dataesr/scientific-paragraphs-categorization huggingface dataset:
Model validation The developed model and parameters obtained during calibration step had to be validated with another dataset. The simulation obtained with calibration parameters correctly reproduced the behavior of the system for the complete period of 28 days as represented in Fig. 3. The main quality of this model is its ability to predict the accumulated methane yield and VFA concentration behaviors with simple data, considering the porosity differences. However, the calibration is a very sensitive step and any process disturbance could modify the set of determined parameters. Asymptotic observers  (Dochain et al. , 1992)  could not be used on this model as only global concentrations could be determined but not mobile and immobile regions concentrations. This is why each kinetic parameter was not identifiable but the global set of parameters could be approached.
Acknowledgments The authors gratefully thank the program MOCOPEE (www. mocopee. fr)and the  FEDER fund  ( FEDER PO Picardie/MOCOPEE PI0012581 ) for the support provided for this work and the PhD grant of  Arnaud Coutu. The authors want to thank also  Denis Dochain  for his help,  Laura André  and  Edvina Lamy  for their technical help; and  Pauline Louis  for her carefully reading of the manuscript.
The duodenoscope is connected to the interventional endoscopy column which manages the incoming/outgoing fluids, the light source of the duodenoscope and the real-time video system (for data acquisition and processing ). An X-ray imager is also used to perform real-time radiographic monitoring of the endoscopic tools (catheter, duodenoscope, instruments, etc. ) in the cavities of the PPBT model. Before inserting the transferred plasma catheter into the duodenoscope to treat the bile ducts, a preliminary maneuver is carried out percutaneously, i. e. without using the duodenoscope. For this, a thin surgical incision is made in the duodenum to introduce the catheter in the bile ducts. Figure  9b  is a night-time photograph which shows that the part of the catheter left outside the porcine model, shows both emissive regions (indicating the presence of plasma) and dark regions (indicating the presence of un-ionized helium).
Referring to (2. 13), we see that the right-hand-side of (2. 15) can be obtained by carrying out a time step, and the matrix-vector product by carrying out a linearized version of the same time step. The Jacobian matrix is thus never constructed or stored. The GMRES algorithm from the NSPCG software library  (Oppe et al. 1989 ) is used as the iterative solver. In the case of the Carreau fluid, the viscous term is no more a simple Laplacian operator. A first possibility we have tested is to calculate the new viscous discretized operator. This operator, however, depends on the local velocities through the viscosity and the shear rate, so that it has to be regularly recalculated at each Newton step. Moreover, with this operator, we cannot use the very efficient diagonalization solver for the velocity at each time step, which is a real handicap to solve large three-dimensional problems.
Aims Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is currently one of the most used devices in refractory cardiogenic shock. However, there is a lack of evidence on how to set the 'optimal' flow. We aimed to describe the evolution of VA-ECMO flows in a cardiogenic shock population and determine the risk factors of 'high-ECMO flow'. Methods and results A 7 year database of patients supported with VA-ECMO was used. Based on the median flow during the first 48 h of the VA-ECMO run, patients were classified as 'high-flow' or 'low-flow', respectively, when median ECMO flow was ≥3. 6 or <3. 6 L/min. Outcomes included rates of ventilator-associated pneumonia, ECMO-related complications, days on ECMO, days on mechanical ventilation, intensive care unit and hospitalization lengths of stay, and in-hospital and 60 day mortality.
Study population and design This is a retrospective, single-centre study including patients in refractory CS supported with peripheral VA-ECMO admitted at La Pitié-Salpêtrière University Hospital in Paris between 1 January 2010 and 31 December 2016. The database for this study has previously been used to analyse the impact of an awake VA-ECMO strategy published elsewhere. 11  was defined as sustained systolic blood pressure < 90 mmHg or requiring vasoactive drugs to maintain it ≥90 mmHg, with concomitant evidence of tissue hypoperfusion. 12, 13 CS was considered refractory when acute cardiovascular failure developed despite high-dose catecholamine infusion (epinephrine ≥ 1 μg/kg/min or dobutamine ≥ 15 μg/kg/min or norepinephrine ≥ 1 μg/kg/ min). Exclusion criteria were patients aged <18 or >75 years old, cannulated during cardiopulmonary resuscitation, post-cardiotomy, or patients with atypical CS aetiologies.
Statistical analysis Continuous variables were expressed as median [interquartile range (IQR)] and compared with Wilcoxon rank-sum tests. Categorical variables were expressed as numbers (percentage) and compared with χ 2 tests. To identify the factors related to 'high-flow' support, a multivariate stepwise logistic regression model was constructed including the baseline variables found to be associated in the univariate analysis with a P value < 0. 10. Kaplan-Meier curves were used to evaluate the association between the VA-ECMO flow classification with 60 day mortality. All statistical tests were two-sided, with a P value ≤ 0. 05 considered significant. Statistical analysis was computed with STATA software, Version 13. 1 (Stata Corp, College Station, Texas).
Regularized image reconstruction We reconstruct the fluorescence profiles at different positions and spectral channel independently, by solving the Tikhonov problem min f m -Pf 2 + f 2 , (7) where is the regularization parameter that sets the trade-off between data fidelity and prior information, and the forward matrix P ∈ R × is given by either Equation  (5)  or Equation  (6). This problem provides the following analytical solution f = P P + I -1 P m. (8) The raw data acquired through the spectral arm extend over a spectral range with [ = 2,560 spectral channels corresponding to the number of pixels in our sensor]. [For visualization or data analysis, it may be convenient to plot the results in some particular spectral bins]. After acquisition, it is possible to reconstruct the binned image f Λ = ∈Λ f directly from the binned measurements m Λ = ∈Λ m , where Λ represents the set of spectral channels that are merged.
Funding. Agence Nationale de la Recherche  ( ANR-17-CE19-0003 ); LABEX  PRIMES  ( ANR-11-LABX-0063 )). Acknowledgments. The authors thank  Dr O. Cochet-Escartin  ( ILM, UCB Lyon ) for providing hydra specimens. [We thank an anonymous reviewer for critically reading the manuscript and suggesting substantial improvements. ].
Strain collection This study includes 197 Lm strains collected from different ecological niches, i. e. food, animal and environment (metadata, including geographic location, year and source of the isolation are listed Supplementary data 1). The matrix of isolation of food strains was defined according to  Painset et al. (2019)  risk food matrixes: "fish and fishery product", "meat and meat product", "dairy product" and "fruit & vegetables"  (Painset et al. , 2019). The strains were selected from surveillance activities and previous studies conducted in Europe  (Dreyer et al. , 2016; Fritsch et al. , 2019; Henri et al. , 2017; Painset et al. , 2019; Papić et al. , 2019). Strains were collected over more than 20 years, with most of them (80%) isolated after 2010, across 16 countries in Central (n = 6), Northern (n = 5), Western (n = 3) and Southern (n = 2) Europe (Supplementary data 1).
In total, 99 strains were isolated from food (dairy, fishery, meat and vegetables), 66 from (wild and farm) animals and 35 from the environment (e. g. vegetation, soil and water). We balanced our dataset with similar relative portions of Lm strains from nature and primary production (animal/environment), as well as secondary and tertiary production (food), for lineage I (~48% vs ~52%) and II (~53% vs ~47%).
Genomic data CCs were defined as groups of 7 locus -MLSTs differing by only one gene from another member of the sequence type (ST)  (Ragon et al. , 2008). For part of the strains collection, the genomic sequences were already available  (Dreyer et al. , 2016; Fritsch et al. , 2019; Henri et al. , 2017; Painset et al. , 2019; Papić et al. , 2019). For the others, newly sequenced genomes were produced using Illumina technologies within ListAdapt project (grant #773830; https://onehealthejp. eu/jrp-l istadapt/). Raw reads for the whole dataset were processed using the "Assembly of reads and typing workflow" (ARTwork) open-source pipeline adopted in the Maisons-Alfort Food Safety laboratory (Anses)  (Palma et al. , 2020; Vila Nova et al. , 2019). Briefly, the ARTwork workflow includes several tools to perform variant calling (i.
Biocides and biocide susceptibility based on MIC Eight biocidal compounds commonly used as disinfectants in medical, veterinary and industrial settings were selected to detect the molecular mechanisms for biocide-tolerance of Lm. The selected biocides along with their principal area of use, main bactericidal action and concentration are reported in Table  1. The MICs of the studied biocides were determined using standard broth microdilution methods and results were reported in Supplementary data 3. Briefly, Lm strains were plated on Tryptone Soya Agar (TSA) with blood (Sigma-Aldrich). Two to three colonies were collected in 4 ml of Tryptone Soya Broth (TSB) with yeast extract (0. 6%) and incubated during 24 h at 37 • C. Then, 300 μl of these precultures were added to 10 ml of Tryptone Soya Broth (TSB) with yeast extract, incubated at 37 • C during 3-4 h and adjusted to OD620nm = 0.
Population structure estimated by phylogenomic reconstruction and homologous recombination detection A phylogenomic reconstruction was performed to determine the overall population structure based on the single nucleotide polymorphisms (SNPs) detected in the coregenome. The alignment of pseudogenomes (including 94,004 variant sites) produced by iVARCall2 were constructed based on mapping of reads against the reference genome EGD-e (accession NC003210) and GATK variant calling analysis  (McKenna et al. , 2010). These pseudogenomes were used to infer trees by maximum-likelihood (ML) using the IQ-Tree software  (Kropac et al. , 2019). The 'ModelFinder' option was applied for an automated substitution model selection, with 1000 SH-aLTR (Shimodaira and Hasegawaapproximate likelihood ratio test) and ultrafast bootstrap support.
Pangenome-wide detection of mutations associated with biocidetolerance The detection of pangenome-wide mutations associated with enhanced tolerance to each biocide under study was performed with GWAS approaches where confounding effects (i. e. clonal population structure, homologous recombination and genome wide significance) are taken into account without losing statistical power to detect associations  (San et al. , 2020). First, a recombination-aware phylogenetic tree-based GWAS approach was applied using the R-package treeWAS  (Collins and Didelot, 2018)  for testing associations between coregenome SNPs and binary (tolerant vs. susceptible) or continuous (MIC values) phenotypes based on MIC data. Then, another GWAS was performed to screen POGs for associations with each studied biocide.
Using the POGs presence/absence matrix produced by Panaroo as input, the Python-based sequence element enrichment analysis (pyseer) tool was run in combination with the continuous MIC data for the eight biocides described above and the phylogenomic reconstruction correcting the population structure with regard to homologous recombination events from the coregenome  (Lees et al. , 2018). Based on the phylogeny_distance. py script provided by the authors, we run pyseer with the linear mixed model (LMM) and the patristic distances matrix generated on the recombination-free core phylogenomic tree (based on the shared branch length between each pair's ancestors and the root). Only POGs present in more than 1% of the total population and presenting 100% of specificity (absent in the less tolerant strains) for each biocide were retained for further analyses.
Origin and molecular sub-types of Lm strains The collection of strains with high-quality genomic data selected for this study encompasses a large genomic diversity of Lm population from lineage I and II, i. e. 29 CCs and 2 STs disassociated from CC. Each CC included 1-19 strains. The distribution of CCs from the lineage I and II for the different isolation sources is reported in Fig. 1  (see Supplementary data 1 for additional details on CCs per source of isolation). The contiguity metrics of de novo assembly showed an average genome length of 2,955,717 bp, a high N50 (2,937,244), a low number of scaffolds (median of 5, 1st and 3rd quartiles corresponding to 2 and 12. 5) and a mean GC% content of 37. 8%. The summary data of the assembly metrics for each genome are listed in the Supplementary data 2.
Genomic signatures of biocide-tolerance across Lm lineage I and II strains and their ecological niches Molecular signals of adaptation to biocide in Lm strains from different ecological niches were investigated at the core and accessory scale. The recombination-aware phylogeny-based GWAS performed using treeWAS did not associate coregenome SNPs with the phenotypes of interest, using either binary or continuous traits. Over the 2706 accessory POGs tested for association with MICs of the eight biocides, the pyseer linear mixed model, taking into account the population structure correction, identified 699 POGs presenting likelihood-ratio test (LRT) p-values lower than 0. 01 (Supplementary data 5). To minimise false associations while preserving causal mutations, we excluded genomic elements identified (i) in the less tolerant strains (i.
, 2017). The CC6 food strain belonging to lineage I and the CC8 and CC9 food strains from lineage II present the highest MICs for the studied QACs (BC and DDAC) and harbour the poly-specific pLMST6_emrC (Fig. 4 ). POGs encoded in the associated pLMST6_emr plasmid and Tn6188_qacH transposon appeared stratified in the Q-Q plots (Supplementary data 7), showing a polygenic effect (i. e. system of non-epistatic genes that influence a phenotypic trait) of QACs-tolerance mechanisms. Among the additional POGs associated with BC tolerance, we also  identified a cluster of 6 POGs (af 10%), including genes that encode for recombination hotspot (RHS) repeat proteins and the putative RNA 2 ′phosphotransferases KptA. By blasting the sequences in public database (NCBI), we found that these POGs are included in a ~12 kbp genomic element 100% homologous to Lm strain 6179 (HG813249.
The genetic elements here discovered by means of hybrid tools, which implement a combination of phenotypic control data, recombination-aware phylogenomics and advanced statistical models might represent universal markers sequences for the prediction of tolerance phenotype within genomics-based epidemiological surveillance systems and databases. Cutting-edge open-source tools for GWAS, including supervised classification technique such as machine learning  (Lupolova et al. , 2017)  or multinomial logistic regression  (Guillier et al. , 2020)  and elastic net pangenome-spanning regressions  (Lees et al. , 2019)  may fit the scope using such genetic elements as predictors to screen the presence of tolerant genotypes across Lm ecological niches. Integration of GWAS into decision-making and risk assessment is expected as technical capacity of European countries is rising and harmonizing across countries.
Acknowledgements We gratefully thank  Arnaud Felten  and  Ludovic Mallet  for providing suitable computing environments. We also thank the  Institute of Microbiology and Parasitology of the University of Ljubljana  and the  Institute for Food Safety and Hygiene of the University of Zurich  for providing part of the Listeria monocytogenes dataset. The " One Health European Joint Programme ListAdapt" ("Adaptive traits of Listeria monocytogenes  to its ecological niches"),  European Union 's  Horizon 2020 research and innovation programme  Grant Agreement Number:  773830 , provided financial support.
[10]  who was limited to studying plate edge profiles, as discussed above. In this paper, a two-dimensional (2D) model, based on CFD simulation carried out using the software COMSOL Multiphysics, is performed to study and examine the performance of a standing wave TAE and a thermally driven TAR comprising a stack of parallel pales. The use of CFD as an analysis tool in thermoacoustics is largely underused, and this tool allows a detailed study of the thermoacoustic effect which is difficult to achieve through experimentation. The novelty of the work is the use of a parallel plate stack made of plates with a corrugated surface. Three shapes of plate surface were tested, flat plates (considered a better reference, especially for comparison with plates of different shapes), plates with rounded ripples (the surface of the plates is formed by a series of circular corrugations of the same diameter), and plates with triangular ripples (the surface of the plates is formed by a series of triangular corrugations).
However, from the 20,000-cell mesh to the most refined, it is observed that the mesh size has less effect on the pressure amplitude. The elements sizes present in the modelspaces were achieved using default "User-controlled mesh" settings within the simulation software Comsol Multiphysics which is a commercial solver and simulation software used to solve the system of timedependent equations associated with appropriate boundary and initial conditions. The solution of the equations is based on the finite element method; it provides the discretization in the considered domain, and it has appropriate criteria to generate the suited mesh. More Fig. 3  Rott's functions (f k ) against the ratio of hydraulic radius (r h ) to the thermal penetration depth (δ κ ) for different stack profiles  [23].
Conclusion In this work, a two-dimensional numerical analysis based on CFD simulation carried out using the software COMSOL Multiphysics is considered to investigate the performance of thermoacoustic couples using a variety of stack plate surface profiles. The comparative performance of three plate shapes noted, flat plate, plate with rounded, and triangular ripples have been estimated. The efficiency of the thermoacoustic engine is examined in terms of the generated acoustic pressure, and the performance of the thermoacoustic refrigerator is measured in terms of the temperature difference along the refrigeration stack. The results show that the plates with triangular and the rounded ripples are noticeable to be more effectively in increasing the acoustic pressure amplitude than the flat plates.
Microscopic structure Many types of researches are recently carried out on straw fibers in its various forms of wheat, barley, oats, or other plant aggregates  [21]. It can be explained by the common worldwide cultivation of the straw  [22]. Fig. 3  shows an example of chopped straw fibers prepared to be investigated by Laborel-Preneron et al. [23]. To determine the size distribution and morphology (width and length) of fibers, Laborel-Preneron et al. [23]  used and analyzed ImageJ software. Only limited numbers of non-spherical fibers are appropriate for this method,  [24] [25] [26]. The fibers were coated with an evaporated gold layer on a metal substrate to observe them under vacuum with a 15-kV accelerating voltage. The data, in the form of a contrasting scanned picture of the particles on a black background, enabled for the estimation of the straw fibers' length and width.
5 detection channel. SPARK: Excitation wavelength: 337 nm with a bandwidth of 20 nm; Emission wavelengths: Eu: 620 nm, bandwidth 5 nm, gain 160; ATTO620: 640 nm, bandwidth 5 nm, gain 180; Tb: 494 nm, bandwidth 5 nm, gain 180; Cy5. 5: 718 nm, bandwidth 5, gain 180. Integration time: 2 ms, lag time: 0. 1 ms. For the KRYPTOR and SPARK comparison tests, the same experimental plate was measured sequentially using both instruments. Complete RCA-FRET procedure overview: Design of DNA sequences: circa 2-3 h; Order of DNA/RNA oligos: circa 7 to 10 days for delivery; Preparation of oligos for assays: circa 1 h; Conjugation of Tb or Eu to the oligos: circa 10 min + overnight incubation + 30 min; Concentration estimation of the lanthanide-oligonucleotide conjugates (spectroscopy measurement): circa 30 min; RCA: circa 5 h 45 min as follows: i) Target-padlock annealing (~1 h 15 min), ii) Padlock ligation (~1 h 15 min); iii) Polymerization (~2 h); iv) RCA product labeling (~1 h 15 min); v) TG-FRET measurements (10 min instrument setup + 5 min measurement + 10 min data analysis).
Acknowledgements We thank  Lumiphore, Inc. for the gift of Lumi804 and Lumi4 reagents. This work was supported by the  Institut National du Cancer  and the  Direction Générale de l'Offre de Soins (INCa and DGOS ; project  PRTk 16158 -Gynomir ),  ITMO Cancer of Aviesan  within the framework of the 2021-2030 Cancer Control Strategy through funds administered by  Inserm  (project " ACTION "), the  Brain Pool program  funded by the  Ministry of Science and ICT  through the  National Research Foundation of Korea  ( 2021H1D3A2A0204958912 ),  Seoul National University, Université Paris-Saclay ,  Université de Rouen Normandie ,  Normandie Université ,  INSA Rouen ,  CNRS ,  European Regional Development Fund ,  Labex SynOrg  ( ANR-11-LABX-0029 ),  Carnot Institute I2C ,  XL-Chem graduate school  ( ANR-18-EURE-0020 XL-CHEM ), and the  Région Normandie.
Test procedures 2. 2. 1. Rheometry The rheological measurements of cement paste and CNF-OPC mixtures were done using a TA Instrument Discovery HR-1 Hybrid Rheometer (New Castle, DE, USA). Different mixtures were prepared based on the prior formulations presented in Table  2  to compare the flow behavior of the bulk cement paste without fibers against those of the CNF-OPC pastes. The rheological behavior of the samples under the strain-controlled mode was measured by vane rotor and grooved cup accessories. The steady state shear-viscosity, time sweep, and frequency sweep tests were done to investigate the rheological properties of bulk CNF-OPC mixtures at 23 • C. The wall-slip effect of the test protocol for the used medium was also checked at three different gaps (5000 ± μm), and the shear-viscosity data were regenerated at all gaps, confirming the absence of wall-slip.
Acknowledgments This project received funding from the  Research Executive Agency of European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No. 101024074. The authors would like to thank  Mr. Jarno Karvonen ,  Mr. Jani Österlund , and  Mrs. Elisa Wirkkala  for their helps at the  Fibre and Particle Engineering Laboratory. Mr. Mohammad Karzarjeddi  is greatly appreciated for his interesting discussions and help with this work.
The BD CSampler Software was used to acquire and treat the cytometric data. Samples were also analyzed after staining with BacLight™ RedoxSensor™ Green (RSG, 1 µM) or propidium iodide (PI, 10 mg/L) (Invitrogen) to detect the metabolic activity and the membrane permeability respectively  [43, 44]. After 488nm laser excitation, green uorescence were collected at 525 nm ± 30 nm for RSG (FL1-A) and the red uorescence signal at 670LP (FL3-A) for PI. Cells were also analyzed at different growth phases (exponential phase, stationary phase and sporulation) on different carbon sources (glucose, xylan and destarched wheat bran) with the same cytometric parameters.