dataesr/scientific-paragraphs-categorization huggingface dataset:
Setting, population and study design The study took place in Kabak (Forecariah Prefecture, Guinea) during the second round of the mass vaccination campaign carried out by the MHPH/MSF in June 2012. The study population corresponded to the population targeted by the vaccination campaign (all residents of Kabak aged one year and above). Individuals were included if they were vaccinated and accepted to participate. They were excluded if they had watery diarrhea on inclusion (to exclude potential cholera cases) and/or a high probability of not being present for all the follow-up visits. The cohort of vaccinated participants meeting study criteria was followed-up prospectively. We estimated that 96 individuals were needed to achieve a minimum precision of 10% around a proportion of 50% of positive RDT, as there were no data on the prevalence of positive tests in the vaccinated population.
Data analysis Qualitative variables were described through their frequency and percentages. Continuous variables were described through their mean, median, standard deviation (SD) and percentiles (P 25 and P 75 ). We calculated the proportion of positive results for O1 or O139 for each day of follow-up including in the numerator the number of positive results and in the denominator the sum of the total number of tests performed and the number of cases for whom follow-up was stopped after obtaining two consecutive negative results. Missing data (absent or no stool sample) were excluded from this calculation. The 95% exact confidence intervals (95%CI) of the proportion estimate were calculated. To estimate the mean time to obtain a negative RDT result after vaccination (time to become negative) we counted the number of days needed to obtain a first negative result in the group of people who obtained previously a positive result for O1 or O139 after vaccination.
A 300 mL aliquot of filtrated endosperm solution, 200 mL of filtrated leaf solution of an internal standard and 400 mL of isolation buffer supplemented with propidium iodide (50 mg mL 21 ) and RNase A (50 mg mL 21 ) were then mixed in a tube. The suspensions were incubated for approx. 5 min at room temperature. After incubation, each sample was run on a flow cytometer. DNA quantities were measured using a FACScalibur laser flow cytometer (Beckton Dickinson, USA) with Cellquest Software. The choice of the internal reference was made according to the expected offspring or endosperm ploidy. To detect non-expected seedlings (triploid in a diploid population or tetraploid in a triploid population), an appropriate internal reference [diploid (639a) or triploid (760a), respectively] was used and the results were interpreted as follows.
EXPERIMENTAL PROCEDURES Human T Cell Isolation-Peripheral blood mononuclear cells (PBMC) were prepared by lymphosep-lymphozyte separation media (BioWest, Nuaille, France) gradient centrifugation. CD25 high cells were isolated using a CD25 MicoBeads II kit for humans (Miltenyi Biotec, Bergisch Gladbach, Germany) and an autoMACS® separator. Half of the recommended beads were used to select only the CD25 high cell population. The CD25 high cells were then labeled with anti-CD4-PerCP-Cy5. 5 (BD Pharmingen, Mountain View, CA), anti-CD127-PE (BD Pharmingen), and anti-CD25-Alexa Fluor 647 (anti-CD25 from Immunotech, Marseille, France) coupled to the fluorochrome using a molecular probe kit from Invitrogen) and sorted using a BD FACSAria TM Flow Cytometer cell sorter and with FACSDiva TM software (BD Pharmingen).
The negative fraction containing the CD25 low cells was then labeled with anti-CD4-PerCP-Cy5. 5 (BD Pharmingen) and anti-CD25-Alexa Fluor 647 (anti-CD25 from Immunotech coupled to the fluorochrome using a molecular probe kit from Invitrogen) and sorted using the BD FACSAria TM Flow Cytometer cell sorter with FACSDiva TM software. Sort gates for CD4 ϩ CD25 Ϫ and CD4 ϩ CD25 ϩ CD127 Ϫ human T cells are shown in Fig. 1A. The purity was systematically Ͼ97% for regulatory CD4 ϩ CD25 ϩ CD127 Ϫ T cells and 96% for CD4 ϩ CD25 Ϫ T cells. Mouse CD4 ϩ CD25 Ϫ and CD4 ϩ CD25 ϩ T Cell Isolation-Splenocytes were prepared by using collagenase D and EDTA on a C57Bl6 mouse spleen. CD4ϩ T cells were isolated using the biotinylated mouse CD4 T lymphocyte enrichment mixture (BD Biosciences) according to the manufacturer's instructions.
CD4 ϩ T cells were then labeled with anti-CD4-FITC and anti-CD25-PE (BD Biosciences) and sorted using the BD FACSAria TM Flow Cytometer cell sorter with BD FACSDiva TM software. Sort gates for CD4 ϩ CD25 Ϫ and CD4 ϩ CD25 high mouse T cells are shown in Fig. 1B. Purity was systematically Ͼ93% for CD4 ϩ CD25 high T cells and 98% for CD4 ϩ CD25 Ϫ T cells. Mouse CD4 ϩ T Cell Isolation-Splenocytes were prepared from C57Bl6 mice. Untouched CD4 ϩ T cells were isolated using the CD4 ϩ T cell isolation kit II, (Miltenyi Biotec, Bergisch Gladbach, Germany) and Automacs pro separator (Miltenyi Biotec, Bergisch Gladbach, Germany). Human Treg Activation-1 ϫ 10 5 Tregs (CD4 ϩ CD25 ϩ CD127 Ϫ ) were cultured in 100 l of RPMI 1640 medium supplemented with 10% AB serum, 2 mM L-glutamine, penicillin, and streptomycin in each well of a round-bottomed 96-well tissue culture plate.
Moreover, a significant correlation was observed between TRIB1 and Foxp3 mRNA expression in human regulatory T cells (r ϭ 1. 0; p ϭ 0,0004; Fig. 2A ) but not in CD4 ϩ CD25 Ϫ T cells, suggesting a strong link between the regulation of TRIB1 and Foxp3 expression in the Tregs. Moreover, these results were confirmed in C57Bl6 mice where, again, an increase in TRIB1 and Foxp3 levels was observed in CD4 ϩ CD25 ϩ Tregs compared with CD4 ϩ CD25 Ϫ cells (p Ͻ 0. 05 for TRIB1 and p Ͻ 0. 01 for Foxp3) (Figs. 1  and 2B ). We also analyzed the protein level of TRIB1 and Foxp3 in Tregs by Western blot and unlike the mRNA level in Tregs, we observed no correlation between the protein level (data not shown).
Tribbles-1 Interacts with Foxp3 in Regulatory T Cells ciency of the anti-TRIB1 antibody was also tested in a Western blot using extract from transfected cells with a plasmid containing the TRIB1 gene followed by the GFP gene or with a plasmid containing the GFP gene alone (Fig. 5B ). TRIB1 Blocks CD4 ϩ T Cell Proliferation-After infection of mouse CD4ϩ T cells, analysis of viability showed no difference between the cells infected with the control lentivirus and with the TRIB1 lentivirus (data not shown). The percentage of infected cells determined by FACS analysis of GFP fluorescence was similar between the negative control lentivirus pULTRA and the TRIB1 lentivirus. Two different MOIs were tested, and there were no significant differences between an MOI of 10 or 50. At an MOI of 10, 6. 3% of cells were GFP ϩ with the negative control and 9.
This interaction was no longer significant when TRIB1 was deleted of its N terminus domain. Such a nuclear interaction fits well with the fact that the N terminus domain of TRIB1 is particularly important for transporting TRIB1 to the nucleus  (3, 43)  and the fact that Foxp3 is principally expressed in the nucleus  (17). This interaction was confirmed by fluorescent microscopy subsequent to the PCA, which again clearly showed the interaction between TRIB1 and Foxp3 in the nucleus. By contrast, when TRIB1 was deleted of its C terminus domain, no difference was observed as compared with the full TRIB1. These data indicate that the C terminus domain is not involved in the interaction of TRIB1 with Foxp3. As the PCA experiment consists in transfecting cell lines with plasmid, we wanted to confirm the TRIB1 and Foxp3 interaction in more physiological conditions.
Isolates and dnA extractions A total of 96 strains corresponding to 85 species were grown on 2 % potato dextrose agar (PDA) plates incubated at 25 ºC. Genomic DNA was extracted from mycelium using the PrepMan TM Ultra protocol (Applied Biosystems). Sequences from additional species were retrieved from GenBank. A total of 140 taxa were included in the ingroup and six taxa in the outgroup (see Table  1  for details).
data analyses Sequences were aligned using MAFFT v. 6 online  (Katoh & Toh 2008 ) and refined visually. In order to retrieve the genetic information from indels, GapCoder  (Young & Healy 2003)  was used to code the gaps contained in the EF1 and the mSSU alignments. Analyses were run both with gaps coded and not coded. The datasets were combined because this is believed to increase phylogenetic accuracy  (Bull et al. 1993 , Cunningham 1997). The six phylogenies resulting from the six data sets were first inspected visually to check whether there were conflicts between the histories of the genes that would preclude the combination of data. Additionally, the Incongruence Length Difference (ILD) test  (Farris et al. 1995a, b)  also known as the partition homogeneity test was run using PAUP v. 4.
0b10  (Swofford 2003). MrAIC  (Nylander 2004 ) was used to determine the best fit model of nucleotide substitutions for each gene. Phylogenetic relationships of the samples were investigated using both Maximum Likelihood (ML) and Bayesian Inference (BI). The ML analysis was conducted using PhyML online  (Guindon et al. 2005). The reliability of each node was assessed using the bootstrap  (Felsenstein 1985)  resampling procedure (100 replicates). The BI was conducted using the software BeaSt v. 1. 7. 4  (Drummond et al. 2012). The phylogenetic relationships were estimated by running 10 000 000 generations and sampling every 100 th generation. Bayes Factors were computed to choose between the different options available in BeaSt (four clock models: strict clock, exponential or lognormal uncorrelated relaxed clocks, and random local clock and two tree priors: Yule process or Birth-Death speciation model).
Phylogenetic relationships The alignment included a total of 4498 bp from six gene portions. The results from the ILD test were not significant and supported a decision to combine the 6 gene datasets. The number of polymorphic and parsimony informative sites ranged from 108 for the SSU, 165 for the mtSSU, 170 for the LSU, 222 for BT, 335 for the EF1 to 361 for the ITS. The Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic reconstructions were similar, and the BI tree is shown on Fig. 1. Species residing in the genera Aplosporella and Bagnisiella (in one clade), Melanops, Saccharata and Kellermania had a basal position on the tree with respect to other genera in the Botryosphaeriales. The remaining genera in the Botryosphaeriales clustered together with a bootstrap support value of 94 % and Posterior Probability (PP) value of 1.
AcKnoWledGeMentS We thank members of the  Tree Protection Co-operative Programme (TPCP) , the  DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) ,  THRIP  (project no. TP2009061100011 ) and the  University of Pretoria ,  South Africa  for financial support. We also thank  Ms Katrin Fitza  and  Ms Fahimeh Jami  for assistance with submissions of sequences.
lepbarcoding. org for details). DNA extraction, PCR amplification and sequencing follow the protocols described in  Vaglia et al. (2008). The taxa included in this study are listed in Table  1. Unfortunately, recently collected material of L. andensis was not available for sequencing. A set of twenty-four specimens of five species was sequenced for the 658 barcode base pairs fragment. Sequences were analyzed using maximum likelihood (ML) and maximum parsimony (MP) methods. MP analyses were carried out with MEGA 5 software  (Tamura et al. 2011). Redescription. Head -Antenna bipectinate, brown with yellow base and brown cilia. Frons light yellowish white, separated at base of antenna by transverse black line. Vertex yellowish white with a prominent black central spot. Palpi erect, yellow with second joint black at sides and third black and very short.
Acknowledgments The authors thank the followings curators for access to specimens in their care:  M. Honey  ( BMNH ),  J. Minet  ( MNHN ) and  I. A. Chacón  (InBio). Thanks also to  B. Espinoza  (InBio) and  J. Barbut  ( MNHN ) for their valued and generous assistance. DNA barcodes were generated at the  Canadian Centre  for DNA barcoding hosted by the  Biodiversity Institute of Ontario, University of Guelph (Canada) , through funding by  NSERC  and by  Genome Canada  to the  International Barcode of Life  (iBOL) project. The second author thanks  J. Barbut  and  A. Levêque  for their help in the organization of the expeditions in Ecuador,  Bolivia, Venezuela, Peru  and  Costa Rica. He  thanks too the  Société Entomologique de France  for its contribution to the entomological project  in Bolivia (Bourse Germaine Cousin 2007 ), the  Société d'Histoire Naturelle Alcide d'Orbigny  for its contribution to the entomological project in Venezuela and Perou.
2008; Raudaskoski & Kothe 2010). During the annotation work, the software Geneious Pro 5. 4. 6 (Biomatter, Auckland, New Zealand) was used. Primer design for mating type proxies Adjacent regions to the MAT genes were selected as proxies to represent the mating types. Primers from MAT A and MAT B were designed based on the annotated genomes using the Primer3 software available as a plugin in Geneious Pro 5. 4. 6. In addition to the genome sequences of the S7. 9 and S7. 3 strains  (Eastwood et al. 2011) , unpublished reads from three Illumina sequenced 108-bp paired-end libraries of three other S. lacrymans strains were available. These reads were searched for the suggested primer sites, to ensure that two alleles could be identified for each strain. A marker for the MAT A region was located in the 39UTR of the MAT A HD2 transcription factor (MATA11_F 59-GCC TCT TGG TTG TTT TTA TTG 39 and MATA7_R 59-GCT GTG AGT GCT AGT GCT ACA-39; Figure  1A ).
The PCR-amplified DNA products from dikaryotic strains were purified using the QIAquick PCR purification kit (QIAGEN) and were cloned into TOPO-TA vector (Invitrogen) following manufacturer's instructions. For each PCR product, eight clones were directly amplified with the T7/M13R primers. All PCR products were purified for sequencing using ExoSAP-IT and run on a 3730 XL DNA analyzer (Life Technologies, Foster City, CA) at the ABI-lab at CEES, University of Oslo. The sequences were trimmed and aligned in Geneious Pro 5. 6. 4. Parsimony trees were made in TNT  (Goloboff et al. 2008) , and strict consensus trees are presented as simplified unrooted cladograms. The sequences from the MAT B linked marker have been accessioned in GenBank with the following accession no. : KC182670-KC182721. The sequences from the MAT A linked marker have been deposited in the Dryad repository: http://dx.
One of these genes (PP8) had a significant sequence identity to a gypsy element when using the tBLASTx algorithm to search the Repbase (a database of transposable elements;  Jurka et al. 2005). Gypsy elements are longterminal repeats retrotransposons, found in most fungal species  (Muszewska et al. 2011). Using the element to search the unmasked S. lacrymans genome, we found that the inserted region has several inverted repeats and that dispersed repetitive elements are found throughout the genome. This finding suggests that at least a part of the inserted region is a retrotransposon. The other putative genes (PP6 and PP7) in the retrotransposon are predicted proteins of unknown function, where homologous sequences of PP6 are found in many other Agaricomycetes. Serpula lacrymans lacks the gene YPL109 (a kinase of unknown function), which is present in all other species in the synteny map (Figure  1A ).
ARE β-GLUCANASE INVOLVED IN THE CELL WALL MODIFICATION? β-1,3-Glucan hydrolyzing enzymes can be divided into exo-β-1,3-glucanases and endo-β-1,3-glucanases. Endo-β-1,3-glucanase activities cleave inside a glucan chain in a more or less random fashion, while the exo-β-1,3-glucanase activities release glucose residues from the non-reducing end (Figure  1 ). Theoretically, the cleavage of long chains of β-1,3-glucan should cause a softening of the cell wall. Therefore, we expect this type of enzyme to be involved in cell wall remodeling that occur during the swelling and germination of conidia or the branching of hyphae. In order to identify all the putative β-1,3-glucanases in the A. fumigatus genome sequenced strain Af293  (Nierman et al. , 2005) , we used the classification of the Carbohydrates enZYmes database [CAZy database (http://www.
cazy. org/)]. This database describes the families of enzymes with structurally related catalytic and carbohydrate binding modules (CBM) that degrade, modify or create glycosidic bonds. In this classification, we selected and further investigated the families which could contain putative β-1,3-glucanases and each potential endo/exo β-1,3-glucanase identified in the A. fumigatus genome was used as a query for BLAST searches to identify possible homologs using cadre genome (http://www. cadre-genomes. org. uk/Aspergillus_fumigatus). This search has led to the identification of twenty nine potential exo-β-1,3-glucanases and endo-β-1,3-glucanases that belong to the CAZy GH families 3, 5, 16, 55, and 81 (Table  1 ). The expression of these different genes in mycelial growth either in liquid or aerial conditions  (Gibbons et al.
EXO-β-1,3-GLUCANASE FAMILIES In the CAZy database, family GH5 represent a group of hydrolases with different substrate specificities such as for example exo β-1,3-glucanases, endo β-1,4-glucanases, endo β-1,6-glucanases. Four proteins belonging to GH5 family in A. fumigatus have been identified in the genome (AfExg1p = AFUA_1G03600, AfExg2p = AFUA_6G09250, AfExg3p = AFUA_7G05610, and AfExg4p = AFUA_2G09350). The characteristics of these proteins are presented in Figure  2A  and Table  1. AfExg1p and AfExg4p have a signal peptide in contrast to the others AfExg2p and AfExg3p. The phylogenetic tree of GH5 proteins is presented in Figure  2B. Recently the respective orthologs in S. pombe have been described  (Duenas-Santero et al. , 2010). SpExg1p is secreted, SpExg2p is bound to the membrane via a GPI anchor and SpExg3p is a cytoplasmic protein.
cerevisiae has been observed  (Larriba et al. , 1995). Moreover, the triple ssg1 exg1 exg2 mutants behave like the simple ssg1 mutant. In S. pombe, the phenotype of the triple exg mutants behave like the parental strain  (Duenas-Santero et al. , 2010). None of the EXG1-4 gene has been deleted or otherwise characterized in A. fumigatus. In the CAZy database, family GH55 includes exo-β-1,3-glucanases (EC 3. 2. 1. 58) and endo-β-1,3-glucanases (EC 3. 2. 1. 39). In A. fumigatus, six proteins belonging to this family are present: AfExg5p = AFUA_6G11980, AfExg6p = AFUA_6G13270, AfExg7p = AFUA_3G07520, AfExg8p = AFUA_1G14450, AfExg9p = AFUA_2G00430, AfExg10 = AFUA_4G03350, (Table  1 ). It has been shown that AfEXG6 encodes a 82 kDa exo β-1,3glucanase enzyme named ExoGI which hydrolyze exclusively a β-1,3-glucan chain with a minimal substrate size of four glucose residues  (Fontaine et al.
OTHERS EXO-β-GLUCANASES In the CAZy database, family GH3 contains exo-hydrolases able to degrade different substrates. They are classified as β-glucosidase (EC 3. 2. 1. 21); xylan 1,4-β-xylosidase (EC 3. 2. 1. 37); β-N-acetylhexosaminidase (EC 3. 2. 1. 52); glucan 1,3-β-glucosidase (EC 3. 2. 1. 58); glucan 1,4-β-glucosidase (EC 3. 2. 1. 74); exo-1,3-1,4-glucanase (EC 3. 2. 1. -); α-Larabinofuranosidase (EC 3. 2. 1. 55). Ten members of GH3 are present in the genome of A. fumigatus (Table  1 ): AFUA_1G05770, AFUA_7G06140, AFUA_7G00240, AFUA_1G17410, AFUA_ 8G02100, AFUA_6G14490, AFUA_5G07190, AFUA_6G11910, AFUA_6G08700 and AFUA_6G03570. The characteristics of the proteins encoded by these genes are summarized in Figure  4A  and Table  1. Half of the proteins are secreted. All the proteins of A.
BRANCHING ENZYME A glucanosyltransferase activity encoded by the BGT1 gene has been identified biochemically in the A. fumigatus cell wall autolysate, Bgt1p belongs to the Carbohydrate-Active Enzyme (CAZy) database Glycosyl hydrolase GH17 (http://www. cazy. org/) (Table  1 ). Bgt1p cleaves a laminaribiose from the reducing end of linear β-(1,3)-glucans and transfers the remaining glucan to the end of another β-1,3-glucan acceptor with a β-(1,6)linkage  (Mouyna et al. , 1998). Such activity had been described originally in S. cerevisiae  (Klebl and Tanner, 1989). We recently characterized Bgt2p in A. fumigatus. This protein presents homology with Bgt1p  (Gastebois et al. , 2010a). Using a recombinant protein produced in P. pastoris, we showed that the enzymatic activity of Bgt2p is a new branching activity, able to cleave two residues of a β-1,3-glucan chain and transfer them to the inside of another chain of β-1,3-glucan with β-1,6-linkage.
ELONGATION ENZYME Elongation of β-1,3-glucan is performed through the action of a β-1,3-glucanosyltransferase, which were originally discovered in A. fumigatus. This enzyme Gel1p splits a β-1,3-glucan molecule internally and transfers the newly generated reducing end to the non-reducing end of another β-1,3-glucan molecule, resulting in the elongation of the glucan chain  (Hartland et al. , 1996). Gel1p belongs to a family of seven members specifically recognized as the unique GH72 family in the Carbohydrate-Active Enzyme (CAZy) database (http://www. cazy. org/) (Mouyna et al. , 2000a)  (Table  1 ). This enzyme activity has confirmed among paralogs of Gelp in A. fumigatus  (Mouyna et al. , 2000b; Gastebois et al. , 2010b)  and orthologs in other species like the GAS family in S. cerevisiae  (Vai et al.
in the CAZy database is quite wide since members of this GH family can act as xyloglucan xyloglucosyltransferases (EC 2. 4. 1. 207), keratan-sulfate endo-1,4-β-galactosidases (EC 3. 2. 1. 103), endo-1,3-β-glucanase (EC 3. 2. 1. 39), endo-1,3(4)- β-glucanase (EC 3. 2. 1. 6); licheninase (EC 3. 2. 1. 73), β-agarase (EC 3. 2. 1. 81), κ-carrageenase (EC 3. 2. 1. 83), or xyloglu- canase (EC 3. 2. 1. 151). The GH16 superfamily has been divided into nine sub-families based on a phylogenetic analysis of conserved domains of members of this super- family (cd00413; http://www. ncbi. nlm. nih. gov/Structure/ cdd/cddsrv. cgi?uid=29534):.
Image Analysis Using the procedure described by  Bax et al. (2012) , gels were scanned with an Image Scanner III using Im-ageMaster Platinum software (GE Healthcare, Uppsala, Sweden). Each liver sample was processed individually, and the value of main bands was calculated by using Image Master Platinum application. Each gel also included a pool of all the samples run and was used as an internal standard. Protease activity was considered as the combination of computerized measurements of both intensity and volume of main bands for each sample. Relative protease activity was estimated as protease activity/pool activity within each gel.
Cathepsin Gelatin Zymography Three major proteolytic bands were detected for the cathepsin proteolytic assay. Unlike MMP-2 protease, these activities of cathepsin isoforms were not affected by the addition of DTT or EDTA, but were inhibited in the presence of PMSF (data not shown). Molecu- 3 D = effect of diet (NFF vs. FF). B = effect of breed (Muscovy vs. Pekin). D × B = effect of the interaction between the diet and the breed. lar weights of the 3 detected acidic proteases ranged from ~37 to ~24 kDa (Figure  1c ). Unfortunately, no specific antibodies directed against cathepsin isoforms from ducks are commercially available to give a better identification of detected isoforms in the present study. Moreover, an identification test of those cathepsins using mass spectrometry analysis failed to give reliable results, probably because of the nonavailability of the full sequence of ducks' genome.