dataesr/scientific-paragraphs-categorization huggingface dataset:
Study design and data source This retrospective nationwide cohort study adheres to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guidelines. It was approved by the institutional review board of Montpellier University Hospital (IRB CHU de Montpellier), who waived patients informed consent because of the retrospective analysis of an anonymised database, and was registered at clinicaltrials. gov (NCT 04163627). Data were extracted from the French Program for the Medicalization of Information Systems database that contains all discharge summaries from all hospitals nationwide. Discharge summaries include information on the patient demographics, principal and associated diagnosis codes according to the tenth revision of the International Classification of Diseases (ICD-10), procedure codes, mode of hospitalization, duration of hospital stay and hospital identification code.
Data extracted All hospital summaries of >18-year-old patients with a diagnosis of HCC (i. e. ICD-10 code C22. 0: liver cell carcinoma e HCC or hepatoma) from 1st January 2010 to 31st December 2019 were extracted from the database. Admissions with the C22. 9 code (malignant neoplasm of liver, unspecified) were also screened and included in the analysis, if they had the C22. 0 code at follow-up. Then, only patients with one or more of the following procedure codes were selected: percutaneous tumour destruction (HLNM001/HLNK001/ HLNN900), operative tumour ablation (surgical approach) (HLNC003/HLNA007), open liver resection (HLFA003/HLFA004/HLFA005/HLFA006/HLFA007/ HLFA009/HLFA010/HLFA011/HLFA017/HLFA018/ HLFA019/HLFA020), minimally invasive (laparoscopic/robotic) liver resection (HLFC002/HLFC003/ HLFC004/HLFC027/HLFC032/HLFC037/HLFC801), orthotopic liver transplantation (OLT) (HLEA002/ HLEA001), trans-arterial chemoembolization or embolization (TACE/TAE) (EDLF014/EDLF015/EDLF016/ EDLF017) and Yttrium 90 SIRT (EDLL001/ EDLL002).
Statistical analysis All analyses were carried out by the Department of Research and Medical Information at Montpellier University Hospital using the SAS statistical software (SAS Enterprise Guide, version 7. 13; SAS Institute; Cary, North Carolina, USA). Quantitative data were expressed as means AE standard deviation (SD), and categorical data as numbers (percentages). For each procedure category, the following data were calculated: total number and percentage of procedures per year and total number and percentage of patients who underwent that procedure per year.
Study population In total, 148,535 hospital admissions for 69,578 patients with the main diagnosis of HCC were retrieved from the database for the study period. Among all these hospitalizations, 68,416 concerned surgical or radiological therapeutic procedures in 34,000 patients (i. e. the study population). The demographic and clinical characteristics of the study population are summarised in Table  1. The annual incidence of HCC remained globally stable over the years (between 9. 9 and 10. 7/100,000 except for 2010), as well as the proportion of newly treated HCC patients (from 9. 1 to 10. 9% of the study population). Conversely, the yearly number of procedures (from 4267 in 2010e8042 in 2019; þ88. 5%) and the yearly number of patients who had at least one procedure (from 3266 in 2010e5750 in 2019; þ76.
A recent study based on a Dutch nationwide cancer registry database  [29]  observed an increase in proportion of patients receiving a treatment from 49% in 2009e2010 to 57% in 2015e2016, which was also observed in our results where more treatments were performed over the years. As the HCC incidence remained overall stable over the years in France, and in the absence of significant changes in screening policies, it is likely that the increase in therapeutic procedures performed was linked to the better accessibility or dissemination of mini-    invasive approaches, which should have made it possible to increase the therapeutic possibilities in patients with hepatic dysfunctions or in borderline general condition. In the BRIDGE study  [30] , mini-invasive treatments such as TACE or ablation also represented a large proportion of treatment performed either in first or second position but the authors did not look for any temporal trends.
The results of our study clearly highlight the strong tendency to offer more therapeutic solutions to cancer patients, and to favour minimally-invasive approaches. Clinicians should be made aware of the importance of referring their patients to health centres where minimally invasive approaches are widely represented. Efforts should probably also be made to widely spread these techniques, currently limited to large hospitals and cancer centres. Yet, many of these mini-invasive treatments are currently being tested in association with immunotherapies. If positive, combination of immunotherapy and mini-invasive treatments could be a major advance in the preservation of the liver function allowing optimising the tolerance while maintaining a good efficacy. Our study has some limitations. Indeed, the analysis was based on data from the French Program for the Medicalization of Information Systems database.
These data are entered and coded by practitioners and/or administrative staff based on the discharge summary and the procedure description. As hospital invoicing is based on this computerised declaration, many efforts have been made to improve and optimise the coding of procedures and patient data when this system was generalised in the mid-2000s. However, some errors or rather omissions remain possible, especially concerning the associated diseases and comorbidities. This could explain the underrepresentation of the diagnosis of cirrhosis in our study population. Moreover, this database only includes procedures performed in hospitalised patients. As procedures performed in outpatients, such as external radiotherapy, are not included, they were not analysed in our study. Finally, to present results in a clear manner, it was decided to perform the analysis according to a per-procedure and per-patient design, and combined treatments carried out during the same hospital stay were not considered.
(2017)  describe a three dimensional (3D) modeling framework that simulates the interactions between waves, flow, and flexible vegetation. Beudin et al. (2017)  evaluated a plant drag model against field measurements in eelgrass canopies and investigated the hydrodynamics in an idealized shallowwater setting. The research presented herein aims to reproduce plant movement under waves and/or current using the SPH method. The method was tested by building numerical two dimensional (2D) and 3D flumes with the GPUSPH model  (GPUSPH official website. www. gpusph. org. Accessed: 2017-03-31. ; G omez-Gesteira et al. , 2010; H erault et al. , 2010 , 2014) , then comparing the simulations with the available data. After a brief description of the SPH method (definition of the two numerical approaches used for plants and water), several tests of the FSI simulations are presented using the proposed model and these are compared with other simulations and experimental data (the FSI was calibrated and evaluated in the open source GPUSPH code  (H erault et al.
Correcting for speed To move the particles, the GPUSPH code uses the XSPH technique  (Monaghan, 1989). For each particle, a term containing the average speed of the surrounding particles is added to the original equation. Particle velocities, v ! , were corrected according to the XSPH scheme to smooth out unwanted numerical peaks. e v a ! ¼ v a ! þ q P b m b p ab ðv b ! À v a ! ÞW ab P b m b p ab W ab (17) The value of q depends on the medium: q ¼ 0:08 for the fluid which is increased to 1 to support high deformation for the solid.
This formulation gave good results for the experiments of  Antoci et al. (2007). However, in cases with large differences in density between the fluid and the solid, when impacts occurred, this formulation created local high pressure. Studies have questioned or perfected these different approaches to boundary conditions  (Crespo et al. , 2007; Ferrand et al. , 2013). In the current case, the standard options in the GPUSPH code worked well enough for the current needs.
Results and discussion The plant movements predicted with the proposed SPH simulations were compared with both experimental results (Le  Bouteiller & Venditti, 2015; Luhar & Nepf, 2011)  and field observations  (Paquier et al. , 2019). Different species of seagrass colonize the shallow coastal waters around the world, often forming large underwater meadows. Seagrass meadows are known to reduce wave height and current velocity near the seabed, but the simulation meadow (see Fig. 4 ), could be also a problem for the simulations. The different datasets used for the current comparisons were collected on real or mimicked plants of different species. Luhar and Nepf (2011)  and  Stratigaki et al. (2011)  worked on mimics of Posidonia oceanica, Le  Bouteiller and Venditti (2015)  workedon mimics of Zostera marina and  Paquier et al.
Acknowledgements The authors gratefully acknowledge the support of the  NVIDIA Corporation  who donated the GTX 780 GPU used for this research. This research was partially supported by the  LabEx Tec   21 program  ( Investissement d'Avenirgrant agreement   ANR-11-LABX-0030 ) and by financial support from the  "Agence de l'Eau RM&C 00  through the  CANOP e research program. AEP was partially supported by the  French National Research Agency (ANR)  through  ANR @RAction chair medLOC  ( ANR-14-ACHN-0007-01eproject  leader Thomas Stieglitz). The authors also thank  M. Luhar  and  H. Nepf  (from  MIT ) for the exchange of information and data.
Communication skills are one of the skills that students must have in the Industrial Revolution 4. 0. Based on the preliminary study at a public senior high school in Karanganyar, Central Java, students' written skills are still low due to the inaccurate method used by teachers. The applied knowledge that utilizes information and communication technology is needed to improve students' written communication skills. This study aimed to determine the effect of Google classroom-based e-learning on students' written communication skills. This research was a quantitative descriptive study. Students' written skills were measured using the written communication skills assessment instrument developed by  Sonseca et al. (2015) , which contains ten indicators. The data analysis technique used in this study was the paired sample t-test to compare the results of the pretest and post-test and the N-gain test.
One form of e-learning that is often used is flipped classrooms  (Ariani, 2018). One of the virtual flipped classrooms is Google classroom. Google Classroom is an ideal learning multiplatform for improving communication skills  (Solikh, Sulisworo, & Maruto, 2018). Google Classroom provides many features that help teachers manage class, manage study time, and improve communication with students without space constraints  (Iftakhar, 2016). One of the features that support communication skills is the communication feature. With this feature, teachers and students can communicate by paying attention to sound and correct language rules and can exchange information without any time and space limitations. Also, both can take advantage of the communication feature to attach files in various forms to improve communication skills  (Iftakhar, 2016).
METHODS This research was conducted in Class 10 th MIPA 5 of Public Senior High School of Kebakkramat, Karanganyar, in the 2019/2020 school year. The validity and reliability test of the written communication skills instrument was carried out on 30 science students of grade 10 senior high school in Surakarta. This research design is the Pre-Experimental Design, which uses the pretest and post-test in one study group. Pretest data was obtained by giving an assignment in writing a report on a biology subject before applied google classroom in the learning process. Meanwhile, the post-test data was obtained by providing an assignment in writing a report on a biology subject after applying google classroom in the learning process. The following is a table of the research design used:   (Sonseca et al.
RESULTS AND DISCUSSIONS The data presented in the form of pretest and post-test scores of each indicator used the observation sheet of written communication skills for class 10 th MIPA 5 Public Senior High School of Kebakkaramat, Karanganyar. Both data were analyzed based on indicators to see differences in students' written communication skills before and after implementing Google classroom-based e-learning. The prerequisite test results used the normality test and the homogeneity test. The normality test used is the Kolmogorov-Smirnov. The results of the Kolmogorov-Smirnov normality test can be seen in table 4. 4  shows that the pretest significance value is 0. 073, and the post-test significance value is 0. 079. Based on the decision criteria according to  Nismalasari, Santiani, & Rohmadi (2016) , if the Kolmogorov-Smirnov significance value is> 0.
Google docs provide a spelling check facility that functions to edit spelling and language. Hence, the student can learn about spelling and vocabulary so that the communication skills can improve  (Putri, 2017)  When the information is completed with a concise and appropriate conclusion, the message recipient, who does not have much time to bring the complete information, can receive the essence of the information conveyed by looking at the conclusion. A formal writing style and format can increase the reader's reading interest in understanding the message. The use of images or graphics in writing can also increase the quality of written communication and convince message readers that the information conveyed is correct. Based on the research results presented, it is known that Google Classroom use in learning can improve written communication skills.
Reading sessions The echocardiography core laboratory randomly selected 10 cases including healthy subjects and at least one group of patients with overt and/or at risk of pulmonary hypertension (PH), according to clinical classification of PH (Table  1 )  [12]. Echocardiographic examinations were performed with commercially available equipment on all subjects (Vivid E9, GE Healthcare, Milwaukee, WI, USA). Data were collected on patients undergoing EDE on a semi-recumbent cycle ergometer with an incremental workload of 25 W every 2 min up to the symptomlimited maximal tolerated workload including resting, 50 W, peak stress and recovery acquisition, as previously described  [6]. All operators directly measured the requested parameters by uploading the same ten cases from the web platform to their echocardiography machine.
Statistical analysis Statistical analysis was performed using standard software (MedCalc version 14. 8. 1, MedCalc Software Ltd. , Belgium; SPSS version 20. 0, SPSS, Inc. , Chicago, IL). Continuous variables were described by mean values ± standard deviation (SD). Normal distribution of the continuous values was assessed by the Kolmogorov-Smirnov test. Accuracy (in %) for each observer was estimated by comparison with the reference standard (core lab reading). Intra-class correlation coefficient (ICC) was calculated along with the 95% confidence interval, in order to quantify the reliability of measurement process. An ICC. Data are presented as mean of the absolute and relative differences (in %) between measurements of all nineteen observers, and ICC for each single parameter was calculated along with the 95% confidence interval.
Study limitations Few study limitations need to be discussed. First, the present study did not validate the echocardiographic measurements against invasive gold standard evaluation of the pulmonary circulation (PAP, wedged PAP and cardiac output), and right ventricular function (indices derived from pressure-volume loops). Second, accuracy and precision were defined by comparison only with the core laboratory measurements. In this regard, it was not logistically possible to repeat the echocardiographic examination of the same patient in each participating center. Third, the study results could have been potentially influenced by the quality images acquired only by the echocardiography core laboratory. For this reason we randomly selected 10 cases with different clinical conditions from a large database to avoid possible bias of selection of best images.
Emission fluorescence was further magnified (× 2) and acquired by an electron multiplying charge-coupled device (EMCCD, QuantEM 512, Princeton Instruments), and the effective pixel size in fluorescent images was 133 nm. The imaging hardwares were all controlled by MetaMorph software (Molecular Devices). For TIRF imaging, each field of view in general contains the footprint of a single astrocyte. In our recording, two to three separate astrocyte culture preparations were used and about three independent coverslips of each preparation for TIRF imaging per condition. Results were derived from signals of all recorded cells. Background was estimated from the autofluorescence signal in non-labeled cells of the same preparation, and then subtracted from the fluorescent images. The contour of the footprint of single astrocytes was delineated with the ImageJ plugin Cell Outliner or with MetaMorph segmentation tool, from which the mean fluorescence was measured over time to generate the time courses of specific signals.
Statistics All data are expressed as mean ± standard deviation (SD), and the t-test was used for assessing the significance. Comparison of non-normally distributed data was also validated using their median ± absolute deviation and the non-parametric tests (Kolmogorov-Smirnov or Mann-Whitney U-test). All statistical operations were performed with Matlab (The MathWorks), with n. s. , denoting non significant, *p < 0. 05, and **p < 0. 01.
Acknowledgements We thank the animal facility and the imaging platform of the  IBPS (Sorbonne Université, Paris, France). We thank  Dr. Nicole Ropert  for the discussion of experiments,  Dr. Tao Xu  for providing the CD63-pHluorin plasmid,  Dr. Kees Jalink  for GFP nd -EPAC(dDEP)-mCherry plasmid and  Dr. Lennart Mucke  of the J. David Gladstone Institutes for hAPPJ20 mice.
4, 100 mM NaCl buffer). Hydrodynamic radius (R h ) or apparent Stokes radius (R s ) and apparent Molecular Weight (MW) of IpgC/IpaB were calculated based on the known standard as described in (La  Verde et al. , 2017). Briefly, Blue Dextran (~2000 kDa) was loaded in a separate run, while protein standards were mixed in two different combinations, in order to avoid peak overlaps. Ferritin (MW = 440kDa; R s = 61Å), Conalbumin (MW = 75kDa) and Carbonic anhydrase (MW = 29kDa; R s = 23,5Å) were mixed in recommended concentrations and loaded to the gel filtration column for the first run while, Aprotinin (MW = 6,5 kDa; R s = 13,5Å), Ribonuclease A (MW= 13,7kDa; R s = 19,4Å), Ovalbumin (MW = 44 kDa; R s = 33,5Å) and Aldolase (MW = 158 kDa; R s = 48,1Å) were mixed together for the second run. Molecular Weight (MW) and Stokes radii (R s ) were provided by the GE Healthcare technical data sheet at that time.
SAXS Data Collection and Processing Two different data sets were collected at 10 °C for various IpgC/IpaB concentrations in 20 mM HEPES (pH 7. 4), 100 mM NaCl, ranging from 0. 58 to 5. 48 mg/ml at the BM29 BioSAXS beamline of the ESRF synchrotron  (Pernot et al. , 2010; Pernot et al. , 2013). Five data sets were collected for IpgC corresponding to three different sample preparations (concentrations ranging from 0. 2 to 7. 8 mg/ml). Samples were either kept on ice or were flash frozen and kept in liquid nitrogen until their arrival to the experimental site. Samples were then thawed on ice, centrifuged and the absorption at 280nm of the supernatant was monitored with Nanodrop. Dilutions were prepared with the same buffer solution and samples were loaded using the beamline's automated system to a 1.
8 mm diameter quartz capillary with a few tens of micron wall thickness using continuous flow during data collection. The SAXS data were recorded using a Pilatus 1 M detector at a sample to detector distance of 2. 84 m, covering the range of momentum transfer 0. 003<q<0. 45 Å -1 (q= 4psin(q)/l where 2q is the scattering angle and l = 0. 9199 Å is the X-ray wavelength). To evaluate radiation damage, ten successive 10 sec exposures of each sample were recorded. Data collection, processing and analysis were performed in an automated manner using the dedicated beamline software BsxCuBE. The PRIMUS software  (Konarev et al. , 2003)  was used for evaluation of the radiation damage and sample monodispersity, buffer subtraction, extrapolation to zero concentration, data scaling and merging. Estimation of the radius of gyration (R g ) and of the forward scattering intensity I(0) (proportional to the number of electrons in the particle) was also performed with PRIMUS using the Guinier approximation  (Guinier, 1939; Guinier and Fournet, 1955).
Molecular weights (MW) were estimated from the I(0) by comparing with a 5 mg/ml BSA solution. The indirect Fourier transform package GNOM  (Svergun, 1993)  was used for the evaluation of the maximum particle diameter (D max ) and the calculation of the pair distribution [P(r)] function as well as the R g. The integrity of the stock samples was verified after the experiment with SDS-PAGE (Supplementary Figure  1 ).
Modeling of the IpgC Dimer The scattering patterns of the high-resolution dimeric models of IpgC (PDB IDs: 3GYZ, 3KS2)  (Lunelli et al. , 2009; Barta et al. , 2010)  were computed and compared to the experimental data using the program CRYSOL  (Svergun et al. , 1995). Because a significant portion of the protein is not present in the crystal structures, we used the program CORAL of the ATSAS package (ATSAS, RRID : SCR_015648)  (Petoukhov et al. , 2012)  to account for the electron density of the missing residues by adding dummy residues.
Modeling of the IpgC/IpaB Complex All handling of PDB files was done using UCSF Chimera (UCSF Chimera, RRID : SCR_004097)  (Pettersen et al. , 2004). The known crystal structure of the IpaB coiled coil domain, covering the amino acid residues 74 to 239, was retrieved from the Protein Data Bank (PDB ID: 5WKQ). The Chaperon Binding Domain (CBD) domain (residues 60 -72) is located directly upstream of the coiled coil domain in IpaB with only one intervening residue. The CBD and the coordinates of the IpgC chaperone bound to it were extracted from the PDB entry 3GZ1. The amino acid sequence of IpaB was introduced as a query in the fold recognition server PHYRE (Phyre, RRID : SCR_010270)  (Kelley et al. , 2015). A total of 162 residues out of the 357 used were modeled with a 99. 7% confidence based on the Aeromonas hydrophila AcrH/AopB chaperone -translocator complex structure (PDB ID: 3WXX)  (Nguyen et al.
, 2015). Similar results were obtained with the HHpred prediction server (Bioinformatics Toolkit, RRID : SCR_010277)  (Zimmermann et al. , 2018)  (Supplementary Figure  2 ). Constraint-based Multiple Alignments (COBALT)  (Papadopoulos and Agarwala, 2007)  are also indicative of the similarity of IpaB to AopB and other translocators (Figure  1B ). Gap penalties used for COBALT were -11 and -1 (opening & extension), end-gap penalties -5 and -1 (opening & extension). RPS BLAST, 'Find conserved columns and recompute' and 'Use of query clusters' options were on. Protein BLAST threshold on 0. 003. 4-mer based sequence similarity. Maximum allowed distance between distances in a cluster at 0. 8. Regular alphabet was used. Accession numbers for sequences analyzed in Figure  1B   The relative positioning of the atomic models and the remaining residues (~25% of the total His-tagged IpgC and IpaB) were modeled with CORAL  (Petoukhov et al.