dataesr/scientific-paragraphs-categorization huggingface dataset:
Both up-and downregulated transcripts (relative to the non-axenic controls) were imported into the gene ontology (GO) enrichment analysis tool based on protein analysis through the evolutionary relationships classification system. The molecular functions, cellular component, and biological process GO categories were considered significantly enriched and represented in the pie charts when their adjusted p values were <0. 05. Up-regulated transcripts were also imported into the pathway enrichment analysis tool of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database.
When life stages were analyzed separately by PCA, replicates from the same treatments did not necessarily cluster together, with the exception of L 1 axenic larvae and pupae from the Paenibacillus D treatment (Fig. 3A ). Pairwise comparisons found a total of 2,359, 10,796 and 6,026 transcripts that were significantly differentially expressed between at least two gnotobiotic treatments in larvae, pupae and newly emerged adults, respectively. As mentioned above, our primary goal was to compare gnotobiotic treatments with one another and we used the non-axenic controls as a shared reference level to facilitate pairwise comparisons. A total of 4,029, 7,240 and 2,844 transcripts were significantly enriched or depleted relative to the non-axenic controls in gnotobiotic larvae, pupae and newly emerged adults, respectively.
Discussion This study builds on our previous work  (Dickson et al. , 2017)  to show that carry-over effects detected at the phenotypic level are associated with massive changes at the molecular level in gnotobiotic Ae. aegypti mosquitoes. Specifically, we found that larval exposure to different bacteria results in transcriptomic and metabolic changes that have consequences on adult physiology and fitness. For two of the four gnotobiotic treatments that we examined in more detail (larval exposure to Flavobacterium S and Paenibacillus D), we noticed that several transcripts related to lipid metabolism were enriched in both larvae and adults. We found elevated lipid content in the adult females emerging from these gnotobiotic treatments, which translated into higher starvation resistance. Together, our results provide evidence that carry-over effects in gnotobiotic Ae.
three in the previous study) since only seven out of 16 bacterial isolates resulted in a consistent effect on adult survival. The influence of larval exposure to bacteria on adult female survival is epidemiologically meaningful because it is one of the most critical determinants of vectorial capacity  (Shaw & Catteruccia, 2019). We used an untargeted approach of transcriptome sequencing to examine the gene expression profiles of gnotobiotic larvae, pupae and freshly emerged adults. We detected substantial variation in transcript abundance between the gnotobiotic treatments both in pairwise comparisons and using non-axenic controls as the reference level. In addition to the expected differences between life stages, we found that most of the transcriptional changes were related to metabolic processes.
Acknowledgments We thank  Catherine Lallemand  for the maintenance of mosquito colonies and the  Lambrechts lab members  for their insights. We are grateful to  Alongkot Ponlawat  for the initial collection of Ae. aegypti in Thailand. We thank  Christophe Paupy ,  Davy Jiolle ,  Diego Ayala ,  Amine Ghozlane ,  Marc Monot ,  Karima Zouache ,  Edwige Martin ,  Vincent Raquin  and  Guillaume Minard  for their input and assistance at earlier stages of the study. This work was primarily funded by the  Agence Nationale de la Recherche  (grant  ANR-16-CE35-0004-01 ). It was also supported by the  French Government 's  Investissement d'Avenir program Laboratoire d ' Excellence Integrative Biology of Emerging Infectious Diseases  (grant  ANR-10-LABX-62-IBEID  to LL), and the  City of Paris Emergence(s) program in Biomedical Research  (to LL).
False positives (FP) are results obtained for samples where a negative result is expected (given the true sample status); similarly, false negatives (FN) are results obtained for samples where a positive result is expected. Calculations used are listed in Table  4. The qualitative input data were the positive and the negative detections derived from each technical replicate from testing the DA of Dss, the stability of the shipped material and the analytical sensitivity. For blind Das, the qualitative result was considered both at (i) the technical replicate level; and (ii) the Das level, i. e. , positivity and negativity was attributed to a Das by coherent results obtained from at least two technical replicates (out of three). The dataset is a binomial distribution, thus the binconf function of the Hmisc package of R  [27]  statistical software was applied to search for confidence intervals (95%) for AC, DSE, and DSP criteria, using the Wilson score method with no continuity correction  [28].
Tests on the equality of AC, DSE, and DSP between laboratories, and the chemistry-based assays were performed using a one-sample t-test. Standard curves were compared according to the following procedure: the average value at each dilution point was subtracted from the corresponding values of a theoretical curve sharing the template values in the x axis (expressed in base-10 logarithm) with experimental curves, but with an exact best fit efficiency (100%) (i. e. , with a regression equation with 3. 32 as the angular coefficient). We thus obtained seven normalized replication values for each curve, which were used in the statistical analysis to compare the various curves and to give a measure of the significance among them. Fisher's test for the analysis of variance (ANOVA) was developed on the dataset obtained after verifying the normality of the distribution with the Shapiro-Wilk test and the homogeneity of the variances with the Bartlett test.
Test Performance Study: Blind Testing of DNA-Aliquot-Samples All the participants laboratories were able to submit the results for a total of 20 data sets and 320 results from blind test items. Specifically, in all three assays-EvaGreen, SYBR Green, and Taqman-all Das which were N + were always correctly detected, at both the technical replicate and the Das level, namely only TP and no FN were obtained. Thus, DSE was 100% at the laboratory and the assay level. A quantitative view of fluorescent detection signals (Ct) obtained with positive Das is depicted in Appendix A, Figure  A1. The Taqman assay performed by PL C with the Rotor-Gene TM 6000 thermocycler clearly revealed that this system ensured the lowest Ct while keeping the highest DSP. Similarly, all detections performed by the laboratories on N -Das showed best fit except in the following cases: (i) six FP technical replications referring to two Das of the same experiment performed with SYBR Green assay; and (ii) two FP technical replications referring to two Das of the same experiment and performed with a Taqman assay (Table  6 ).
Regarding detection of blind samples, all three assays obtained either very high or best fit CO, as derived from the (nearly) best fit performance parameters obtained by each PL. In practice, we analyzed data starting either from results on technical replicates or from those at the Das level (i. e. , those derived from in-agreement results from at least two replicates out of three). While the former is more stringent, the latter can mask any inconsistent results within the technical replicates, i. e. , if one replicate out of the three is an FP or an FN. In Table  6 , we present results obtained with the first method while in Spreadsheet S1 both are presented. With regard to N -samples (n = 360 at the technical replicate level), a total of eight FP (2. 2% of all N -) were detected. Six of these were detected in SYBR green by a single PL, which had a substantial impact on the performance of the method by this PL.
Acknowledgments: The test performance study was developed in kind within Euphresco project 2015-A-118 "Identification and early detection of Cryphonectria parasitica and Ceratocystis platani occurring on trees in Europe, CERACRY". We wish to thank the coordinator of the project, Gerard Van Leeuwen, for creating the necessary international network to accomplish the project. We also thank Miriam Levenson for English language reviewing.
Both groups didn't show any extension of flagella. Moreover, molecular identification was performed as different microalgae species can have similar morphologies, plus same strains can present different shapes in the different growth stage  [42]. Full obtained sequences were blasted into the NCBI BLAST software, and the results were compared with the gene bank. Table  1  gives an overview of the strains, their identified genera according to 16S rDNA analysis, accession numbers as well as their sampling location (Habitat, GPS coordinates). The comparison of the 16S rDNA sequences of the four axenic isolates together with the morphological studies confirmed the presence of 4 different genera. From the alignment of the sequences, and the resulting phylogenetic tree (Fig. 2 ), we concluded that QUCCCM 34 and QUCCCM 54 showed high similarities to the genus Chroococcidiopsis and Pleurocapsa, respectively, whilst the other strains QUCCCM 77 and QUCCCM129 displayed an homology with the existing sequences published in the GenBank for Euhalothece and Cyanobacterium respectively.
Habitat nature GPS (N, E) QUCCCM 34 Chroococcidiopsis GenBank: MZ817054 Marine Seawater N 25. 59. 183, E 51. 0101. 418 QUCCCM 54 Pleurocapsa GenBank: MZ817055 Marine Soil N 25 59 125, E 051 01 617 QUCCCM 77 Euhalothece GenBank: MZ817056 Marine Clay N 25 43 894, E 051 33 336 QUCCCM 129 Cyanobacterium GenBank:.
Statistical Analyses Statistical analyses were performed using R version 4. 0. 3 (13). Differences in percentages of protection were analyzed using the Fisher's exact test followed by pair-wise comparisons using the "fisher. multcomp" function from RVAideMemoire package version 0. 9-79  (14). All other quantitative parameters were analyzed using Kruskal-Wallis test followed by Fisher's least significant difference test with Holm adjustment method for multiple comparisons using the "kruskal" function from the package "Agricolae" version 1. 3-2  (15).
To check the lack of interference of the anti-coagulant, HI testing was performed again after adding CaCl 2 to the plasmas to induce clotting. No difference in HI titers was observed after this treatment (data not shown). At both time-points, blood leukocyte counts revealed significant differences in B cell concentrations between virus strains. At 15 days of age, prior to NDV vaccination, both control groups exhibited concentrations close to 1,000 B cells/µL (Figure  3D , left panel). For I1 vaccinated birds, the median concentration significantly dropped to 143 B cells/µL. For I2 vaccinated birds, the drop was even more pronounced (median of 42 cells/µL, p < 0. 05). For I+1 and I+3 vaccinated birds, B cell counts were statistically lower than in I vaccine groups, with medians below the detection limit of 8 cells/µL.
2015; Martin et al. 2016; Nagy et al. 2017; Miyauchi et al. 2020; Ruiz-Dueñas et al. 2021). Despite the undoubted contribution of class II peroxidases to lignin decomposition, their exclusive role in this process is debated. Indeed, substantial lignin degradation seemingly occurs in the absence of organisms producing these enzymes, as in the case of the termite gut  (Li et al. 2017). On the other hand, other microbial enzymes have been shown to be able to cleave phenolic and/or nonphenolic bonds of artificial lignin substrates (e. g. β-O-4dimers = adlerol) and/or oxidize Mn 2+ to Mn 3+ and therefore behave similarly to either class II LiP/VPs or MnPs  (Fernández-Fueyo et al. 2015). One such enzyme family is that of "dye-decolorizing peroxidase" (DyP) (pfam no. PF04261, E. C. 1. 11. 1. 19 ) (Celis and Dubois 2015).
2017). In the absence of forward genetic data and in the presence of uncertain biochemical activities, the objective of the present study has been to further evaluate the potential biological functions of fungal DyPs, including their putative contribution to lignin decomposition using phylogenetic and correlative approaches. Two strategies were followed. One was to establish a comprehensive view on the evolution of the DyP (sub)family in the fungal kingdom, using available genomic data, and to confront these data to our current knowledge on DyPs' catalytic mechanisms and evolution of trophic modes in fungi. A second strategy was to isolate new fungal DyP genes expressed in different environments (soils and decomposing wood) in an attempt to characterize potentially divergent DyP sequences distantly related to sequences present in public databases.
Species and sequence datasets Publicly available DyP sequences were extracted from Gen-Bank and the JGI Mycocosm portal (https:// genome. jgi. doe. gov/ progr ams/ fungi/ index. jsf;  Grigoriev et al. 2014 ) databases as well as from our own unpublished whole-genome sequences. DyP protein sequences were identified in public databases using BlastP searches  (Altschul et al. 1990 ) using as queries the protein sequences of two biochemically characterized DyPs from Auricularia auricula-judae (accession No. JQ650250) and Bjerkandera adusta (CDN40127. 1). A threshold E-value of 10 -5 was retained for the inclusion of the sequences in the dataset. DyP sequences extraction from the unpublished genomes was performed using HMMER (http:// hmmer. org/). A HMMER profile was first created starting from a Clustal Omega alignment  (Sievers and Higgins 2014)  of 150 DyP sequences from the public databases.
2016 )), was used to find the best substitution model (LG + R). IQ-TREE Web Server was also used to perform a maximum likelihood phylogenetic analysis  (Nguyen et al. 2015). One thousand bootstrap replicates were performed to assess tree topology. A fungal species phylogeny that encompassed all examined fully-sequenced basidiomycetous species was obtained by modifying a publicly available phylogenetic tree (#Tr106951,  Zhao et al. 2017) , built using an alignment of six genes, downloaded from TreeBase (www. treeb ase. org/). Species whose genomes have not been sequenced were removed from the original six-genes alignment while the corresponding six genes from newly sequenced species were added to it to construct a new species tree following the approach presented in  Zhao et al. (2017). Species taxonomy was assigned using the MycoBank database (www.
mycob ank. org). Both gene and species trees were edited using the online software iTOL (https:// itol. embl. de;  (Letunic and Bork 2016) ). We inferred gene loss and duplication along the species phylogenetic tree using a comparative genomics method with NOTUNG 2. 9 as described in the original article of  Chen et al. (2000). To visualize similarities between fungal DyP protein sequences, a sequence similarity network (SSN) was computed using the EFI-Enzyme Similarity Tool (https:// efi. igb. illin ois. edu/ efi-est/;  (Gerlt et al. 2015) ) starting from the complete set of DyP protein sequences. The lowest pairwise alignment score limit for the output file was set to 66. The full-network output file was visualized with Cytoscape 3. 5. 1  (Shannon et al. 2003). The network was represented with an "organic" layout, and only edges with a pairwise alignment score above 110 were visualized.
bioin forma tics. org/ sms2/;  (Stothard 2000) ). Principal component analysis (PCA) was performed to cluster DyP protein sequences according to their protein features in the R environment using the R 3. 6. 3 (R Core Team 2019). Principal components were extracted with the prcomp function of the R base package and visualized with the ggbiplot package v0. 55. Kmeans analysis was performed with the kmeans function of the R base package. Variable's (i. e. protein features) contribution to principal components (PC) was determined using the fviz_contrib function from factoextra v1. 0. 6 R package. Statistical differences were tested using the nonparametric Kruskal-Wallis test and Dunn's post hoc tests with dunn. test package v1. 3. 4  (Dinno 2015). DyP abundance comparisons among different fungal guilds were performed with the Yates-corrected Chi-square test.
Probes design for gene capture by hybridization From 1267 publicly available fungal DyP DNA-coding sequences, we designed 69 (70 bp long) degenerated probes (Supplemental Table  S1 ) with the KASpOD software (https://g2im. u-clermont1. fr/kaspod/index. php, (Parisot et al. 2012) ). In silico probe coverage evaluation, on the 1267 fungal DyP sequences detects 94. 2% of the ascomycetous sequences and 81. 5% of the basidiomycetous ones (with four allowed mismatches). Oligonucleotides corresponding to probe sequences were synthesized with two flanking adaptor sequences for their PCR amplification and conversion to biotinylated RNA probes using the T7 RNA polymerase, as described in  Bragalini et al. (2014).
e -05 and a minimal identity of 50%). Matching cDNA sequences were translated using the Expasy  (Gasteiger 2003 ) translate tool and further analyzed for the presence of the DyP peroxidase domain using ScanProSite and the Prosite database  (de Castro et al. 2006; Sigrist et al. 2012). Identified DyP proteins were clustered using a 90% identity threshold using CD-HIT v4. 7  (Fu et al. 2012). Sequences are available on NCBI with the accession numbers OM674899-OM674912.
3 ). The first two axes of the PCA altogether explained 52% of the variation in the dataset. Clade VI-2 was particularly well separated from all other clades with significantly lower average pI values and significantly higher GRAVY indices (Fig. 2 ), as well as the number of putative N-glycosylation sites per polypeptide (Dunn's post hoc test, p < 0. 05) (Supplemental Fig. S1 ). Furthermore, 69% of the proteins affiliated with clade VI-2 also possessed a predicted N-terminal signal peptide for secretion (Fig. 2 ). Outside of clade VI-2, only four proteins from Puccinia spp. , belonging to clade II, also processed a putative signal peptide. Interestingly, 13 of the 16 purified and characterized fungal DyPs identified in the literature belong to clade VI-2; the three others were affiliated with clade VI-1.
We predicted the number of gene loss or gene gain events, using the NOTUNG software, separately for the most sequence-rich clades VI-1 and VI-2. Diversification at the level of the tree leaves (species-level) of clades VI-1 and VI-2 was not systematically coordinated between DyP clades (Fig. 4 ). To further evaluate the potential contribution of agaricomycetous DyP genes to organic matter conversion, and more specifically, to lignin degradation, we compared the prevalence of the different DyP clades in Agaricomycotina with respect to their trophic modes. The first observation from the cluster analysis is that clade VI-2 (putatively secreted extracellular DyPs) encompassed sequences exclusively from WR and OS species and none from BR or EM ones (Fig. 1 ). This distribution is specific to clade VI-2.
Diversity of fungal DyPs expressed in the environment A set of 69 biotinylated degenerated RNA probes, whose sequences spanned the known phylogenetic diversity of fungal DyP sequences, was designed and used to capture homologous cDNAs synthesized from mRNA directly extracted from different environmental matrices (decaying wood, forest and grassland leaf-litter, and soils). DNA recovered after two successive rounds of capture (enrichment) was randomly sequenced, and the reads were successfully assembled to recover 14 full-length or nearly full-length DyP cDNAs. All of these environmental sequences encode different DyP not present in the database. They were clearly affiliated with either clade VI-2 (5 sequences) or clade VI-1 (9 sequences) (Fig. 2 ). In clade VI-1, three environmental DyP sequences were related to reference sequences from Ascomycota and six to sequences from Basidiomycota.
Clades VI-1 and VI-2 sequences represent altogether about two-thirds of all DyP present in databases. The exclusive presence of clades VI-1 or VI-2 DyPs among environmental sequences suggests that fungal species harboring DyPs belonging to these clades are either overrepresented and/or that the corresponding genes are overexpressed in the studied environments. These observations are comforted by the data of  Kellner et al. (2014) , who used PCR to obtain partial DyP sequences from different forest soils. Affiliation of these 61 partial sequences to the different clades showed that 81% originated from clades VI-1 (42%) and VI-2 (24%), while a minority of the sequences came from clades I (4 sequences), III (6), and V(1). The absence of environmental sequences that define novel DyP clades may signify that fungal genome sequencing may have already captured the entire phylogenetic diversity of the DyP D subfamily or those additional clades are too divergent to be captured by the designed probes or too rare to be easily identified using this approach.
Acknowledgements We would like to acknowledge  Dr. Francesco Venice  ( University of Turin ) for the suggestions in bioinformatics. The study was performed in the framework of the  PeroxiDiv  project co-funded by the  ANR (Agence Nationale de la Recherche, France ;  ANR-RF-2015-01 ) and the  DFG (Deutsche Forschungsgemeinschaft, Germany). Martino Adamo  was supported by a grant from the  Italian Ministry of Education, University and Research (MIUR)  and the  CMIRA (Coopération et mobilité internationales Rhône-Alpes) program of region Région Auvergne-Rhône-Alpes. We are grateful to the  Mésocentre Clermont Auvergne University and AuBi  platform for providing computing resources.
Data collection The data were collected between March and October 2021 from two sources: a literature review and interviews with surveillance stakeholders. The aim of the literature review was to: (i) analyse the institutional context and the scientific and technical framework in which anthrax surveillance is carried out at the international, regional and national (central and local) levels; (ii) describe the organization and functioning of the surveillance programmes in place, including the roles and missions of the different categories of actor; and (iii) identify the existing collaboration between these different programmes. The documents were selected by consulting the websites of the various bodies involved in the epidemiological surveillance of zoonoses at international (OIE, FAO, and WHO) and regional levels (RAHC and WAHO) or by contacting them directly.
Data analysis We first conducted a qualitative descriptive analysis of the data collected from literature review and interviews to characterize: (i) the organization of the anthrax surveillance system in Burkina Faso in terms of the programmes included and the actors involved; and (ii) the collaboration in place between the different sectors. The characteristics of these programmes and actors were identified against a list of organizational and functional attributes identified from similar studies  [12]  or inductively identified during the study (Table  1  and Supplementary file 1). Collaboration was identified and analysed at both governance and operational level, following the conceptual framework defined by Bordier et al. , 2019  [13]. In a second step, we conducted a thematic analysis of the informants' discourse in order to identify what represents an obstacle or, conversely, a lever for a more integrated approach to anthrax surveillance in Burkina Faso.