dataesr/scientific-paragraphs-categorization huggingface dataset:
Since PilQ is essential for type IV pilus secretion across outer membrane  [63] [64] [65] , it is tempting to speculate that the T4P of Xff 4834-R is unfunctional. However, the truncated PilQ of Xff 4834-R still contained a secretin domain (IPR011662) according to Interproscan software, thus suggesting that PilQ could still be functional in Xff 4834-R. This is in agreement with our previous study, which show that T4P should be functional in Xff 4834-R  [16]. Indeed, a mutant deleted in pilA displayed altered adhesion capacities on bean seeds relative to wild-type 4834-R, and a decreased aggressiveness. Therefore either the frameshift observed in pilQ has no major consequences on the protein function, or alternative secretins such as XpsD and or XcsD are recruited. Bacterial attachment, the first step of biofilm formation, depends mainly on adhesion factors such as T4P, Type 1 pilus, and non-fimbrial adhesins.
Xff 4834-R genome possesses a cluster of genes encoding a Type 1 pilus, belonging to γ1 fimbrial clade of the Chaperon-Usher system  [66]  and sometimes referred to as Type 7 secretion system  [67]. This cluster (XFF4834R_chr30690-XFF4834R_chr30740) is highly similar to that of Xac 306 with two genes encoding the putative pili assembly chaperones, two genes encoding candidate structural fimbrial subunits containing each a spore coat U domain (IPR007893), and one gene coding a predicted usher protein, i. e. an outer membrane protein corresponding to the assembly platform. A conserved secreted hypothetical protein (XFF4834R_chr30730) is also predicted in this cluster as in Xcc ATCC33913 genome, i. e. between one gene coding a candidate structural fimbrial subunit and a putative pili assembly chaperone at the end of the cluster.
biotoul. fr// accession number: FO203524), ISXfu2 (https://www-is. biotoul. fr// accession number: FO203525), ISXcd1 (AF263433), and ISXac2  [42] , and three types of degenerated ISs (belonging to IS3-, IS5-, and IS1595-families)  [137]. ISXfu1  has not yet been identified in any other sequenced genome but an isoform was previously sequenced (accession number: AY375317) from another bean-associated xanthomonads strain. There are 26 insertions or remnants of ISXfu1 found all over Xff 4834-R chromosome, none are plasmidic. There are 33 insertions of ISXfu2 in Xff 4834-R genome. No complete copy of ISXfu2 is identified so far in other xanthomonads genomes. However, exact copies of the transposase TXfu2 are present in Xfa ICPB10535 translated genome. Overall, Xff 4834-R contains more ISs than Xac 306  [138]  and less ISs than X.
Around 76-fold coverage of Illumina reads (36 bp) were mapped, using SOAP (http://soap. genomics. org. cn), for the polishing phase as it is described by Aury et al. [157]. The sequences reported here have been deposited in the EMBL GenBank database, and accession numbers are FO681494, FO681495, FO681496, and FO681497 for the chromosome and for the three plasmids, respectively.
Gene prediction and annotation Sequence analysis and annotation were performed using iANT (integrated ANnotation Tool;  [158]  as described for X. albilineans  [34]. The probabilistic Markov model for coding regions used by the gene prediction software FrameD  [159]  was constructed with a set of CDS sequences obtained from the public databank Swiss-Prot as revealed by BLASTX analysis. The alternative matrices were built using genes first identified in ACURs (Alternative Codon Usage Regions) based on homology and taken from the X. albilineans annotation process  [34]. The corresponding products were automatically annotated using a protocol based on HAMAP scan  [160] , InterPro domain annotation and BLASTp analysis. Predicted CDSs were manually annotated individually gene by gene by an international consortium of scientists with expertise on different gene functions on xanthomonads (http://www.
Phylogeny of organisms used for genomic comparison The complete nucleotide sequences of a set of six housekeeping genes (atpD, dnaK, efP, glnA, gyrB, rpoD) were extracted from the 15 genomes (Table  2 ). Whole amino acid sequences were aligned using ClustalW with a BLOSUM protein weight matrix and transposed back to nucleotide sequence level to gain a codon-based alignment. The alignments were manually edited with Bioedit Sequence Alignment Editor Software 7. 0. 9. 0  [164]. Sequences were concatenated following the alphabetic order of the genes using Geneious 4. 8. 4. A phylogenetic tree was constructed using the Maximum Likelihood method (ML). The model of evolution for the ML analysis was determined using ModelTest 3. 7 in Paup. Both hierarchical likelihood ratio test (hLRT) and the standard Akaike Information criterion (AICc) were used to evaluate the model scores.
Primers were selected upstream and downstream of the frameshift in order to amplify a unique sequence in Xff 4834-R genome. Primers were validated by blast on Xff 4834-R genome with parameters for short queries with a minimum number of nucleotide matches of 15 nt and a maximum number of 5 mismatches. Primers were then checked in silico for specific and efficient gene amplifications (Amplify software version 3. 1. 4). Primer description is available in Additional file 9. PCRs were performed as previously described  [17]  and amplicons were sequenced using Sanger technology (Genoscreen, France). Presence of CDSs that are putative pseudogenes in Xff 4834-R genome was assessed in the 15 genomes used in genomic comparisons by BLAST of the nucleic sequences (Additional file 3). When available, nucleic sequences of the corresponding genes were used to build a Neighbor-joining (Nj) tree using Phylip 3.
Acknowledgements AI is funded by a PhD grant from  INRA-SPE  and region  Pays de la Loire, France. EG was funded by a PhD grant from the  French Ministry of National Education and Research and French Guyana. SC, EG, MA, EL and LDN are funded by the  LABEX TULIP  ( ANR-10-LABX-41 ), LSG is funded by  ANR-2010-GENM-013  Xanthomix.
fuscans subsp. aurantifolii (Xfa) ICPB10535 Non-vascular pathogen Citrus [45] PRJNA63615 X. gardneri (Xg) ATCC19865 Non-vascular pathogen Tomato and sweet pepper [46] PRJNA153105 X. oryzae pv. oryzae (Xoo) PXO99A Vascular pathogen Rice [47] PRJNA54411 X. oryzae pv. oryzicola (Xoc) BLS256 Non-vascular pathogen Rice [39] PRJNA63613 X. vesicatoria (Xv) ATCC35937 Non-vascular pathogen Tomato and sweet pepper [46] PRJNA57869 Xylella fastidiosa (Xf) Temecula1 Vascular pathogen, insect-transmitted Grapewine [48].
Recruitment for each of these studies has been reported previously  [4, 5, 6]. Strains were stored at 270uC in the Laboratorio de Investigacion de Enfermedades Infecciosas of Universidad Peruana Cayetano Heredia (UPCH) in Lima. Available patient data was limited to gender, age and HIV status; strain data included first line drug susceptibility profile and name of source study with date of collection of original clinical sample. Spoligotyping was undertaken at UPCH in batches over several months and films were interpreted by two independent readers; for the rare occasions where there was lack of independent agreement and subsequent failure to resolve discrepancies between both readers spoligotyping was repeated and the new film was used. Phylogenetic analyses and the construction of phylogenetic trees and spoligoforests (drawn using the SpolTools software available through http://www.
emi. unsw. edu. au/spolTools; [7, 8] ) permitted identification of clusters and orphan strains by comparison with the SITVIT2 database (Institut Pasteur de Guadeloupe). The minimum spanning tree (MST), based on spoligotyping patterns, was drawn using BioNumerics software version 3. 5. The MST is an undirected connected graph which links all the strains together with the fewest possible linkages between nearest neighbours. Contrarily to the MST, the spoligoforest trees are directed graphs which only evolve by loss of spacers. In these trees, nodes are not necessarily all connected (indeed, in case of too many changes between two strains, there are no edges linking them. In combination with SpolTools software, GraphViz software (http://www. graphviz. org) [9]  was used to colour the orphan strains on the spoligoforest trees.
Strain diversity Of 794 strains from 794 patients there were 149 different spoligotypes identified. Of these there were 27 strains with novel, unique orphan spoligotypes, 718 which mapped to spoligotypes already described at least twice, and 49 which were newly created shared types either within the present study or after a match with an orphan in the database. Descriptions of the orphan strain spoligotypes and the demographics of the source patients are given in table 1. In table 2 the 122 already known spoligotype international types (SITs) and corresponding lineages detected in this strain set are shown along with the frequency that each occurred in this strain set as compared with the comparison global database. (The complete original dataset of 794 spoligotypes with accompanying clinical data is made available in table  S1 ; the comparative frequency of the predominant SITs in this study with those reported elsewhere in Latin America is shown in table  S2 ).
Discussion In this report of strain diversity from Peru covering the period 1999-2005 3. 4% of spoligotypes observed were from novel, orphan strains. The nine most frequently observed spoligotypes (out of 149 observed) accounted for over 60% of all disease and the eight of these also featured amongst the nine most frequently Table  1. Description of spoligotypes with corresponding spoligotyping defined lineages/sublineages and demographic information for 27 orphan strains identified from amongst 794 strains of M. tuberculosis isolated from adults with pulmonary tuberculosis in Lima, Peru. **Lineage designations according to SITVIT2 using revised SpolDB4 rules; ''Unknown'' designates patterns with signatures that do not belong to any of the major clades described in the database. ***Clustered strains correspond to a similar spoligotype pattern shared by 2 or more strains ''within this study''; as opposed to unique strains harboring a spoligotype pattern that does not match with another strain from this study.
Unique strains matching a preexisting pattern in the SITVIT2 database are classified as SITs, whereas in case of no match, they are designated as ''orphan'' (see Table  1 ). doi:10. 1371/journal. pone. 0065873. t002 *Worldwide distribution is reported for regions with more than 3% of a given SITs as compared to their total number in the SITVIT2 database. The definition of macro-geographical regions and sub-regions (http://unstats. un. org/ unsd/methods/m49/m49regin. htm) is according to the United Nations; Regions: AFRI (Africa), AMER (Americas), ASIA (Asia), EURO (Europe), and OCE (Oceania), subdivided in: E (Eastern), M (Middle), C (Central), N (Northern), S (Southern), SE (South-Eastern), and W (Western). Furthermore, CARIB (Caribbean) belongs to Americas, while Oceania is subdivided in 4 sub-regions, AUST (Australasia), MEL (Melanesia), MIC (Micronesia), and POLY (Polynesia).
Note that in our classification scheme, Russia has been attributed a new sub-region by itself (Northern Asia) instead of including it among rest of the Eastern Europe. It reflects its geographical localization as well as due to the similarity of specific TB genotypes circulating in Russia (a majority of Beijing genotypes) with those prevalent in Central, Eastern and South-Eastern Asia. **The 3 letter country codes are according to http://en. wikipedia. org/wiki/ISO_3166-1_alpha-3; countrywide distribution is only shown for SITs with $3% of a given SITs as compared to their total number in the SITVIT2 database. doi:10. 1371/journal. pone. 0065873. t003 observed in a previous study in north Lima  [2] ; 5. 5% were SIT1/ Beijing family. Strains belonging to Haarlem, T, LAM and Beijing families predominated, and drug-resistance was not shown to be associated with any specific family, including Beijing, findings consistent with the single previous report from Peru  [2].
After multivariate analysis to control for the effects of HIV infection, gender and year Figure  2. Discrete spoligotypes relationships for all isolates (n = 794) presented through spoligoforest tree drawn as a ''hierarchical layout'' using the SpolTools software (available through http://www. emi. unsw. edu. au/spolTools; Reyes et al. 2008 [11] ). Each spoligotype pattern from the study is represented by a node with area size being proportional to the total number of isolates with that specific pattern. Changes (loss of spacers) are represented by directed edges between nodes, with the arrowheads pointing to descendant spoligotypes. In this representation, the heuristic used selects a single inbound edge with a maximum weight using a Zipf model. Solid black lines link patterns that are very similar, i.
In summary, we report the strain distribution of M tuberculosis isolates in Lima, Peru, highlight a significant proportion of novel spoligotypes, and hypothesize a prolonged, clonal, hospital-based outbreak of MDR disease amongst HIV patients but no evidence to support a hypothesis of strain-specific propensity for the acquisition of resistance-conferring mutations. Figure  S2  Discrete spoligotypes relationships for all isolates (n = 794) presented through a Fruchterman Reingold spoligoforest tree drawn using the SpolTools software (available through http://www. emi. unsw. edu. au/spolTools;  Reyes et al. 2008 [11] ). Each spoligotype pattern from the study is represented by a node with area size being proportional to the total number of isolates with that specific pattern. Changes (loss of spacers) are represented by directed edges between nodes, with the arrowheads pointing to descendant spoligotypes.
Supporting Information Table  S1  Detailed genotyping and drug-resistance data and demographic information on M. tuberculosis strains (n = 794) isolated from adults with pulmonary tuberculosis in Lima, Peru. (PDF) Table  S2  A comparison of the proportion of the most predominant SITs found in Peru as compared to neighbouring countries (Brazil, Colombia) and regions (Central America and Caribbean), recorded in the SITVIT2 database as consulted on 9 April 2013. (PDF).
of 100/122 SITs (n = 718) matched a preexisting shared-type in the database, whereas 22/122 SITs (n = 49 isolates) were newly created either within the present study or after a match with an orphan in the database. A total of 66 SITs containing 711 isolates were clustered within this study (2 to 130 isolates per cluster), while 56 SITs contained a unique strain within this study. Note that SITs followed by an asterisk indicates ''newly created shared-type'' (n = 22 containing 49 isolates) due to 2 or more strains belonging to an identical new pattern within this study or after a match with an orphan in the database. SIT  designations followed by number of strains: 2961* this study (n = 2); 3000* this study (n = 3); 3001* this study (n = 8) and USA (n = 1); 3004* this study (n = 2); 3005* this study (n = 2); 3006* this study (n = 2) and South Africa (n = 1); 3007* this study (n = 1) and USA (n = 1); 3008* this study (n = 1) and USA (n = 1); 3009* this study (n = 2); 3010* this study (n = 1) and USA (n = 1); 3011* this study (n = 4); 3012* this study (n = 2); 3013* this study (n = 3) and USA (n = 1); 3014* this study (n = 1) and Argentina (n = 1); 3015* this study (n = 2); 3016* this study (n = 1) and Panama (n = 1); 3017* this study (n = 3); 3089* this study (n = 2) and Mexico (n = 1); 3168* this study n = 1, Sweden (n = 1); 3431* this study (n = 2); 3432* this study (n = 2); 3433* this study (n = 2), BRA (n = 1).
The veterinarian collected data on the characteristics of suspected case and the unaffected calves by face-to-face questionnaire-based interview (Questionnaire S1). A case was therefore defined as a calf that had developed one or more BNP clinical signs on or before 28 days of age and had bone marrow depletion on histopathology and/or had thrombocytopenia (,150610 9 /litre) and leucopenia (,5610 9 /litre). A control was defined as a calf on the same farm as a case, aged 10-28 days at the time of case reporting, no clinical signs of BNP up to 28 days of age, and normal blood results (thrombocytes. = 300610 9 / litre, leucocytes. = 5610 9 /litre). Farmers were contacted again when control calves were 28 days of age to confirm that they had not developed BNP signs. If the laboratory results subsequently indicated that a suspected case did not meet the case definition then the case and its matched controls were excluded from the study, and if a control calf did not have normal blood results then it was excluded from the study.
The questionnaire was developed in English, translated into French and German, and field-tested by researchers with experience of BNP cases from the four countries. In the Netherlands and Belgium the English questionnaire was used and the interview conducted in Dutch. There were 91 questions, of which 36 collected descriptive data on calf, dam and sire identification, calf characteristics, clinical signs and laboratory results, and 55 collected data on potential risk factors related to colostrum and milk feeding, dam and sire characteristics, and dam vaccination history. Data were entered into an internet-based form created in Open Source software (Lime-Survey http://www. limesurvey. org/), exported to Microsoft Excel and then to Stata IC 12. 1 for coding, cleaning and analysis. Thirty (6 descriptive, 24 potential risk factor) questions were dropped due to a low number of responses or differences in interpretation between countries.
Five variables identified the calf, dam and sire. Twenty two variables describing clinical and post-mortem signs and laboratory results were used to define cases and controls. Thirty four variables were used in the statistical analysis and an additional 15 variables were created by recoding, to give a total of 49 exposure variables (3 descriptive and 46 potential risk factor). Due to the matched design, conditional logistic regression with farm as the matching variable was used for univariable analysis to obtain matched odds ratios (mOR), 95% confidence intervals (ci) and Wald test p values. It was first conducted on the dataset of 1559 calves, but due to missing observations the sample size for each variable was different. Variables with greater than 30% missing observations were excluded.
The number of calves in the final multivariable model was 1296 due to missing observations in the retained variables, so univariable analysis was repeated with the smaller dataset. Variables with p values greater than 0. 2 in univariable analysis were excluded from multivariable analysis. Pair-wise associations between the exposure variables were examined by the chi-squared test, and polychoric correlation was used to check for collinearity. Multivariable analysis was conducted using conditional logistic regression with farm as the group variable. The model was built using forward stepwise regression starting with the variable with the highest odds ratio and lowest p value on univariable analysis. Variables were retained if the likelihood ratio test indicated that inclusion led to a better model fit (p,0.
05). For variables from the same risk factor group (e. g. colostrum management, dam vaccination) that were likely to be collinear, the variable with the highest number of observations was added first. It was then removed and the other collinear variables were added and removed one by one. If more than one of the collinear variables improved the model then the one with the most observations and/ or that was most biologically relevant was retained, as described below. The population attributable fraction, PAF (proportion of cases in the total population that would be avoided if the exposure was removed, assuming the exposure is causal), was estimated using the punafcc package for Stata  [12].
Results Data were collected for 502 suspected cases and 1583 potential controls from 410 farms. However, 62 suspected cases did not fit the case definition, 122 potential controls had incomplete blood results, and 210 potential controls had ''atypical'' blood results (thrombocytes ,300610 9 /litre and/or leucocytes ,5610 9 /litre). Exclusion of these led to the loss of 97 confirmed controls with no matching case and 35 confirmed cases with no matching control. The remaining 405 confirmed cases were matched to 1154 confirmed controls from 330 farms with an overall case control ratio of 1:2. 8 (Table  1 ). The proportions of dairy, beef and mixed farms that were included in the study from each country approximately reflected the proportions of those types of farms in each country. In the Netherlands, dairy farms predominate so almost all suspected calves came from dairy farms.
DNA analysis and prediction the effects of coding nonsynonymous variants on protein function Sequences were analyzed using the Megalign program with the Lasergene sequence analysis software package (DNAStar, Madison, WI, USA). The possible functional impact of amino acid changes was predicted by the PolyPhen-2 (Polymorphism Phenotyping)  [23]  (http://genetics. bwh. harvard. edu/pph2/) which is an automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein. SIFT (sorts intolerant from tolerant) (http://sift. bii. a-star. edu. sg/www/SIFT_BLink_submit. html) was also used for predict possible functional impact of amino acid changes based on sequence homology  [24, 25]. To investigate whether the identified variants were present in natural or autism-free populations in other database, we explore the Exome Variant Server from the National Heart, Lung, and Blood Institute (NHLBI) 1000 genomes project (http://evs.
Statistical Analysis Deviation from Hardy-Weinberg Equilibrium (HWE) for genotype frequency distributions was tested using the chi-square goodness-of-fit test. All those with frequencies of minor alleles greater than 5% were used as genetic markers in this study. The Haploview program (version 4. 0) was used to determine pairwise D9 linkage disequilibrium (LD) to detect haplotype block  analysis using the option of determining blocks based on the criteria defined by Gabriel et al  [29, 30]. Allele and genotype frequencies for each polymorphism were compared between patients and controls using Pearson's chi-square analysis. The Fisher's exact test was used instead of the Pearson's chi-square test when calculated minimum expected count was less than 1. In addition, continuity correction of chi-square was used when calculated minimum expected count was less than 5 but more than   1.
The SPSS statistical software was used for all analyses, and significance was set at p,0. 05 (2-sided). The power of sample size for association tests was evaluated using the Genetic Power Calculator program (http://pngu. mgh. harvard. edu/,purcell/gpc/). For the disease locus, a prevalence of 0. 006, a genotype relative risk Aa = 1. 5 and AA = 1. 5, and a Dprime = 1 were used to perform the analyses.
W257X) (Table  3 ). The locations of rare nonsynonymous variants identified in patients with autism were shown in Figure  2  and Figure  S1 , S2, S3, S4, S5, S6. Four nonsynonymous variants (p. R115W, p. V166I, p. V179G, and p. W257X) were only found in children with autism. These coding rare variants in autism were inherited. Three variants (p. R115W, p. V179G, and p. W257X) were not present in database such as Exome Variant Server. Moreover, functional prediction of impact of amino acid was performed using two pieces of software. The consistent results showed that p. R115W might affect protein function. Importantly, the four variants (p. R115W, p. V166I, p. V179G, and p. W257X) affecting the protein sequence were observed in 6 of 398 (1. 51%) patients with autism and none in 437 controls (Chi-Square test, Continuity Correction p = 0.