dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Methods Statistical analyses were carried out using SPSS version 20. 0 (IBM Corp, Armonk, NY, USA). P-values less than 0. 05 were considered statistically significant. Data were summarized in frequencies with percentages for categorical variables and means with standard deviation for continuous variables. The chi-square (χ 2 ) test was used to compare categorical variables, and analysis of variance (ANOVA) was used for the analysis of quantitative variables (age, BMI, and stool form). Significant ANOVA analysis led to posthoc tests with Bonferroni adjustment for multiple tests. In addition, a linear regression model adjusted for age, BMI, gender, clinical group, the presence of painful constipation, pelvic floor dysfunction, and symptom intensity was used to assess the relationship between total and segmental CTT.
β-actin served as a loading control. After washing, the membranes were incubated with an alkaline phosphatase-labeled anti-rabbit or anti-mouse secondary IgG antibody (Santa Cruz Biotechnology, USA) and visualized using a BCIP/NBT AP Conjugate Substrate Kit (Bio-Rad, USA). Determination of the relative intensities of the bands was performed using Quantity One software and the values were calculated as relative absorbance units (RQ) per mg protein.
Scratch wound cell migration assay Cells (5 × 10 5 /well) were seeded in 24-well plates and grown in serum-reduced medium overnight. On the following day confluent cell layers were scratched with a tip and wells were rinsed with warm PBS buffer in order to remove detached cells. Next, fresh serum-reduced medium containing the indicated concentrations of the test compounds was added and each well was photographed using a JuLI FL miscroscope (NanoEntek, Korea). Photographs of the same areas were taken again after 7, 13 or 18 h (t x ). The time of incubation was different for each cell line depending on the individual cell migration dynamics so that the wound area would not become closed in vehicle-treated cells. The area covered by cells was assessed for each well at both time points using JuLI FL software and the difference in cell coverage area between t x and t 0 was calculated.
Cell cycle analysis Cells (1 × 10 5 /well) were seeded in 12-well plates and, after overnight pre-incubation, medium was replaced with fresh medium containing the test compounds after which the cells were grown for another 48 h. Vehicle treated cells were used as negative controls and cells treated with topotecan were used as positive controls. Next, cells were collected by trypsinization, washed with PBS buffer and fixed in 70% ethanol. After at least overnight storage at -20 °C, fixed cells were collected by centrifugation and cell cycle distributions were analyzed using a Muse Cell Cycle Kit (Merck, Germany) according to the manufacturer's protocol. Briefly, cell pellets were washed with PBS buffer and next incubated with propidium iodide in the presence of RNase A. Flow cytometric analysis of the stained samples was performed using a Muse Cell Analyzer (Merck, Germany) and data from two independent experiments were analyzed using Muse 1.
Acknowledgements. Our interest for devices with electrostatic doping has developed during the accomplishment of REMINDER, a project funded by the  European Union. Vivid thanks are due to all our partners, especially to  F. Gamiz ,  Y. Taur ,  J. Wan ,  A. Zaslavsky ,  H. El Dirani ,  P. Fonteneau ,  C. Le Royer ,  P. Galy ,  J. Lacord , and  J-P. Colinge. M. Bawedin  is thanked for illuminating critical comments.
11 ituximab is a chimeric, humanized anti-CD20 monoclonal antibody  12  believed to exert its clinical effects in pemphigus through depletion of Dsg-specific lymphocytes. 13 The efficacy of rituximab in the treatment of severe, recalcitrant pemphigus has been reported in the literature for the past decade. In patients with newly diagnosed pemphigus, Joly et al. demonstrated that rituximab plus shortterm CS was safe and significantly more effective than CS alone (the Ritux 3 study; ClinicalTrials. gov NCT00784589). 14 he U. S. Food and Drug Administration (FDA) granted Orphan Drug Designation and Breakthrough Therapy Designation to Roche for rituximab in the treatment of PV. The lead investigator, Rouen University Hospital and Roche then collaborated, and Roche independently analysed data collected from patients diagnosed with PV (excluding patients with PF) in the Ritux 3 study and submitted applications to seek regulatory approvals for rituximab as a treatment for moderate-tosevere PV in the U.
Statistical analyses and methods Trial data and associated documents (such as case report forms and randomization specification) were obtained from Rouen, translated into English and formatted according to regulatory submission requirements [Clinical Data Interchange Standards Consortium Data Exchange Standards and coding of adverse events (AEs) using the Medical Dictionary for Regulatory Activities] and analysed according to an independent statistical analysis plan prepared by Roche. Descriptive analysis was used to compare the rituximab plus prednisone arm with the prednisone-alone arm for the proportion of patients who achieved complete remission (CR) off CS therapy (CRoff), the median cumulative dose of prednisone and the proportion of patients who relapsed. Last observation carried forward imputation was used to impute prednisone data for missed visits.
Acknowledgments We thank the investigators in the French Study Group on Autoimmune Bullous Diseases who designed the Ritux 3 study and collected data on their study patients, and the patients who participated in the Ritux 3 study. We would like to thank  Rouen University  who allowed  Roche  to have access to the study database and supporting documents and we also thank  Everest Clinical Research for assisting Roche  with the independently conducted data analysis and review of document translations. Support for third-party writing assistance for this manuscript, furnished by  Health Interactions Inc. , was provided by  F. Hoffmann-La Roche.
ACKNOWLEDGEMENTS  Donatella Marazziti, Stefano Baroni, Armando Piccinni,  Liliana   Dell'Osso planned the study, wrote and revised the paper. Donatella Marazziti ,  Armando Piccinni ,  Federico Mucci ,  Enrico Massimetti ,  Claudia Carmassi  and  Ilenia Moroni  selected the subjects to be included in the study. Stefano Baroni ,  Lionella Palego  and  Gino Giannaccini  carried out the biological assays and the statistical analyses. All the authors revised and approved the final version of the paper.
Emission light from the sample was collected after passage through the appropriate emission filters (Semrock, Rochester, NY, USA). Images were acquired using an electronmultiplying charge-coupled device camera (C9100-13; Hamamatsu, Hamamatsu, Japan). Image acquisition was performed using MetaMorph software (Molecular Devices, Sunnyvale, CA, USA). Raw image data files were processed using Adobe Photoshop CC 2015 and assembled in Adobe Illustrator CC 2015. Pearson correlation coefficient (PCC) analysis was performed on ;100 cells to quantify colocalization between proteins.
All experimental samples were acquired using an LSR II Flow Cytometer (BD Biosciences, San Jose, CA, USA) located in the MGH Center for Regenerative Medicine Flow Cytometry Core Facility and analyzed using FlowJo software (Treestar, Ashland, OR, USA). Compensation was performed using single-color controls prepared from BD Comp Beads (BD Biosciences) for cell surface staining and live/dead cell staining (Thermo Fisher Scientific) for viability. Compensation matrices were calculated and applied using BD FACS Diva software.
Emitted fluorescence for each reaction was measured 3 times during the annealing-extension phase, and amplification plots were measured using Roche LightCycle 96 (Roche). Data were analyzed with MX4000 software, v. 3. 0 (Stratagene, San Diego, CA, USA). The quantity of gene expression was generated by comparison of the fluorescence generated by each sample with standard curves of known quantities and normalized by dividing by the number of copies of the housekeeping gene b 2 -microglobulin. Normalized values from each cell line were then divided by the normalized WT value to calculate the expression ratio.
1G ), these levels were significantly less than WT mice. As expected, TLR9KO mice did not produce TNF-a in response to CpG + D-GalN (Fig. 1G ). Mice injected with D-GalN alone did not produce TNF-a. To determine whether CD82 regulation of serum TNF-a was TLR9 specific, we tested response to the activation of TLR4. We injected intraperitoneally WT and CD82KO mice with LPS and D-GalN only and assessed serum TNF-a levels 1. 5 h postinjection. WT mice injected with LPS produced elevated serum levels of TNF-a (Supplemental Fig. S2 ), as previously shown by Blanqué et al. (39). Similarly, CD82KO mice injected with LPS produced comparable amounts of TNF-a as the WT mice (Supplemental Fig. S2 ), demonstrating that CD82 is not required for TLR4 signaling in vivo. Our data indicate that CD82 controls TLR9-induced TNF-a production in macrophages and in vivo (Fig.
We observed an interaction between VAMP3 and TLR9-GFP in both unstimulated and CpG-stimulated WT macrophages, but this interaction was absent in UNC93B1-KO macrophages, despite robust VAMP3 expression in both cell types (Fig. 5B , top blot and third blot). In the WT macrophages, we observed both full-length and cleaved TLR9-GFP in the TLR9-GFP immunoprecipitates, whereas only the full-length TLR9-GFP was found in the UNC93B1-KO macrophages (Fig. 5B , second blot). These data indicate that UNC93B1 controls the trafficking of TLR9 to VAMP3positive compartments. We next sought to determine whether the interaction between TLR9 and VAMP3 requires CD82. We stimulated WT and CD82KO macrophages stably transduced with TLR9-GFP with CpG. The lysates were immunoprecipitated for TLR9-GFP, resolved by SDS-PAGE, and probed for endogenous VAMP3.
CD82 controls TLR9-dependent myddosome assembly MyD88 is a TLR adaptor protein critical for the activation of NF-kB and cytokine production. MyD88 forms a complex with IRAK4, which sequentially recruits IRAK2 and forms a myddosome complex  (21, 23). Based on our data demonstrating that CD82 regulates TLR9-dependent NF-kB activation (Fig. 1G ), we sought to determine whether CD82 affects TLR-dependent myddosome assembly. To assess the role of CD82 in TLR9-induced myddosome assembly, we stimulated WT, TLR9KO, CD82KO, and CD82KO + CD82-mRFP1 macrophages with CpG and immunoprecipitated endogenous MyD88. The proteins from the immunoprecipitates were resolved by SDS-PAGE and probed for IRAK2 and IRAK4. In unstimulated cells, the presence of IRAK2 and IRAK4 in MyD88 immunoprecipitates indicated baseline levels of myddosome formation (Fig.
ACKNOWLEDGMENTS The authors thank  Nicole Wolf  for the artwork displayed in the graphical abstract (Fig. 7),  Shizuo Akira  ( Osaka University, Osaka, Japan ) for the TLR9 knockout ( TLR9KO ) mice, and  Douglas Golenbock  ( University of Massachusetts Medical Center, Worcester, MA, USA ) for the TLR9KO macrophage cell line. The authors also thank  Kensuyke Miyake  and  Ryutaro Fukui  ( University of Tokyo, Tokyo, Japan ) for the TLR9 monoclonal and polyclonal antibodies (41), and  Gregory Barton  and  Bo Liu  ( University of California-Berkeley, Berkeley, CA, USA ) for the TLR7-FLAG construct. This work was supported by  U. S. National Institutes of Health, National Institute of Allergy and Infectious Diseases Grants   R01 AI092084  and  R01 AI097519  (to J. M. V. ) and  R01 AI025780  and  R01 AI139615  (to S.
, 2007a). Mihalache et al. (2017)  also spotted deeply folded, shrunken, wrinkled and partially distorted hyphae, as well as subterminal vesicles and intercalary swelling on F. oxysporum mycelium, under M or SM treatments, using SEM. More recent data, from  Park et al. (2019) , have shown vesicle-like structures with surfactin (from B. velenzenis) on Colletotrichum gloeosporioides. The surface of the mycelium was rugged and unusually swollen and rough, suggesting the peptide affects directly the fungal cell wall components (chitin, glucans, and glycoproteins) to exhibit antifungal activity  (Park et al. , 2019). Clear disruptions were observed after linking antifungal activity data with morphological microscopic observations. Indeed, on S755, for the same level of antifungal activity, we did not observe the same type of morphological modifications according to treatments: large vesicle-like structures could be seen in the presence of fengycin, while small oval-shaped swollen structures, of small sizes, could be observed with tebuconazole.
Methods A computerized search was done by the bibliographer in different databanks (MEDLINE, Scopus, EMBASE) and citations were included for the period between January 1990 and August 2018 using the primary search strategy: kidney, injuries, trauma, urogenital, adult, pediatric, hemodynamic instability/stability, angioembolization, management, nonoperative, conservative, operative, surgery, diagnosis, follow-up, combined with AND/OR. No search restrictions were imposed. The dates were selected to allow comprehensive published abstracts of clinical trials, consensus conference, comparative studies, congresses, guidelines, government publication, multicenter studies, systematic reviews, meta-analysis, large case series, original articles, and randomized controlled trials. Case reports and small case series were excluded.
Euler and URANS approaches Euler and Unsteady Reynolds-Averaged Navier Stokes (URANS) solvers compute the aerodynamic forces by solving a set of conservation laws (mass, momentum, energy) at discrete space/time intervals. While the Euler equations are non-linear, they ignore viscous effects. URANS solvers are as Euler solvers, with the addition of the viscous stresses. Turbulence is typically modelled via the eddy viscosity assumption. The aerodynamic solver used is NSCODE (A. T. Levesque, 2015) , which uses a cell-centered multiblock structured approach. In this work, we use an implicit LUSGS (Lower-Upper Symmetric Gauss-Seidel) time integration scheme with classical acceleration methods such as multigrid and implicit residual smoothing. For turbulent calculations, the Spalart-Allmaras turbulence model  (Spalart & Allmaras, 1992 ) is selected.
The single copy SAG101 from pepper grouped within the SAG101b branch. SAG101 isoforms from outside the Solanaceae (Coffee canephora (Cc) and Arabidopsis) were more closely related to, but did not directly cluster with, SAG101b (Figure  1a ). SAG101 homologs were not detected in species lacking TNL receptors (here Musa accuminata (Ma) and Mimulus guttatus (Mg)), as previously described  (Wagner et al. , 2013). A public RNAseq dataset from plants treated with different bacterial isolates or the MAMP flgII-28  (Rosli et al. , 2013)  was assessed using the TomExpress platform  (Zouine et al. , 2017)  to analyze expression of tomato EDS1 family genes (Figure  S2 ). Transcription of all four genes was detected in mock-treated plants, confirming general expression of both SAG101 isoforms. Treatment with Pseudomonas fluorescens (Pfo 55) and Pseudomonas putida bacteria, inducing robust MTI responses in Solanaceae  (Chakravarthy et al.
Life Cell Imaging and FRET-APB Analysis Images were taken on a Zeiss LSM780 laser scanning microscope. For imaging of GFP and mCherry, fluorophores were excited with 488 nm and 561 nm laser lines, and emission detected at 493-556 nm and 597-636 nm, respectively. For intensity-based FRET (FRET-APB), mCherry was bleached using the 561 nm laser at 100% intensity, and GFP fluorescence measured pre-and post-bleach. At least 15 measurements per donor/acceptor combination were done per experiment, and data was reproduced in four independent repetitions.
The Reverse Transcriptase Core Kit was used for cDNA synthesis, and the Takyon No ROX SYBR 2X MasterMix blue dTTP qPCR Kit (both Eurogentech) for quantitative real time PCR using a CFX96 detection system (Bio-Rad). The previously described reference genes Protein Phosphatase 2A (PP2A) and Elongation Factor 1-α (EF1α) were used for data normalization  (Liu et al. , 2012)  with similar results, and data from normalization to PP2A is shown. Primers used for quantitative real PCR are listed in Table  S4. All primers had efficiencies of 90-105%, as evaluated by dilution series.
Protein Modeling Structural models of Solanum lycopersicum EDS1-SAG101a and EDS1-SAG101b complexes were modeled using the structure of the Arabidopsis thaliana EDS1-SAG101 as template (PDB: 4NFU) (PDB: 4NFU;  Wagner et al. , 2013). Sequences of SlSAG101a and SlSAG101b share 38% and 36% sequence identity with AtSAG101, respectively, while SlEDS1 and AtEDS1 share 40%. All three sequence-template pairs could therefore be confidently aligned using hhpred algorithm  (Zimmermann et al. , 2018)  and structural models were generated and relaxed based on these alignments using rosettaCM  (Song et al. , 2013)  with limited need for manual re-alignment in the regions with insertions. Sequence conservation was calculated using the rate4site algorithm  (Pupko et al. , 2002)  and mapped at the surface of structural models using pymol (The PyMOL Molecular Graphics System, Version 2.
0 Schrödinger, LLC). Structural models and analysis thereof are provided in Appendix S1. S5c  for details) and under control of Arabidopsis promoter fragments. Segregating T 2 populations were selected with BASTA, and three week-old plants infected with Hyaloperonospora arabidopsidis isolate Cala2. True leaves were used for Trypan Blue staining 7 dpi. At least four independent T 2 populations were tested for each construct with similar results. Lines expressing untagged proteins were used for infection assays. Lines expressing epitope-tagged proteins were used for immunodetection (Figure  S5d ). hr -hypersensitive response; fhfree hyphae. Supplemental Figure  S2 : Expression of tomato EDS1 family genes A public RNAseq dataset from treatment of tomato "Rio Grande" plants with di erent MTI-inducers  (Rosli et al.
Acknowledgements We acknowledge  Bianca Rosinsky  for taking care of plant growth facilities and growing plants. Ulla Bonas  is acknowledged for generous support. Martin Schattat  is acknowledged for assistance with FRET experiments. This work was funded by  GRC  grant  STU 642-1/1  ( Deutsche Forschungsgemeinschaft, DFG)  and seed funding by the  CRC 648 (DFG)  to  Johannes Stuttmann.
Acknowledgments This work was funded by  Region of Normandy  and the  European Regional Development Fund of Normandy (ERDF)  in the frame of the  MAGMA  project. The authors would like to thank  F. Danoix ,  F. Vurpillot ,  H. Zapolsky  and  D. Blavette  for useful and fruitful discussions about APT. Corresponding authors: lindor. diallo@etu. uni-rouen. fr.
The absence of fiber orientation is associated with the combined lack of stress transmission between fibers and PLA and the small BUR and TUR used during film blowing. Indeed BUR and TUR were not large enough to impart anisotropy to the films crystalline properties. This lack of crystalline anisotropy is reported in Tab. 1. The same degree of crystallinity was computed from WAXD spectra of films sampled along TD and MD. Data in Tab. 1 also indicate that the degree of crystallinity X decreases with the amount of DPLF compounded with PLA.
Design of a modified Delphi study To achieve consensus, we followed a modified Delphi procedure (Figure  1 ). We carried out a systematic literature search and formed a focus group of Dutch experts to identify relevant items for niche assessment and design a questionnaire on niche measurement, which would be answered online anonymously by the experts participating in the Delphi study. A modified Delphi procedure was applied, with repeated rounds of the questionnaire, to enable the participating experts to reflect on the results of each previous questionnaire round in a structured manner. Thus, in each round, after analysis of the collective opinion of the group, the results of one round were used as the basis for formulating the next. It was predetermined that the process would include at least three rounds (two online questionnaire rounds and one face-to-face meeting) and additional rounds if required until data saturation was achieved.
Literature search to collect data for first Delphi round A systematic search of the literature up to October 2015 was performed in PubMed and EMBASE databases, with the assistance of a clinical librarian. We searched for all possible methodological items describing ultrasonographic evaluation of uterine scar in non-pregnant women (see Appendix S1 for search strategy). Duplicate articles were excluded. We included any English or Dutch article that reported on niche measurement by ultrasound and reported on one or more of a set of questions that was predetermined by J. H. , R. L. and I. J. The questions concerned: (1) the optimal timing for measuring a niche following CS; (2) the best infusion fluid (gel or saline); (3) whether 2D or 3D ultrasonography should be used; (4) what features of the niche should be measured; (5) the best time in the menstrual cycle for measurement; (6) the relevance of pressure from the transvaginal probe; (7) the relevance of Doppler ultrasound; and (8) the relevance of measuring the distance between the vesicovaginal (VV) fold and the internal os.
Focus group participation and Delphi procedure The focus group discussion took place on 10 January 2016. It was recorded and transcribed, resulting in an analysis of 50 keywords using Atlas. ti. software  25. Analyzing these keywords, 40 relevant items comprising 79 questions emerged for inclusion in the first online questionnaire. These questions could be categorized as: definitions and methods of measurement and their relevance, general ultrasound methods (including machine settings), additional tools (including Doppler ultrasound) and the use of gel or saline contrast. Appendix S4 gives an overview of questions of both questionnaires and subjects discussed during the face-to-face meeting. During successive rounds of the procedure, a further two items were added. A total of 15 experts were involved in the first round of the Delphi procedure and completed the first online questionnaire.
The relevance of these parameters in terms of related symptoms, subfertility or problems during fertility treatment, prediction of obstetric complications in a subsequent pregnancy and prediction of treatment risks and success, needs to be elucidated. To determine the optimal timing for niche measurement after a CS, future studies are needed as data are limited. An ongoing trial with this aim is registered in the trial register (NTR6921). A previous study reported a difference in niche measurements using saline contrast sonohysterography between those made at 6-12 weeks and those at 12 months following CS  26. Based on the expected duration of the scar healing process, and until future data become available, we advise evaluating a niche at least 3 months after CS. This is in line with a large ongoing study in 2290 patients (NTR5480), in which niches are measured at 3 months follow-up after doubleor single-layer closure of a uterine CS scar.
DSC ANALYSIS DSC data were acquired using a Pyris Diamond calorimeter (Perkin Elmer, U. S. A) beforehand calibrated with an indium standard. The samples weight was 10 mg encapsulated in an aluminum pan. They were heated from 20 to 150°C at 50°C. min -1. Measurements are performed when the samples are maintained at 150°C, 160 min in order to follow the vulcanization process. This one is evidenced by the appearance of an exothermic peak on the thermogram (cf. Fig. S2  in SI). Then, samples were quenched at 20°C and submitted again to the same thermal program to ensure the end of curing. The DSC thermogram obtained during this second isothermal treatment at 150°C provides the baseline needed to calculate the previous peak enthalpy.