dataesr/scientific-paragraphs-categorization huggingface dataset:
External Validation and Application External validation is one of the strictest approaches in model testing and consists of applying a new dataset within a final model to determine the accuracy and reproducibility of the model and in which conditions it would be applicable. Different strategies and steps are possible in order to adequately evaluate models from the literature. For more information on these strategies, refer to the Supplementary Materials. In this review, most studies performed at least advanced internal validation (n = 13) but only three of them validated their model with another dataset  [19, 29, 33] , resulting in adequate bias and inaccuracy values. Although each of these three models was externally validated using data from independent patients, this does not imply that these models could be easily applied into other datasets from similar populations.
Moreover, while external validation is highly preferred during model evaluation, the number of studies performing it is rather insufficient  [61]. This lack of external validation could be due to the difficulty of collecting data from enough patients with similar characteristics from another ICU to build a high-quality validation dataset. Furthermore, external validation in antimicrobials is known to often lead to inadequate bias and inaccuracy values  [62] [63] [64] , thus suggesting that a certain challenge still remains. The conception of a meta-model for each aminoglycoside may also be feasible by including the characteristics (covariates, error models, initial estimates) from the bestperforming models following external validation with an independent dataset. The development of this meta-model is, therefore, derived from the independent dataset while also being based on previously published PK models.
Characterization of catalysts X-ray diffraction data were collected at low angles to obtain information about structural properties of the synthesized materials, i. e. , the degree of structural ordering. The XRD method was also used to determine the distance between parallel crystal lattice planes (d 100 ) and the distances between mesopore centres (a 0 ). The elementary cell parameters were determined from the formula: a 0 ¼ dO2. Low-angle X-ray scattering measurements were performed using a Bruker AXS D8 Advance having Johannson monochromator with CuKa radiation, which generated the wavelength of l ¼ 0. 154 nm. All measurements were made with a step 0. 02 in the range 2q ¼ 0. 6-8. Nitrogen adsorption/desorption isotherms and pore size distributions (PSD) were determined at À196 C with a Quantachrome Nova 1200e analyser.
All samples were degassed for 24 hours at 90 C before the actual measurements. The specic surface area of the samples studied was determined using the BET method and the PSD functions were obtained using the BJH algorithm. Microscopic images of the materials were taken using a transmission electron microscope JEOL JEM-1200 EX II at 80 kV. This type of microscopy was used to determine the degree of ordering of mesopores and their distribution. The TEM image, aer setting the scale and threshold for the whole image, were analyzed using "Analyze Particles" option to generate a table with data of the particle areas and diameters. These data were exported into Origin program to construct the histogram plots. The samples were also analysed using a Zeiss scanning electron microscope type EVO at 17 kV.
The imaging data were used to evaluate the surface texture and morphology of all synthesized catalysts. Scanning electron microscopy with X-ray energy dispersion option was used to assess the structure of ordered silica modied with transition metal atoms. For this purpose, the LEO 1430 VP microscope (SEM measurement) and Quantax 200 with XFlash 4010 detector by Bruker AXS (EDX) were used. The content of transition metal was determined using inductively coupled plasma optical emission spectrometry with ICP-OES VISTA-MPX spectrometer by Varian. Prior to measurement the samples were mineralized in aqua regia in a microwave oven. Spectroscopic measurements of X-ray excited photoelectrons were performed using the SPECS UHV analysis system with AlK a radiation (E ¼ 1. 487 keV). All samples were neutralized using a low energy electron gun.
, 2011 ; Tac- Notes. Galaxies with low µ H 2 are identified with †. Galaxies with CO upper-limits are identified with *. ( a) Galaxy with z LDP as z spec. coni et al. 2010 , 2013 , 2018; Freundlich et al. 2019; Spilker et al. 2018; Hayashi et al. 2018; Daddi et al. 2010; Noble et al. 2017 Noble et al. , 2019;; Rudnick et al. 2017a ). The galaxy stellar masses of these comparison samples were originally derived by SED fitting, assuming either a 'Chabrier' or a 'Kroupa' IMF  (Kroupa 2001; Chabrier 2003). We converted all masses to a Chabrier IMF using the relation of  Zahid et al. (2012) : M star, C = 0. 94 × M star, K. Most existing datasets have focussed on field galaxies, with the exception of  Geach et al. (2009 Geach et al. ( , 2011)) ,  Jablonka et al. (2013) ,  Cybulski et al. (2016) ,  Rudnick et al.
Acknowledgements. This paper makes use of the following ALMA data: ADS/JAO. ALMA# 2017. 1. 00257. S. ALMA is a partnership of  ESO  (representing its member states),  NSF (USA)  and  NINS (Japan) , together with  NRC (Canada) ,  MOST  and  ASIAA (Taiwan) , and  KASI (Republic of Korea) , in cooperation with the  Republic of Chile. The Joint ALMA Observatory is operated by  ESO ,  AUI/NRAO  and  NAOJ. The authors are indebted to the  International Space Science Institute (ISSI), Bern, Switzerland , for supporting and funding the international team 'The  Effect of Dense Environments on Gas in Galaxies over 10 Billion Years of Cosmic Time '. We are grateful to the Numpy (Oliphant 2006; Van Der Walt  et al. 2011), SciPy (Virtanen et al. 2020), Matplotlib (Hunter 2007), IPython (Pérez & Granger 2007), and  Astropy  (Robitaille et al.
This new cell line was submitted to the same procedure using the TMPRSS-2 encoding lentivirus and then selected with Neomycin G418 at 250µg/ml to generate U87 cell line stably expressing both ACE-2 and TMPRSS2 proteins. The monitoring of ACE2/TMPRSS2 expression by RT-qPCR revealed that both genes were e ciently expressed. SARS-CoV-2 serology of blood donors SARS-CoV-2 serology of blood donors was determined on plasma diluted 10 times using Simple Western technology, an automated capillary-based size sorting and immunolabeling system (ProteinSimple TM ). The SARS-CoV-2 Multi-Antigen Serology Module (SA-001) was used with Wes device and all procedures were performed according to manufacturer's protocol. Wes device was associated with Compass software for device settings and raw data recording (ProteinSimple/Biotechne).
Exposure to wt SARS-CoV-2, inactivated wt SARS-CoV-2 or recombinant active trimer Spike SARS-CoV-2 SARS-CoV-2 strain (BetaCoV/France/IDF0571/2020, GISAID Accession ID = EPI_ISL_411218) was cultured on Vero E6 cell line (ATCC®CRL1586™) for virus production. PBMC, U87 and Vero cells were infected with SARS-CoV-2 at a multiplicity of infection (MOI) 0. 1. PBMC infection was performed in RPMI-1640 medium (Gibco, 61870-010) completed with 2% of heat inactivated Human AB serum (Sigma, H4522), U87 and Vero infections were performed in DMEM medium (DMEM, Gibco TM ) completed with 2% of heat inactivated FCS. 2 h later, the concentrations of AB-human serum or FCS were respectively increased to 5 and 10%. Recombinant non-stabilized trimer Spike SARS-CoV-2 (ACROBiosystems, USA; Ref. SPN-C52H8) treatment was performed at 0.
Antibody solutions were prepared in the previously described saturation buffer. After three washes in PBS 1X, cells were incubated during 1 hour with secondary antibodies mix containing 1µg/mL goat anti-mouse Alexa Fluor 488 (ThermoFisher Scienti c, A11029), 1µg/mL donkey anti-rabbit Alexa Fluor 647 (ThermoFisher Scienti c, A31573) and DAPI 1/2000 (Sigma, D9542) diluted in the previously described saturation buffer. Finally, cells were washed three times in PBS 1X and mounted using the Fluoromount-G mounting medium (Southern Biotech, 0100-01). Pictures were acquired on NIKON Eclipse TS2R microscope and analyzed on ImageJ software.
Stained cells were acquired on a BD LSR Fortessa, uorochrome emissions from the pool of antibodies were compensated using OneComp Beads (Invitrogen, 01-1111-42) and data analyzed with FlowJo software (v. 10). Quantitative RT PCR (RT-qPCR) At several time points after infection or recombinant Spike exposure, cells were harvested and total RNA extracted. 200 ng of DNase-treated RNA were reverse-transcribed into cDNA using iScript cDNA Synthesis Kit (Bio-Rad, 1708891) according to the manufacturer's protocol. A control with no-RT was prepared in parallel, to con rm the absence of contaminating DNA in PCR experiments. An amount of 5 ng of initial RNA in RT reaction has been used to quantitatively evaluate the transcriptional levels of HERV-W ENV, HERV-K ENV, N SARS-CoV-2 (Ferren et al. preprint 2021.
Acknowledgments We acknowledge World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) and UTMB investigator,  Dr. Pei Yong Shi  for kindly providing recombinant NeonGreen virus based on 2019-nCoV/USA_WA1/2020 isolate and VirPath from the  CIRI, Centre International de Recherche en Infectiologie, Lyon, France  ( B. Lina ,  A. Pizzorno ,  O. Terrier  and  M. Rosa-Calatrava ), for providing us with the BetaCoV/France/IDF0571/2020 virus and  C. Goujon  ( CNRS, Montpellier, France ) and  Olivier Moncorgé  ( IRIM, CNRS, Montpellier ) for providing the plasmids used for the lentifection. This work was supported by  ANR-CoronaPepStop  ( ANR-20-COVI-000 ) and  Fondation de France  to BH and  Agence Nationale de la Recherche  ( ANR, France)-COVERI  to HP. HP, BC, JB, JP and NQ receive compensation from  Geneuro-Innovation  for their work.
Cells, virus and reagents Human synovial fibroblasts (HSF) were obtained from ScienCell Research Laboratory (Scien-Cell, 4700; Clinisciences). The primary cultures of HSF were maintained in Minimum Essential Medium eagle (MEM eagle, PAN Biotech P0408500) supplemented with 10% of decomplemented fetal bovine serum (PAN Biotech, 3302 P290907) and completed with L-glutamine 2 mM (Biochrom AG, K0282), 100U/mL-0. 1 mg/mL penicillin-streptomycin (PAN Biotech, P0607100), 1 mM sodium pyruvate (PAN Biotech, P0443100) and 0. 5 μg/mL fungizone (PAN Biotech, P0601001). The double-stranded polyribonucleotide PIC (cat. no. 27-4732-01) was purchased from Amersham Biosciences. Interleukin-1β (IL-1β; cat. no. 200-01B), Tumor necrosis factor-α (TNFα; cat. no. 300-01A) and Interferon β (IFNβ; cat. no. 300-02BC) were purchased from Peprotech.
Hence, we investigated potential CHIKV direct and indirect effects on HSF PGE2 biosynthetic pathway. Our histological assessments were restricted to a synovial biopsy collected from one patient with CHIKVD relapses. However, our novel immunohistological data strongly support the aforementioned hypothesis for several reasons. First, we observed a strong leukocyte infiltration (CD45 staining) and synovial cell proliferation (Ki67 staining) which may argue for a status of cell activation favoring the production of cytokines by both cell types. Growth factors such as VEGF detected in the synovial tissues may also contribute to angiogenesis (as indicated by robust CD31 and CD34 staining) and further contributing possibly to leukocyte infiltration. T cells (CD3 and CD8 + cells) may produce cytokines such as IFN-gamma and contributing to the activation of CD14+ monocytes and CD68+ macrophages.
15-PGDH expression levels were found to be reduced in RA synovium compared to normal synovium  [34]. We demonstrated that PIC stimulation as well as CHIKV MOI 10 -1 infection significantly reduced 15-PGDH mRNA levels in HSF. MTX treatment did not interfere with the expression of 15-PGDH in basal conditions as well as after PIC stimulation or CHIKV infection. 15-PGDH was shown in recent published microarray data  [57]  to be strongly downregulated by the dsRNA PIC in cultured normal human epidermal keratinocytes (NHEKs). This downregulation of 15-PGDH by PIC, together with an observed marked upregulation of COX-2, is consistent with our observations about the ability of the dsRNA PIC to modulate the expression of several enzymes of the PGE2 biosynthetic pathway. MTX treatment ability to affect the expression levels of 15-PGDH was assessed in both RA biopsies ex vivo and in cultured RAFLSs.
| AVAIL AB LE G ENOMI C DATA Since the first whole-genome sequence published in 2013  (Darrasse et al. , 2013) , 70 Xcf-Xpp genomes have been released to date at the National Center for Biotechnology Information (Table  1 ). These genomes represent a diversity of 51 Xcf-Xpp strains, 13 of which were Genome: The genome consists of a single circular chromosome plus one to four extrachromosomal plasmids of various sizes, for a total mean size of 5. 27 Mb with 64. 7% GC content and an average predicted number of 4,181 coding sequences. Disease control: Management of CBB is based on integrated approaches that comprise measures aimed at avoiding Xcf-Xpp introduction through infected seeds, cultural practices to limit Xcf-Xpp survival between host crops, whenever possible the use of tolerant or resistant bean genotypes, and chemical treatments, mainly restricted to copper compounds.
(b, c) Subtrees of rep-PCR group 9. 6, from trees constructed using CVtree  (Qi et al. , 2004)  on the same strain dataset as for the tree presented in (a). These trees are based on the frequency of appearance of overlapping oligopeptides of length K = 6. The tree in (b) was constructed based on the same 1,335 core genes as in (a), while the tree in (c) was constructed based on the pan-genome consisting of all predicted coding sequences. Topologies in (a) and (b) are congruent with each other sequenced more than once. Most sequenced strains were isolated from common bean except for Xpp CIAT XCP123, which was isolated from lima bean, which lacks a XopJ5 homolog encoded in other Xpp and is phylogenetically an outlier within GL1 (Figure  1a ;  Aritua et al. , 2015). According to PacBio assemblies, the genome consists of a single chromosome plus one to four extrachromosomal plasmids of various sizes.
This region comprises 28 genes, including Xfutal1, and seven genes encoding proteins from the type IV conjugal transfer system. In all, whole-genome data revealed that the pathological convergence observed between Xcf and Xpp is associated with horizontal gene transfers and highlighted the role of plasmids in these transfers. Functional validation is still needed to confirm the role of these genes in pathogenicity. No evidence of horizontal gene transfer was observed between Xcf-Xpp and lablab-associated strains, indicating that they have undergone an evolutionary history distinct from the other CBB strains  (Aritua et al. , 2015). Although the dichotomy between Xpp and Xcf has clearly been established, the phylogenetic positions of the fuscans, GL2, and GL3 lineages have never been clearly elucidated with respect to other strains from rep-PCR group 9.
| IMPAC T AND D IS TRIBUTI ON CBB is one of the five major diseases of common bean  (Broughton et al. , 2003). Yield losses up to 45% were reported in susceptible genotypes  (Saettler, 1989; Wallen & Jackson, 1975; Yoshii et al. , 1975). In the field, CBB directly affects yield either by degrading edible fresh materials or by reducing the area of photosynthetic tissues. Materials with symptoms become unsaleable, and additional losses are due to the time and costs involved in controlling the disease. A major threat posed by CBB concerns seed quality, impacting both the seed industry and edible seed production. In particular, infected seed lots cannot be sold in disease-free areas, even in the absence of symptoms. According to the EPPO global database, CBB is widely distributed over 104 countries across the five continents (Figure  2 ).
Accepted Article This article is protected by copyright. All rights reserved after a 45 min run at 100 V. The amplified regions were sent to GenoScreen (Lille, France) for direct Sanger Sequencing with primer EF1. The sequences were analyzed with Geneious prime v10. 0. 4 (Biomatters, Auckland, New Zealand). Raw sequences showing more than 15 % of Low-Quality bases were removed from further analyses. The remaining sequences were aligned with Geneious using default parameters and species were identified using both databases of Fusarium MLST (https://Fusarium. mycobank. org/) and Fusarium ID (http://isolate. Fusariumdb. org/blast. php). Neighbor-joining trees were built with the Geneious Tree Builder default parameters (1000 bootstrap replicates and 50% consensus support threshold) to visually confirm the molecular identification (not shown).
(2012). Due to lack of polymorphisms for the rpb1, rpb2 and ITS region sequences, three consensus trees were constructed with sequences of the tef-1α and IGS regions. All tef-1α sequences obtained during the molecular identification of strains (n=1171) were included in the analysis in addition to 139 sequences of F. proliferatum strains and 118 sequences of F. oxysporum strains isolated from garlic, maize (Zea mays), onion (Allium cepa), welsh onion (Allium fistulosum) and wheat (Triticum sp. ) from the GenBank collection (https://www. ncbi. nlm. nih. gov/genbank/). These reference strains had been isolated from China, Finland, France, Iran, Japan, Malaysia, Mexico, Serbia, South Africa, Spain and in the USA (Table  2 ). Sequences were analyzed with Geneious prime v10. 0. 4 (Biomatters, Auckland, New Zealand).
They were aligned (Pairwise alignment) and ends were trimmed. Unique sequences were extracted and underwent iterative pairwise alignment and trimming until all sequence lengths were strictly identical. Trees of the F. proliferatum and the F. oxysporum sequences were constructed with MEGA-X v10. 1. 8 software using the maximum-likelihood method in order to get a more detailed picture of the strains distribution. For each tree, the best model was chosen using ModelTest include in the software. All trees were constructed using the bootstrap method with 1000 replicates. Gaps and missing data were treated as deletions. The neighbor joining method was used in cases where the objective was to distinguish groups of strains. To the 1171 tef-1α sequences of strains isolated from French garlic, we added 12 tef-1α sequences from strains isolated from Spanish garlic, non-garlic sources or garlic leaf debris.
Statistical analyses All statistical analyzes were conducted with RStudio software (v 1. 2. 1335) and Statistica software (v. 10). Incidences of garlic rot on all garlic types were compared with ANOVAs and Tukey's HSD post hoc test. Relative aggressiveness of haplotypes were compared with ANOVAs. A generalized linear model (GLM) was used to explore the proportional differences of Fusarium species. A linear model (LM) was used to compare the link between aggressiveness and several factors.
One contained strain FA122-E11 and the other contained the 13 others strains. The strains collected in this study were dominated by a tef-1α gene haplotype of F. proliferatum that accounted for more than 75 % of the strains collected from garlic (Haplotype 1, Table  3 ). Strains from garlic (from cloves or leaf debris from France and elsewhere) constituted 25 additional haplotypes of which 17 haplotypes represented less than 1 % of the strains collected from garlic. The strains tested for aggressiveness on garlic represented 8 of the 9 haplotypes with more than 10 strains in the collection and 3 of the haplotypes with fewer than 10 strains. To those sequences, we added 80 tef-1α GenBank database sequences corresponding to strains isolated from different hosts and geographical areas. Of these 119 tef-1α haplotypes, 66 corresponded to strains of F.
proliferatum. The 505 bp sequences of these 66 haplotypes showed high nucleotide identity with each other, ranging from 99. 8 to 98. 41 % except for the sequence of KU847789 sequence whose similarity to other sequences ranged from 98. 03 to 96. 45 %. Sequences of F. proliferatum strains from French garlic cloves were partially clustered but no correlation with geographic origin of host could be determined (Figure  4a ). The 5 strains representing the minor rpb1/rpb2 haplotype were also clustered in a unique branch on the tree obtained with the partial tef-1α sequences. F. oxysporum sequences (574 bp) showed 99. 87 % to 96. 03 % nucleotide identity. Sequences of F. oxysporum strains isolated on French garlic cloves showed affiliation across the whole range of available sequences of F. oxysporum from the GenBank database (Figure  4b ).
Acknowledgments This study benefited from a PhD scholarship provided by  ANRT (Association Nationale Recherche Technologie, CIFRE  grant  n°2017/1440 ) and by the  French garlic industry  ( Coopérative Alinéa, Prosemail, Syndicat de l'Ail Rose de Lautrec ). This study was supported in part by a grant from the  Plant Health and Environment research division  ( OCARINA  project) of  INRAE  ( National Research Institute for Agriculture, Food and Environment ). The authors thank the  French garlic industry  for providing garlic bulbs used in the present study and the  FNAMS  for providing onions plants used to isolate Fusarium strains. The authors thank  Claire Troulet ,  Magali Eygrier ,  Erine Amorim-Pinto ,  Alice Alarçon ,  Emma Borelly  and  Jeanne Hamet  for their technical help. The authors are grateful to  Dr.
Results RNA-seq analysis of Pst-infected field samples can be used to define wheat varieties A set of 156 Pst-infected bread wheat (T. aestivum) samples collected between 2013 and 2016 were used to explore the genetic diversity of Pst-infected host wheat varieties across Europe (Supplemental Data Set 1). This set included 130 Pst-infected samples previously used to study Pst population dynamics  (Hubbard et al. , 2015; Bueno-Sancho et al. , 2017). Total RNA was extracted from the remaining 26 samples and subjected to RNA-seq analysis (Supplemental Data Set 1;  Hubbard et al. , 2015). As each sample gives rise to both wheat and pathogen-derived reads, we determined the proportion of wheat reads by filtering the raw reads from a subset of 131 samples for quality and mapping them to the Chinese Spring wheat reference genome  (IWGSC RefSeq v1.
Co-expression cluster analysis reveals varietalspecific gene expression profiles To reduce dataset complexity and identify biological processes linked to varietal-specific expression, we performed co-expression cluster analysis. As samples from the same wheat variety were sourced from different environmental conditions and were at different developmental stages, we hypothesized that this approach could lead to identification of genes linked to Pst susceptibility because the main commonality between samples was their response to Pst infection. A total of 61,700 differentially expressed transcripts were identified and classified into 12 co-expression clusters (Figure  2A ). Gene ontology (GO) terms were assigned to each gene where possible. This analysis highlighted 16 biological processes, 12 cellular components and 16 molecular functions as second level GO terms that were present in all co-expression clusters (Supplemental Figures  4 5 6 ).
RNA-seq of Pst-infected wheat samples A total of 156 Pst-infected bread wheat (T. aestivum) leaf samples were collected between 2013 and 2016 and stored to maintain nucleic acid integrity in RNAlater solution (Thermo Fisher Scientific, Paisley, UK), of which 130 were previously processed for RNA-seq analysis  (Hubbard et al. , 2015; Bueno-Sancho et al. , 2017 ; Supplemental Data Set 1). The remaining 26 samples were subjected to RNA extraction using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions (Qiagen, UK), and cDNA libraries were prepared using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, USA). Libraries were sequenced on the Illumina HiSeq 2500 machine (Earlham Institute, UK and GENEWIZ, Germany), and adapter and barcode trimming and quality filtering were performed on the resulting 101-bp pair-end reads using the BBDuk tool in BBtools version 37.