dataesr/scientific-paragraphs-categorization huggingface dataset:
Funding This study was supported by the " Fondation Méditerranée Infection " and by the  French Government  under the " Investissements d'avenir" (Investments for the Future ) programme managed by the  Agence Nationale de la Recherche  ( ANR , fr:  National Agency for Research) , (reference: Méditerranée Infection  10-IAHU-03 ). This work was also supported by the  Région Provence-Alpes-Côte d'Azur and European funding FEDER PRIMI.
Housekeeping gene amplification and sequencing Sequences from three isolates (Xcc DZ114. 10, Xcc DZ113. 5 and Xcc DZ1388. 2) were selected from the main varieties cultivated in Algeria to be compared with those available in the database with BLASTN  (Altschul et al. , 1990). Fragments of four housekeeping genes were sequenced for each isolate, including gyrB (DNA gyrase subunit B), rpoD (RNA polymerase sigma-70 factor), atpD (ATP synthase beta chain), and DnaK (heat shock protein 70), according to  (Fargier et al. , 2011)  (Table  2 ). The amplifications were each carried out in a thermocycler (iCycler; Bio-Rad), in a final volume of 20 μL containing 1× green GoTaq Hot Start buffer, 1. 5 μL of 25 mM MgCl 2 , 0. 2 mM of dNTP, 0. 5 μM of each primer and 1U of GoTaq Hot Start DNA polymerase (Promega) and 3 μL of target DNA.
The amplification program consisted of 5 min at 95°C followed by 35 cycles of 30 s at 95°C, 45 s at Tm (Table  2 ) and 1. 30 min at 72°C, and finished with 72°C for 5 min. The PCR products were analysed on 1. 5% agarose gel in 1× TBE buffer. The two strands of the amplicons obtained from the three isolates were sequenced by the GATC Biotech laboratory, Germany. The sequence electropherograms were analysed using the software 4 peaks 1. 7. 2 (https://nucleobytes. com/4peaks/index. html). The DNA sequences were aligned using the Multalin software (Corpet, 1988: http://multalin. toulouse. inra. fr/multalin/).
5% agarose gel in 1× TBE buffer, and also by Nano-Drop ND-2000 (ThermoFisher Scientific). The 96 amplicons were sequenced at the GATC Biotech laboratory, Germany. DNA sequences were analysed using the software 4 peaks 1. 7. 2. and were aligned using the Bioedit program  (Hall, 1999). Only sequences having average lengths of 500 bp were used for analyses. The sequence data of the two genes were concatenated according to the alphabetical order of the gene, the gyrB gene followed by the rpoD gene, using the GENEIOUS software Version 4. 8. 5 (BIO-MATTERS). Phylogenetic analyses were carried out on individual genes as well as on the concatenated sequences using the DNA Sequence polymorphism (DnaSP) software version 5. 10  (Rozas et al. , 2010). This analysis is based on the Tajima's method  (Tajima, 1996) , allowing a multiple alignment by determining pairwise nucleotide diversity.
The differentiation between the haplotypes is based on the presence of a single nucleotide different per sequence  (Wicker et al. , 2012; Tancos et al. , 2015). The phylogenetic tree was constructed using Mega software version 6. 06  (Tamura et al. , 2013)  based on the Maximum likelihood (ML) method  (Tamura and Nei, 1993). This software allows quick analysis of a large number of sequences, and evolutionary phylogenetic reconstruction based on statistical bootstrap analysis at 1000 replications. The tree was constructed with the DNA sequences of each gene and with the concatenated sequences. Sequences of Xcc strains (Xcc-C168, Xcc-C278, ICMP 6541, strain 0407, strain 0470, ICMP 13, CFBP 5241, 70 genome, ICMP 4013, ATCC 33913, 21080, Xcc-8004), published on the NCBI database were used for comparisons with sequences from the Algerian strains, and the sequence from X.
Amplification of housekeeping genes Sequence amplifications from the three isolates of Xcc (Xcc DZ114. 10, Xcc DZ113. 5 and Xcc DZ1388. 2) using four housekeeping genes, gave four bands of the expected sizes of 904 bp for the gyrB gene, 1313 bp for the rpoD gene, 868 bp for the atpD gene and 1034 bp for the dnaK gene  (Fargier et al. , 2011). The DNA sequences of the four genes from the three Algerian isolates showed high percentage similarities of 98 to 100%, in comparison with Xcc sequences, and less than 96% similarity with other Xanthomonas species available in the NCBI database (Table  3 ). The partial nucleotide sequences of the strains Xcc DZ114. 10, Xcc DZ113. 5 and Xcc DZ1388. 2 were deposited in the NCBI database under the following accession numbers: the atpD gene (KU556302 to KU556304), the DnaK gene (KU556305 to KU556307), the gyrB gene (KU556308 to KU556310) and rpoD (KU556311 to KU556312).
DISCUSSION Th is study reports for the fi rst time the presence of Xcc in Algeria, aft er the investigation conducted in cabbage and caulifl ower fi elds from 2011 to 2014. A total of 170 Xcc isolates was obtained from 45 fi elds. Th ese isolates were identifi ed as Xcc by morphological, physiological and molecular tests. Th e analysis of four housekeeping genes (gyrB, the rpoD, the atpD and the dnaK) performed on partial DNA sequences of three representative Algerian strains showed 98 to 100% similarity with homologous Xcc sequences available in the GenBank database (Table  3 ). Results obtained from this survey indicate the importance of black rot in Algeria, and how widespread the disease is in the main Brassica growing areas of the country. However, the sampling method used did not allow assessment of how the disease spreads in this country, because each region was not monitored each year.
Most questions required answers by "yes" or "no" answers, except 2: "impact of disease and treatment on pregnancy wish" and "consequences of disease and transplant on sexual life" for which additional free text answers were required. Data from free text answers were analyzed through a thematic analysis approach. In the absence of a response, a reminder phone call was provided 1 month after inclusion. Two members independently compiled the answers to each survey. The descriptions considered meaningful were then sorted into themes. Differences of opinion about the themes were reviewed by 4 of the co-authors (N. F. , M. J. , C. P. , and N. D. ). Findings from this process are reported as descriptive information. Explorations for post-transplantation ovarian function evaluation were performed at least 3 months after discontinuation of hormonal replacement therapy (HRT) in patients with amenorrhea or on day 3 of menstruation in patients without amenorrhea.
Hormonal analyses included follicular-stimulating hormone (FSH), luteinizing hormone (LH), estradiol, and anti-M€ ullerian hormone (AMH). Transvaginal pelvic ultrasonography reported antral follicle count for each ovary. Data concerning diagnoses, HSCT procedure, occurrence of GVHD, and FP techniques were collected from patient medical records. An update of survival and pregnancy outcomes was performed in January 2019.
ACKNOWLEDGMENTS The authors thank all the study contributors for their assistance with data collection, especially  Sylvie Lengay , as well as the medical and nursing staff who took care of the patients and especially the patients who participated in this study. Financial disclosure: No part of the work presented has received financial support from any source. There are no financial or other conflicts of interest in relation to this manuscript. Conflict of interest statement: There are no conflicts of interest to report. Authorship statement: N. D. conceived the study. N. D. and C. P. designed the survey and acquired the data. N. D. , C. P. and D. V. included the patients. N. D. , C. P. , N. F. and M. J. independently reviewed survey answers. N. F. and M. J. performed data curation and formal analysis and wrote the original draft.
PMMA Biotransformation Products Four TPs were found in the biotic reactor experiments, namely TP-166 and TP-196(a-c) (Table  1 ). The chromatographic peak of the TP-166 (m/z 166. 1215) at 3. 01 min could be attributed to two different compounds, the N-demethylation or O-demethylation product of PMMA according to the suspect database. This TP was observed after 2 h at relatively low levels (absolute peak area) (Figure  1 ) and according to accurate mass, retention time, and MS/MS spectra the TP-166 was the O-demethylation product of PMMA (Figure  3 ). The retention time prediction model calculated a t R of 5. 87 min for the N-demethylation product and 3. 14 min for the O-demethylation one. Hence, the N-demethylation product was excluded as a potential TP according to the prediction model. Furthermore, the product ions of the MS/MS experiments corresponded to loss of NH 2 CH 3 (m/z 135.
0797) and a further loss of C 2 H 4 (m/z 107. 0491) (Figure  3 ), which matched the product ions of p-OHmethamphetamine  [5, 40]. c) (Table  1 ). The chromatographic peak of the TP-166 (m/z 166. 1215) at 3. 01 min could be attributed to two different compounds, the N-demethylation or O-demethylation product of PMMA according to the suspect database. This TP was observed after 2 h at relatively low levels (absolute peak area) (Figure  1 ) and according to accurate mass, retention time, and MS/MS spectra the TP-166 was the O-demethylation product of PMMA (Figure  3 ). The retention time prediction model calculated a tR of 5. 87 min for the N-demethylation product and 3. 14 min for the O-demethylation one. Hence, the N-demethylation product was excluded as a potential TP according to the prediction model.
DHM Biotransformation Products Six TPs were found in the biotic reactor (Table  2 ). TP-210 and TP-178 were characterized as the major TPs and TP-166, TP-164, TP-192a, and TP-192b, as the minor TPs according to their abundance (Figure  2 ). The TP-210 with m/z 210. 113 and retention time of 1. 82 min was detected after 8 h of incubation. Three isomeric compounds were proposed according to the suspect database, but the retention time prediction model was not able to distinguish the isomeric forms of TP-210. The predicted retention times (from 3. 1 min to 3. 3 min) of isomers were within the limits of the model  [37]  and, therefore, it could be assigned to one of the isomeric TPs. The formation of TP-210 (Figure  4 ) was proposed to be done by two biotransformation pathways. Oxidation of the primary alcohol on DHM was the first one, following the formation of a ketone group on the β-carbon (forming TP-178) and, after that, dihydroxylation.
Identification of Transformation Products by Suspect Screening Detection and identification of PMMA and DHM TPs was performed by a postacquisition approach  [36]. A suspect database of potential TPs was built using two in silico prediction tools, the Eawag-Biocatalysis/Biodegradation Database Pathway Prediction System and the MetabolitePredict software, and a list of reported metabolites and TPs from the literature  [5, 15, 16, 40, 41, 51, 53]. Samples were screened using specific criteria  [52]  and an in-house retention time prediction model  [37]. Finally, the confidence levels for the identification of a compound proposed by  Schymanski et al. (2014) , were used  [39].
Funding:  Juliet Kinyua  acknowledges the  "Sewage Analysis CORe group Europe (SCORE)" for her Short-Term Scientific Mission (STSM)  grant and the  EU International Training Network SEWPROF (Marie Curie -Grant number  317205 ) for her PhD fellowship. The APC was funded by the  Special Account for Research Grants of NKUA  (Grant #  7737 ). Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
(4. 9) With the help of LiteRed  [118, 119] , a Mathematica package performing the IBP reduction to master integrals, this combination can be reduced to four master integrals: f 1 ≡ -q 2 G 2,0,0,1,0,1,1,0,1 , f 2 ≡ -q 2 G 2,0,0,1,0,0,1,1,1 , f 3 ≡ -q 2 G 1,0,1,1,0,0,1,1,1 and f 4 ≡ -q 2 G 2,0,0,1,1,1,1,1,1. Once the master integrals are known, we can cast I as a linear combination of these. Note that since we are considering a cut two-loop integration, one must use the CutDS option in LiteRed in order to perform the correct IBP reduction. The set of propagators in eqs. (4. 4) and (4. 5) and the four master integrals above are enough to solve our four topologies in eq. (3. 7). At this point, we can use the differential equation methods  [85] [86] [87] [88]  to solve these integrals. It is convenient to replace the dependence on γ of the master integrals by that on the kinematic variable x, defined by x ≡ γ -γ 2 -1  [81].
The observed variations are probably due to ion channel activity modulations with no toxic effect on the airway epithelium. Original experiments on the efficacy of SNH have been included in the present report. The airway epithelium represents a primary defense mechanism against respiratory challenges and functions as a physical barrier and immune response modulator from the nostrils to the lung by means of MCC  [27]. MCC relies on mucus secretion and cilia beating and its measurement expresses the rate of foreign particle, pathogen, and chemical clearance. SNH significantly increased MCC at Day 4 in comparison to untreated cultures. Overall, these data suggest a beneficial effect of SNH on MCC which is compromised in sinonasal diseases such as chronic rhinosinusitis  [28]. Additionally, levels of secreted mucins were measured.
Study design Using the local Programme de Medicalisation des Systemes d'Information (PMSI) database,  11  among 5661 consecutive cases of TV surgery performed in adult patients at 12 tertiary French centres between 1 January 2007 and 31 December 2017, we identified 466 patients who underwent an ITVS on native valve for severe non-congenital TR. The design of the study has been previously reported. 4 Clinical information and immediate and mid-term outcome were retrospectively collected locally at each centre. Right-sided heart failure signs were defined as severe jugular venous distention, ascites, and/or marked peripheral oedema. Tricuspid regurgitation mechanism was classified as functional (no intrinsic TV disease) or organic (due to abnormalities of the tricuspid leaflets or chordae). Glomerular filtration rate was calculated using the Cockcroft-Gault formula according to sex.
67 and 0. 63, respectively). In an attempt to better assess the surgical risk of ITVS, LaPar et al. 10  proposed a dedicated risk score model derived from a subset of the STS database from the states of Virginia and Michigan. Although the authors should be commended for their seminal work and indeed their risk model was an important step towards a better risk stratification of patients referred for ITVS, it suffered from two important limitations. First, because of the limited granularity of the STS database, important prognostic factors in the setting of TR as RV consequences and liver function were not accounted for. 26 econd, their risk model was not well calibrated for high-risk patients with a maximum predicted mortality rate of 34%. The Model for End-Stage Liver Disease (MELD) score, which is used to stratify patients awaiting liver transplantation, has also been shown to predict mortality after TV surgery in a cohort of 168 patients but in whom only 22 patients underwent ITVS.
The Genome of U. pustulata We used the genome assembly by Greshake Tsovaras et al. [56]  as reference for TE prediction and annotation (accession GCA_008636195, BioProject: PRJNA464168). The haploid genome of U. pustulata is 32. 9 Mbp long, with 43 scaffolds and an N50 length of >1. 8 Mbp.
39  [57]  with a length cutoff of 80 bp and a quality cutoff of 26 in a window of 5 bp. Reads with Ns were removed and an additional quality trimming using a modified Mott algorithm was performed using the script trim-fastq. pl from the PoPoolation v1. 2. 2 pipeline  [58]. After trimming, the sequencing depth varied between 24. 3 and 37. 3 million paired-end reads (Table  1 ). We used the TEdenovo pipeline from the REPET package v2. 5  [59, 60]  to generate a TE consensus library in U. pustulata. Briefly, the pipeline was used to perform a self-alignment of the reference genome to detect repeats, to cluster the repetitions and to perform multiple alignments from the clustered repetitions to create consensus TE sequences. Consensus TEs were subsequently classified using the PASTEClassifier pipeline v2.
0  [61] , which follows Wicker's classification  [7]  using structural and homology-based information (i. e. , terminal repeats, poly(A) tails, ORFs, tandem repeats, etc. ) and the following databases: 'rep-base20. 05_ntSeq_cleaned_TE. fa', 'repbase20. 05_aaSeq_cleaned_TE. fa' and 'ProfilesBank-ForREPET_Pfam27. 0_GypsyDB. hmm' (https://urgi. versailles. inra. fr/download/repet (accessed on 9 January 2018)). We set the minNbSeqPerGroup parameter to 3 (i. e. , 2n + 1) because U. pustulata is haploid. All remaining parameters used for these analyses can be found in the TEdenovo and TEannot configuration files (Additional Files 1, 2). We then performed extensive automated as well as manual curation of the TE consensus library to minimize redundancy as well as false positives. For this purpose, we first performed a two-step annotation  [62]  on contigs longer than 5 Kbp, i.
e. , 1st round: steps 1 -taking all matches found by BLASTER, RepeatMasker and CENSOR, 2-normal and random, 3-using Grouper, Recon and Piler as clustering methods and 7-removing duplicated/spurious fragments and applying the long join procedure for nested copies of TEs identified by the TEannot pipeline part. We only retained TE consensus sequences having at least one full-length copy (FLC, i. e. , length of fragments between 95% and 105% of consensus length) to build the final TE library. This was followed by a 2nd round consisting of TEannot steps 1, 2, 3, 4, 5, 7 and 8, using the final TE library to annotate the genome. Finally, we performed a copy divergence analysis of TE classes based on Kimura distances by calculating Kimura 2-parameter divergence  [63]  between each TE copy and its consensus sequence using the utility scripts provided in the RepeatMasker package.
pustulata populations via a subsampling and a rescaling approach: In order to balance the loss of information with the homogeneity of the TE frequency, we used the stat-coverage tool from PoPoolationTE2 to obtain information on the physical coverage in our dataset. We then used the subsamplePpileup tool (-target-coverage 16) to discard positions with a physical coverage below 16x and rescale the coverage of the remaining sites to that value. We identified signatures of TE polymorphisms from the previously subsampled file using the identifySignature tool following the joint algorithm (-mode joint; -min-count 3; -signature-window minimumSampleMedian; -min-valley minimumSampleMedian). Then, for each identified site, we estimated TE frequencies in each pool using the frequency tool. Eventually, we paired up the signatures of TE polymorphisms using pairupSignatures tool (-min-distance 100; -max-distance 500), yielding a final list of TE loci in the reference genome with their frequencies for each pool.
Each TE insertion was manually checked using IGV v2. 5  [68]. TE loci predictions with unusually high read coverage, i. e. , resulting from spurious alignments to unmasked repeats, were discarded from further analysis. The stringent filters applied here, together with the inability of PoPoolationTE2 to detect nested TEs  [64] , may lead to an underestimation of TE activity across U. pustulata populations. On the other hand, such a conservative approach almost certainly eliminates false insertions. TE loci supported by significant physical coverage were considered polymorphic if they had a frequency difference of at least 0. 05% among populations. TE loci with frequencies ≥0. 95% were considered fixed in the populations. The similarity of populations based on their TE composition was investigated using nonmetric multidimensional scaling (NMDS) on all detected TE insertion frequencies using the function metaMDS from the vegan package  [69]  for R  [70].
e. , 'sync' file containing the allele frequencies for every population at every base in the reference genome) and the script subsample-synchronized. pl (-without-replacement), excluding positions with a coverage exceeding the 2% of the empirical coverage distribution of each pool. Genetic differentiation (F ST ) was calculated with fst-sliding. pl in PoPoolation2 on the subsampled sync file (F ST dataset available at: 10. 6084/m9. figshare. 14784579 (accessed on 8 November 2021)). We only considered SNPs with a minimum read count of 4 and a minimum mapping quality of 20. A more detailed description of the methods can be found in  [54].
TE Landscape in U. pustulata The mobilome spans 21. 26% of the U. pustulata genome length (Table  S1 ). We annotated 119 TE consensus sequences (available via the INRAE data repository: https://doi. org/10. 1 5454/KXPSUY (accessed on 13 November 2021) and at: 10. 6084/m9. figshare. 14784579 (accessed on 8 November 2021)) for a total of 5956 TE copies (704 of which are full-length) and 6758 TE fragments, for a cumulative coverage of 6,996,427 bp (Table  2 , Tables  S1  and S2 ). Retrotransposons (Class I) cover 15. 6% of the genome of U. pustulata, while DNA transposons (Class II) cover 3. 5%. Among the Class I elements, Gypsy are the most represented (8. 8% of the genome), followed by Copia elements (4. 1%). Helitron are the most abundant elements within the Class II elements (1. 7%), followed by terminal inverted repeats (TIR; 1.
TE Variation across U. pustulata Populations We used the PoPoolationTE2 pipeline  [64]  on the U. pustulata reference genome  [56]  to detect variations in TE frequencies in 15 natural populations across three replicated elevational gradients. After manual curation, we retained 182 TE loci belonging to 12 superfamilies with a minimum physical coverage of 16 (Table  3  and Table S4 ). Of these, 68 insertions were fixed across populations, i. e. , they had a minimum frequency of 0. 95 within each population. Copia elements were the most frequently detected loci, representing 43% (49 loci) of all polymorphic insertions, followed by TIR elements (19. 3%, 22 loci) (Table  3B ). We further compared population structure based on 447,470 genome-wide SNPs (dataset available at: 10. 6084/m9. figshare.
Crystals for FBA C were obtained at 20°C in a reservoir containing 0. 1 M sodium acetate trihydrate pH 4. 5, 2. 0 M ammonium sulfate, and a ratio of protein and reservoir with 25 and 75%, respectively. FBA P crystals grew at 8°C with 50% protein and 50% reservoir containing 20% PEG 4000, 0. 2 M imidazole/malate buffer at pH 6. Crystals were flash cooled in liquid nitrogen for storage and data collection. X-ray diffraction data of FBA C were collected in-house at 100 K on a Rigaku MicroMax 007HF rotating anode X-ray generator equipped with amar research mar345dtb image plate detector. Data of FBA P were collected on beamline X06DA with PILATUS 2 M-F detector (Dectris) at Swiss Light Source (Villigen, Switzerland). The FBA structures were solved by molecular replacement with MOLREP  (Vagin and Teplyakov, 2010)  using aldolase from Bacillus anthracis (PDB ID code 3Q94;  Tan et al.
2021) , Using the cloud model technique applied to the Mg II line profiles we identified explosive clouds with supersonic Alfvén velocities. A stratification thermal model of the atmosphere at the time of the reconnection was proposed. The Mg II spectra show extended wings like in IRIS bombs  (Peter et al. 2014; Grubecka et al. 2016). Twist and bald patch reconnection was confirmed with the analysis of the IRIS spectra (Si IV, C II, Mg II) by  Joshi et al. (2020). In this paper we extend the IRIS data analysis of the mini flare studied in  Joshi et al. (2020 Joshi et al. ( , 2021) )  and present the Balmer continuum around 2832 Å observed with IRIS (Sect. 2). Section 3 presents the IRIS spectra and 2832 Å slit-jaw images (SJIs) analysis. Further, we analysed the hard X-ray (HXR) emission detected by FERMI/GBM (Sect.