ) of 300 mL/min, a dialysate flow rate ( Q d ) of 200 mL/min, and 50 mL/min predilution with a targeted treatment duration of ≥8 h. Other clinical and demographic data were collected on the day of plasma sampling, including age, sex, total body weight and body mass index (BMI). Clinical data included Acute Physiology and Chronic Health Evaluation (APACHE) II score as well as serum albumin and serum creatinine (SCr) concentrations.
Population pharmacokinetic modelling To describe total ticarcillin concentrations, one-and twocompartment models were developed with the Nonparametric Adaptive Grid (NPAG) algorithm within the Pmetrics software package for R v. 1. 5. 1 (Keck School of Medicine of USC, Los Angeles, CA). Elimination from the central compartment and intercompartmental distribution into the peripheral compartment (two-compartment model) were modelled as first-order processes.
Model diagnostics Goodness of fit was assessed by linear regression, with an observed-predicted (both population-and individual-predicted concentrations) plot, coefficients of determination and loglikelihood values. Predictive performance was based on mean prediction error (bias) and mean bias-adjusted squared prediction error (imprecision) of the population and individual prediction models. The internal validity of the population pharmacokinetic model was assessed by the bootstrap resampling method ( n = 10 0 0) and normalised prediction distribution error (NPDE). Using the visual predictive check method, parameters obtained from the bootstrap method were plotted with the observed concentrations. NPDE plots were checked for normal distribution characteristics and trends in data errors.
Study limitations Although this study is the first descriptive pharmacokinetic study of ticarcillin in critically ill patients undergoing EDDf, it has some limitations. First, the sample size is small, therefore describing all possible correlations between pharmacokinetic parameters and covariates may not have been possible. Second, ticarcillin plasma concentrations were measured and not concentrations at the site of infection, which may provide better mechanistic data regarding the effectiveness of dosing. Finally, this study was not designed or powered to examine the effect of ticarcillin exposure on patient outcome, and larger studies are required to explore this question further.
2018 ) combined with both shipboard and newly published biostratigraphic data  (Kamikuri et al. 2017)  to construct high-resolution, high-precision age models at the two sites. Physical properties measured at high resolution during the cruise were utilized to correlate the sediment records between holes and between coring sites. These physical properties were also used to support orbital tuning because sedimentary cycles were clearly evident in the high-resolution record (e. g. ,  Lourens et al. 2005; Tian et al. 2008).
Correlation with logging data Continuous sedimentary records are required to apply cyclostratigraphy to sedimentary sequences. IODP expedition 346 drilled two or more holes at sites U1425 and U1430, from which a continuous Miocene-Pliocene stratigraphic record, or splice, was assembled for each site. During the expedition, the cores at each site were stratigraphically correlated onboard using physical properties such as natural gamma radiation (NGR), gamma ray attenuation (GRA), and color reflectance  (Tada et al. 2015b (Tada et al. , 2015c)). On the shore, core photographs were examined to identify small faults and disturbances that could not have been identified in the physical property profiles. The initial splice was revised on the basis of several new tie points within core intervals corresponding to lithological units I and III to correct miscorrelations and avoid intervals containing sponge plugs and other discontinuities (detailed in  Irino et al.