dataesr/scientific-paragraphs-categorization huggingface dataset:
acknowledgements The continuing beach monitoring program has been funded by  Observatoire Aquitaine des Sciences de l'Univers (OASU) ,  Agence Nationale de la Recherche (ANR)  through grants  ANR-10-JCJC-602 ,  ANR-14-ASTR-0004  and  ANR-17-CE01-0014 ,  Service National d'Observation (SNO) Dynalit labeled by Centre National de la Recherche Scientifique -Institut National des Sciences de l'Univers (CNRS-INSU) and Observatoire de la Côte Aquitaine (OCA). The daily topographic data in 2008 was acquired in the frame of  ECORS program  supported by the  French "Service hydrographique et oceanographique de la marine" (Shom). NORGAS-UG wave hindcast data provided by  LOPS-Ifremer. French Centre d' Archivage National de Données de Houle In Situ (CANDHIS)  buoy network operated by  French Centre d'Etudes et d' expertise sur les Risques, l'Environnement, la Mobilité et l' Aménagement (CEREMA).
code availability All data files created and used in processing are formatted in the Network Common Data Form (NetCDF), providing detailed metadata for each variable within the file, and can be read using MATLAB, Python, Fortran, C, C++, Java, and other languages. A Code file used to interpolate the raw sand elevation data is included in the repository folder. Code is written in MATLAB (R2019a) and is fully commented. Although MATLAB is a proprietary language, the. m files can be read with a text viewer.
Methods Study design and participants. A cross-sectional population-based serological survey and household interviews was conducted in French Guiana between June and October 2017. We reproduce here details on the random household selection, sampling weights, interviews, ethical considerations that were described in Flamand et al. 18. The French Guianese territory is composed of 22 municipalities that we broke down into seven geographical areas for the statistical analysis. The areas and number of participants are given in Supplementary Table  1. We estimated the sample size for this survey at 2500 persons distributed in the French Guiana territory based on a 50% seroprevalence, 95% confidence, 90% power and a cluster effect. To reach the desired sample size, a total of 1600 households were randomly selected for possible participation in the study from household databases maintained by the Geographic information and knowledge dissemination unit of the Regional environment, planning and housing agency and the National Institute of Economic and Statistical Information (INSEE).
The study was recorded on Clinicaltrials. gov (ID: NCT03210363) and approved by the Multiplex microsphere-based immunoassay. Collected sera were tested using an in-house microsphere-based multiplex immunoassay (MIA) based on recombinant antigens. The recombinant ectodomain of the CHIKV and MAYV envelope E2 glycoproteins were used for the capture of specific IgG antibodies, whereas a recombinant human protein (O6-methylguanine DNA methyltransferase) was used as control antigen in the assay. Distinct MagPlex microsphere sets (Luminex Corp. , Austin, TX) were, respectively, bound to viral and control proteins using the amine coupling kit (Bio-Rad Laboratories, Hercules, CA) according to manufacturers' instructions. The MIA procedure was performed as described previously with minor modifications  24.
g. , the prior of the ratio male/female is the same as the prior female/male)  25. Estimation using MCMC. Parameters were estimated using a Markov Chain Monte Carlo (MCMC) algorithm implemented in the rstan package (version 2. 19. 2)  26. The No-U-Turn sampler variant of Hamiltonian Monte Carlo was used to update parameters. Four independent chains of 20000 iterations were ran; the first 10000 iterations correspond to a burnin period. Ninety-five percent credible intervals were defined as the 2. 5% and 97. 5% percentiles of the posterior distributions. Parameter estimates for the model for antibody dynamics are given in Supplementary Table  5. Models were compared using the deviance information criterion (DIC). A smaller DIC indicates a better fit. Models with DIC under the smallest DIC+5 were considered equally adequate explanations of the data.
As opposed to the model with cross-reactivity, here, a circulation model in which French Guiana experienced a recent MAYV outbreak was as adequate as a model of constant circulation (DIC = 3599 and DIC = 3600); age (OR: 0. 8, 95% CrI: 0. 4-1. 3) and sex were no longer significant risk factors for MAYV infection (OR: 1. 2, 95% CrI: 0. 9-1. 6). The reason for these discrepancies between the model-based classification and the simple cutoff is that MAYV and CHIKV have contrasting risk factors for infection: males (respectively, females) are more exposed to MAYV (respectively, CHIKV). Many children and women infected by CHIKV in the urban areas are tested positive for MAYV with the simple cutoff, therefore leading to estimate that MAYV was recent and urban in French Guiana. Model adequacy. We assessed model adequacy by simulating 100 surveys in a population with the same characteristics (age, sex…) as in the dataset and with parameters drawn from the posterior distribution.
01. In the second, we assumed an outbreak that happened in 1980 and infected 20% of the population. We fitted the epidemic and constant model on the two datasets. The DIC shows we are able to identify the correct scenario: we obtained a difference of DIC of 35 for the constant model survey and of 42 for the epidemic model survey. We also estimated the posterior distribution of the parameters. The probability of infection in the first model is 0. 94% (95% CrI: 0. 78-1. 11%) (real value = 1%). For the outbreak model we found T to be 1979 (95% CrI: 1977-1981) and the probability of infection is 22% (95% CrI: 16-28%). Evaluation of the statistical framework. We also performed a simulation study to evaluate the performance of our statistical framework. One survey was simulated with parameters equal to the posterior mean we estimated in our analysis.
Acknowledgements We wish to thank  Mirdad Kazanji  ( Institut Pasteur in French Guiana ),  Félix Djossou  (Cayenne hospital center),  Sandrine Fernandes-Pellerin  ( Institut Pasteur -CRT ), and  Léna Berthelot ,  Séverine Matheus ,  Laetitia Bremand ,  Bhety Labeau ,  David Moua , and  Marine Rangon  from the  Arbovirus National Reference  Center for their valuable contribution in the laboratory analyses. We thank  Juliette Paireau  and  Quirine ten Bosch  for insightful discussions. This study was supported by the  "European Regional Development Fund " under EPI-ARBO grant agreement  ( GY0008695 ), the  "Regional Health Agency of French Guiana", the "National Center of Spatial Studies". C. Fl. and C. Fr. acknowledge funding from  Calmette  and  Yersin  allocated by the " Pasteur Institut Department of International Affairs ".
To further confirm that PP7L was involved in TE silencing, we analyzed the recently published RNA-seq dataset for pp7l-1  (Xu et al. , 2019)  for TE expression and found that 11 TE-encoded loci were among the significantly increased transcripts. Notably, 10 of these loci were among the transcripts that were also found as upregulated in the published RNA-seq datasets for mail1-1 and main-2  (Ikeda et al. , 2017)  (Figure  3d  and Table  S2 ). It should be noted that two of the loci that showed significant increase in both pp7l-1 and pp7l-3 in our RT-qPCR experiments, namely At1g6680 and At3TE58495, were not detected as significantly upregulated in the pp7i-1 RNA-seq data. This difference might be explained by the different growth conditions or age of the sampled seedlings: for the pp7-1 RNA-seq analysis 4-day-old seedlings were used, whereas we used samples of 6-day-old seedlings.
Co-immunoprecipitation Transgenic seedlings expressing MAIL1-GFP, MIPP-GFP or GFP were grown for 6 days and 3 g material was used for each GFP pull down. MS analysis was performed on a Q-Exactive Orbitrap and quantitative analysis was carried out using MAXQUANT and PER-SEUS software. Protocols are described in  Wendrich et al. (2017b).
Root growth assay and propidium iodide staining For the analysis of root growth, plants were germinated and grown on vertical plates. The plates were scanned every 3 days and measurement of root length was carried out using IMAGEJ software (http://imagej. nih. gov/ij/). The final values were calculated by determining the arithmetic mean of the root length values of three biological replicates, which were themselves the average of at least 20-30 plants. For treatment with zeocin, seedlings were transferred to liquid medium containing zeocin or, as control, no zeocin and incubated for the indicated time. Staining of cell wall and dead cells was performed by submerging seedling for 1 min in a 10 lg/ml PI/water solution and imaging was carried out using confocal microscopy.
ACKNOWLEDGEMENTS We thank  Judith Mehrmann ,  Teresa Wulf ,  Sotoodeh Seyedehyasaman , and  Zsuzsanna Darula  for technical assistance and experimental support and to  Paul Larsen  ( University of California, Riverside ) for providing the seeds for the sog1-7 line. This work was funded by the  Deutsche Forschungsgemeinschaft (DFG)  grant to MW ( WE 4506/6-1 ). C. L. -H. was supported by a  UHH fellowship , work in the Mathieu lab was supported by  CNRS ,  Inserm , and  Universit e Clermont Auvergne  and  AP-Sz  was supported by the  GINOP-2. 3. 2-15-2016-00032.
, data not published). Massive blooms of O. cf. ovata have been observed at the remote equatorial oceanic island of St. Paul's Rocks  [29]  and at the coastal subtropical Currais Archipelago  [30]. High O. cf. ovata abundances were also found at the Brazilian tropical coast in Bahia, although no biofilm was observed  [31]. The current study reports molecular data based on the D1-D3 and D8-D10 regions of the LSU rDNA and ITS loci and the morphology of O. cf. ovata isolates and field populations from locations along the Brazilian tropical and subtropical coastal regions and three oceanic islands. Additional ITS sequences from three single cells sampled from the tropical coast are provided. Toxin profiles and quantities of PLTX and analogues produced by two clonal cultures and two field blooms from Rio de Janeiro were investigated.
LSU rDNA D1-D3 Phylogeny Phylogenetic reconstructions based on D1-D3 region included three new sequences from the current study and other 75 sequences retrieved from GenBank, totaling 78 OTUs and 720 aligned nucleotides. The overall tree topology was similar to that observed with ITS and D8-D10 sequences in the current study, and with D1-D3 sequences by other authors  [8, 9, 33]  (Figure  6 ). There are no D1-D3 sequences available for Ostreopsis sp. 3, Ostreopsis sp. 4 and Ostreopsis sp. 8. Concerning the O. cf. ovata clade, the five subclades (A to E) observed in the ITS analysis (Figure  5 ) were recognized in the LSU D1-D3 phylogenetic tree (Figure  6 ). Strains UNR-03 and UNR-05 grouped into O. cf. ovata subclade A together with sequences of strains from the Mediterranean Sea, the Atlantic coast (Europe and Brazil), as well as Japan and Hong Kong.
LSU rDNA D8-D10 Phylogeny The   7 ). Sequences of O. fattorussoi and Ostreopsis sp. 8 were not included in this analysis since they were not available in GenBank. Ten main clades were recovered for the Ostreopsis genus, the same observed by Chomérat et al. [16]  when D8-D10 sequences were considered. Four subclades of Ostreopsis cf. ovata were recognized in the LSU rDNA D8-D10 tree (subclades A to D, Figure  7 ). The subclade E (observed in the ITS and D1-D3 trees) was not observed in the D8-D10 tree since there were no sequences from this lineage available in GenBank. Strains UNR-03, UNR-05 and UNR-60 from Brazil grouped in the O. cf. ovata subclade A together with sequences of strains isolated from Italy, Hong Kong and Japan. The fourth strain from Brazil, UNR-10, grouped in the O. cf. ovata subclade B together with sequences of strains from Japan.
Toxins The toxin profile determined for strains UNR-03 and UNR-05, as well as for bloom samples collected from Rio de Janeiro were similar and were composed mainly of ovatoxin-a (average 63. 1%) and ovatoxin-b (average of 31. 7%). In previous studies, OVTX-a and -b were dominant in the toxin profile of O. cf. ovata strains isolated from a nearby area in Rio de Janeiro  [26] , from Bahia  [47]  and from Currais Archipelago  [30] , all in Brazil. Dominance of OVTX-a and -b was also frequently reported in an extensive study assessing the toxin profiles of 55 O. cf. ovata strains along the Italian and French Mediterranean coast  [48]. The toxin profile of O. cf. ovata from Rio de Janeiro was similar to that of 67% of the strains analysed by Tartaglione et al. [48]  in the latter study. The toxicity data of ovatoxins is limited, as only ovatoxin-a has been isolated in a sufficient amount for full structure elucidation (the other OVTXs are minor congeners) and it is possible that different analogues may present different toxin potencies  [48].
1. 0, 2012). Neutral Lugol iodine solution preserved cells of Ostreopsis cf. ovata strain UNR-60 were observed using an upright light microscope (ImagerA2, Zeiss, Germany) equipped with phase contrast. Images were obtained using an AxioCam MRc digital camera (Zeiss, Oberkochen, Germany) in this case. The dorso-ventral (DV) diameter (or depth) and width (W) of cells were measured in lugol preserved cells using the Axiovision software (Zeiss, Oberkochen, Germany). In this study, a modified Kofoid tabulation system  [55]  as described in Besada et al. [32]  was followed to name the plates, and this enabled comparisons with other genera. Additionally, the dorso-ventral diameter (DV), width (W), and DV/W of cells from field Ostreopsis cf. ovata populations were measured either using the Axiovision software (Zeiss, Oberkochen, Germany) or with a microscope eyepiece ruler.
Reactions with ITS primers comprised an initial 5 min heating step at 94 • C, followed by 40 cycles at 94 • C for 1 min, 45 • C for 1 min, 72 • C for 1 min, and a final extension at 72 • C for 5 min. The sequencing of samples was performed by Macrogen Inc. using both forward and reverse primers. Sequences were manually checked and edited using the software BioEdit v7. 2. 5  [59]. The new sequences obtained in the present study were BLAST-searched against the GenBank database (www. ncbi. nlm. nih. gov/blast) to test for sequence homology with non-target taxa. The sequences were then aligned with other Ostreopsis sequences retrieved from GenBank using MAFFT v7  [60]. Phylogenetic analyses were conducted separately for each molecular marker. Sequences of Coolia spp. were used as outgroup. Amplified samples that did not result in good quality sequences were cloned in pGEM T-Easy vector ® (Promega), and the final constructs were introduced into DH5α cells.
D8-D10 dataset included four new sequences from the present study and 71 sequences from GenBank, totaling 75 OTUs and 821 aligned nucleotides. Phylogenetic analyses included sequences of O. cf. ovata, O. lenticularis, O. cf. siamensis, O. rhodesae, Ostreopsis sp. 1, Ostreopsis sp. 2, Ostreopsis sp. 3, Ostreopsis sp. 4, Ostreopsis sp. 6 and Ostreopsis sp. 7 (Figure.
The GP measurement could not be performed on the whole bacterium, because the probe detects mainly the bacterial motility in the surrounding environment of the vesicles (data not shown). As the initial packing of the lipid bilayers depends on the curvature, the initial GP value of the vesicles with different diameters was normalized by subtracting the GP value in the absence of flagella for each size of liposome (ΔGP) (Fig. 2C ). The presence of H7 with vesicles allowed slight changes in the lipid order only for vesicle diameters greater than 2 m. This confirms the existence of a threshold diameter above which the interaction becomes significant. Role of phospholipid head groups in flagellar adhesion. We next evaluated more thoroughly how different lipid species may affect EHEC flagellar adhesion.
The former lipid is not available in simulation databases, whereas the latter lipid has already been parameterized in the Charmm force field. These two lipids are structurally very close (same head group and only one difference in unsaturation), and very similar behaviors of the lipid bilayers are likely  (33). Moreover, anisotropy values were measured for PC 18:2/18:2 (PC 18:2), and no difference was observed compared to those for PC 18:3 (Fig. 5C ). All correlations between bacterial adhesion numbers and the other parameters were high except those for laurdan anisotropy, which were moderate. To favor more adhering bacteria with pure PC GUVs, the membrane thickness needs to be around 40 Å and the area per molecule should be 60 Å. A thinner plasma membrane and too much space between molecules do not help bacterial adhesion.
In total, 3,072 repetition experiments were performed leading to a total acquisition time of 6 h. After data processing and phase and baseline corrections, the areas of the peaks of interest were determined by integration, and the molar ratio of lipids was calculated with relative integrations. GC-FID. Fatty acids from seeds, seedlings, and plant tissues were directly transmethylated as described before  (69). Heptadecanoic acid (C 17:0 ) was used as an internal standard. Fatty acid methyl esters were extracted in heptane and separated by gas chromatography with flame ionization detection. Lipid extraction. The fatty acid content of the cells or GUVs was determined after extraction with a modified method according to Bligh and Dyer  (70). Three hundred seventy-five microliters of a mixture of chloroform/methanol (2:1 [vol/vol]) containing butylated hydroxytoluene (BHT; 1 mM) was added to 100 l of aqueous solution containing lipid vesicles or cells.
MS 2 scans were performed on the sixth most intense ions. Two internal reference masses were used for in-run calibration of the mass spectrometer (121. 0509 and 922. 0098 in positive-ion mode and 112. 9856 and 1033. 9881 in negative-ion mode). MassHunter B. 07 software enabled the control of the parameters of the machine and acquired and processed the data. The mass spectra were acquired in positive-and negative-ion modes. Data processing and annotation. Agilent generated files (*. d) were converted to *. mzXML format using MSConvert  (72). File (*. mzXML) data sets were processed using MZmine 2 v2. 37  (73). The noise level was 2. 0E3 for MS 1 and 0E00 for MS 2 in centroid. The chromatogram builder was used with a minimum time span of 0. 10 min, a minimum of height of 1. 0E3 and m/z tolerance of 5 ppm.
ACKNOWLEDGMENTS We thank  David Gally  and  Eliza Wolfson  for Stx-negative derivative strain of  TUV 93-0  and its isogenic mutants (ΔfliC and ΔmotA). We also thank  Ashleigh Holmes  for her critical review and  Muriel Vayssade  for providing HT29 cell line. This work was supported by the  European Regional Development fund ERDF  and the  Region of Picardy  ( CPER 2007-2020 ) and the  French Ministry of Higher Education, Research and Innovation  (to H. C. and L. L. ).
Simulation settings The simulations were performed with the finite element software COMSOL Multiphysics, on a workstation with 256 GB RAM and an Intel® Xeon® CPU E5-2680 v3 processor, 12 cores, 2. 50 GHz. The mesh of the entire geometry, on which the electromagnetism is solved, is composed of 17,672 tetrahedra measuring no more than 6. 88 mm. The heat equation is solved in a sub-geometry with a more refined mesh of 1318 tetrahedra, measuring no more than 1. 00 mm. When solving both the electromagnetism and the heat equation, a previous study showed that mesh independency is obtained for a maximum element size of 1. 75 mm  (Sadot et al. , 2017).
Conclusion A laboratory scale microwave assisted freezing process was designed to conduct experiments with parameters and conditions that were controlled as much as possible. The thermophysical and dielectric properties of the methylcellulose gel were accurately measured and the incident power was determined by the inverse method. A numerical model, developed previously, was improved by using a hybrid method to solve the heat equation in 2D and the Maxwell equations in 3D. The significant reduction of computational time allowed the validation of the model in comparison to the experimental data with this geometry. The results showed that the ice mass fraction approach that we proposed is relevant for describing all the evolutions of all the thermophysical and dielectric properties during phase change.
Acknowledgements This work received financial support from the  French National Research Agency (ANR)  in the framework of the  FREEZEWAVE  project  (ERANET call "SUSFOOD ", grant number  ANR-14-SUSF-0001 ). M. SADOT's PhD work is co-funded by the  FREEZEWAVE  project and the  Région Pays de la Loire. The authors would also like to thank  C. Couëdel  for his technical contribution.
Materials and methods The study population included 19 adult critically ill patients on CRRT, receiving 1 g of meropenem in 1-h infusions every 8 h. Blood samples were collected prior to (time zero) and  15,  30, 45, 60, 75, 90, 120, 180, 240  and 480 min after the start of meropenem administration. Population nonlinear mixed-effects modeling was conducted using NONMEM software, Fortran, and Wings for NONMEM. Results A two-compartment model was used to describe the available data. Typical values of the central and peripheral volume of distribution, and the CRRT and inter-compartmental clearance for a theoretical patient with 24. 6 g/l albumin concertation were V 1 = 27. 9 l, V 2 = 33. 7 l, Cl CRRT = 15. 1 l/h, and Q = 21. 1 l/h. A significant covariate relationship between V 1 and albumin concentration was observed in the data that was described by a power relationship with -2.
Population PK methods The population PK modeling was performed with NON-MEM software (version 7. 3, Icon Development Solutions, Ellicott City, Maryland, USA), Fortran compiler (version 4. 6. 0) and Wings for NONMEM (version 741, https ://wfn. sourc eforg e. net). The FOCE with interaction method using ADVAN3, TRANS4 routine was employed throughout the model-building procedure. Matlab ® (version 7. 0, The Math-Works, Inc. , Massachusetts, USA) was used to process and visualize data generated by NONMEM. Models obtained in this work were assessed and compared using the minimum value of the NONMEM objective function (OFV), typical goodness-of-fit (GOF) diagnostic plots, and the evaluation of the precision of pharmacokinetic parameter and variability estimates.
Model evaluation The model performance was assessed using visual predictive checks (VPC). For VPC the predicted PK profiles for 1000 virtual datasets were generated from the final parameters and variances estimates. The observed and predicted concentrations were binned across time. The predicted median along with 5th and 95th percentile of the simulated concentrations was plotted against time with the median and 5th and 95th percentiles of the observed concentrations. When the percentile from the experimental data falls outside the 90% confidence interval derived from predictions, it indicates model misspecification. A nonparametric bootstrap analysis was used to evaluate the uncertainty of model parameters. The data for individual patients were randomly sampled with replacement from original dataset to form 1000 new data sets.
Dosing simulations Monte Carlo dosing simulations were performed using NONMEM for short-term infusion (0. 5, 1 and 3 h) of 1 g of meropenem every 8 h (q8h) and every 12 h (g12h) for patients with three different albumin concentrations (15. 6, 24. 6 and 31. 8 g/l). They correspond to the lowest, median, highest observed values. Each simulation generated steadystate concentration-time profiles for 1000 subjects using the final estimated population PK parameters. From these data the %T > MIC was calculated for each subject and then PTA was obtained by counting subjects who achieved 40% or 100% T > MIC for MIC values ranging from 0. 064 to 64 mg/l and for albumin concentrations spanning the range of values observed in this study. The linearity of meropenem PK allows to calculate PTA for different doses based on the values obtained for the standard dosing (i.