dataesr/scientific-paragraphs-categorization huggingface dataset:
1 ). Retrospective identification of previous isolates from patient 1 recovered from 2000 to 2008 (50 sputum samples) rectified the identification as P. pulmonicola (misidentified as A. xylosoxidans) and was used to assess whether patient 1 was chronically colonized with P. pulmonicola. From March 2009 to December 2009, five additional patients acquired P. pulmonicola. Demographic, bacteriological and clinical data for the six patients are summarized in Table  1. Concerning bacterial identification, one strain from each patient was identified by ARDRA, 16S rDNA gene sequencing and MALDI-TOF MS, which had the same results as patient 1. In order to analyze the clonality of the strains, one strain per patient was used for PFGE analysis. All strains displayed the same PFGE type, demonstrating a clonal link between strains (Fig.
pulmonicola by MALDI-TOF MS. The API20NE results were not reliable with an identity score of 58. 9 % (T = 0. 64) for the species A. xylosoxidans and an identity score of 22. 2 % for Alcaligenes faecalis 2 (T = 0. 6, biochemical profile: 0040476). Biochemical identification of Pandoraea spp. was not suitable because this genus is not included in the API20NE database. This explains the misidentification of the strain recovered from patient 1 prior to molecular identification. Previous studies have reported the misidentification of P. sputorum as A. xylosoxidans  [11]  and the misidentification of other Pandoraea species as A. faecalis, A. denitrificans, CDC IV C2 and Acinetobacter spp. [21]. ARDRA, as well as 16S rDNA-based PCRs, resulted in a genus level identification of the Pandoraea sp. , but could not discriminate between P.
After 2003, all recovered strains from patient 1 displayed the same AST pattern as the epidemic strain (resistance to piperacillin, piperacillin-tazobactam and imipenem). Jørgensen et al. already reported intermediate susceptibility to ceftriaxone in P. apista strains  [10]. Susceptibility to trimethoprim-sulfamethoxazole was also reported in P. sputorum strains  [8]. Analyses of hospitalization periods for patients 1, 2, 3, 4, 5, and 6 are consistent with the chronological acquisition of P. pulmonicola (data not shown). In 2009, the source patient was hospitalized eight times. The clonality of the strains isolated from all six patients was assessed by PFGE analysis. The main hypothesis to explain the bacterial spread between patients is droplet crosstransmission. In our center, all patients have to follow standard precautions and are asked to use an alcohol hand rub.
18379 T. MALDI-TOF MS found the closest match with reference strain Pandoraea sp [2]  65 RLT (score value > 2 for all six strains). Interestingly, Pandoraea sp [2]  65 RLT displayed 99. 8 % sequence identity with Pandoraea pulmonicola (accession number AF139175) and 99. 5 % sequence identity with Pandoraea pnomenusa (accession number AY268170) (data provided by Bruker Daltonics).
Acknowledgements CC acknowledges long term support for malaria vaccine development at  ICGEB  from the  Department of Biotechnology (Govt. of India) ,  Biotechnology Industry Research Assistance Council (BIRAC) ,  Malaria Vaccine Initiative at PATH ,  European Vaccine Initiative (EVI) ,  Bill and Melinda Gates Foundation (BMGF)  and  WHO-TDR. CC also acknowledges  Institut Pasteur  for support for malaria vaccine development projects through internal funding schemes including PTR and PasteurInnov. IM acknowledges support from  National Health & Medical Research Council (NHMRC, Australia , grants # 1021544  and # 1043345 ) and the  Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.
Ly6C + cells did not expand in the spleen or epidermis of either DT-treated WT or Langerin. DTR mice (Supporting Information Fig. 2D ). Together, these data suggest that the loss of CD11c + cells drives expansion of monocytes and neutrophils in the spleen of CD11c. DTR mice. These observations agree with other published studies that have reported monocytosis and neutrophilia after depletion of DCs in other, more specific, models of DC depletion  [27, 28, 31, 32]. In particular, depletion of DCs, but not macrophages, results in monocytosis in zDC. DTR mice  [27]. Therefore, together these studies strongly suggest that the loss of DCs is sufficient to drive expansion of myeloid cells in these mice. To compare monocytes from PBS-or DT-injected mice, we initially examined the cells by microscopy.
All control populations were validated against publically available Immgen datasets (http://www. immgen. org, see materials and methods). Multidimensional scaling analysis, which offers a visual representation of the proximity of the datasets, demonstrated that DT-Ly6C + monocytes were transcriptionally distinct from classical Ly6C + and Ly6C neg monocytes, and were more distant from precursor cells than both these populations, suggesting the development of a more differentiated cell type (Fig. 3A ). To explore the lineage relationship between PBS-and DT-Ly6C + monocytes further, we specifically analyzed the expression of a panel of genes that encode transcriptional factors implicated in monocyte differentiation  [3, 9]. The heat map in Figure  3B  shows the relative expression of the panel of genes by macrophage/DC precursors (MDPs), cMoPs, and Ly6C + monocytes from PBS-and DT-treated mice.
A representative panel of the 12 most significant expression differences between PBS Ly6C + and DT Ly6C + monocytes was elected using the limma procedure. The heat map shows that the G-CSF Ly6C + samples show a strongly similar expression pattern to DT Ly6C + according to these genes: PBS-Ly6C + n = 9, DT-Ly6C + n = 4, G-CSF-Ly6C + n = 3. (E) Heat map showing differential Z-scored expression of a neutrophil/monocyte gene panel in the three sets of samples: Neu (n = 4), PBS Ly6C + (n = 9), and DT Ly6C + (n = 4). The gene expression profile for neutrophils was obtained from the Immgen database. dot plots  [20, 33, 40, 46]. This phenotypic transition as monocytes egress out of the vasculature is associated with the expression of a distinct tissue-dependent transcriptional signature (Fig. 2 )  [20].
Flow cytometry Spleens were digested with Collagenase IV (Worthington Biochemical Corporation). The following antibodies were used for flow cytometric analysis, all from eBiosciences or BD-Biosciences: FcBlock (clone 2. 4G2), anti-CD11b (M1/70), anti-CD11c (HL3), anti-Ly-6C (AL-21), anti-Ly-6G (1A8), anti-CD45. 1 (A20), anti-CD45. 2 (104), anti-MHCII (M5/114. 15. 2), anti-CD115 (AFS98), anti-CD64, anti-F4/80 (BM8), anti-CD135 (A2F10), anti-CD117 (2B8). FSC-W and a lineage dump gate were used in some experiments to exclude irrelevant cells (anti-CD3 (145-2C11), anti-CD19 (1D3), anti-B220 (RA3-6B2), anti-NK-1. 1 (PK136), and anti-Ly-6G (1A8)). Samples were acquired using a BD LSR Fortessa Cell Analyzer (BD Bioscience), and analyzed using FlowJo software (Treestar).
Acknowledgements: The authors thank the members of the  Bennett and Chakraverty labs  for their helpful discussions of this work. This study was supported by research funding from  Leukaemia and Lymphoma Research, UK , to S. S. , S. W. , T. M. , L. Z. , R. C. and C. L. B. (grants  10007  and  12006 ) and from the  APHP (Assistance Publique-Hôpitaux de Paris, France) ,  Cancéropôle d'Ile de France , and the  Institut National du Cancer, Paris, France , to M. D. , O. H. , and M. -T. R.
The following amplification protocol was used: denaturation at 95°C for 5 min, 45 cycles at 95°C for 10 s, 55°C for 30 s, and 72°C for 10 s. These conditions were used for all the primer pairs. For the species determination, a melting curve analysis determined the melting temperature (Tm). To test the reproducibility of the Tm determination, three strains of different species were tested in 10 separate runs with the selected primers. For the subspecies determination, after PCR cycling with the VNTR primers, the samples were heated from 65°C to 95°C with continuous acquisition. For each VNTR locus, a normalization region of the melting curve was selected to improve the analysis per the recommendations of the Rotor-Gene ScreenClust HRM Software User Guide (Qiagen, Courtabeuf, France). Two normalization regions were selected: one before and one after the melting curve transition.
The highest fluorescence value was 100 and the lowest fluorescence value was zero. The data were analyzed using ScreenClust HRM (Qiagen, Courtabeuf, France) in unsupervised mode (i. e. , there were no known controls for each cluster and the number of clusters was unknown). The unsupervised mode was also employed to analyze Leptospira DNA fluorescence data obtained with human samples, and the results from the control strains were employed as pseudo-unknowns. The data were analyzed by ScreenClust using the principal component analysis statistical method  [41] , which enabled the maximum separation of genotypes. A cluster plot was built in three dimensions (principal components) and ellipses representing each cluster were drawn. The probability of each sample fitting into a specific cluster was calculated and required to be at least 0.
Application of ScreenClust software to biological samples (Table 2, Figs 2 and 3) The 42 Leptospira DNAs that were extracted from patient serum samples showed a Tm corresponding to that of the species L. interrogans using the primer pairs lfb1F/R and G1/G2. Using VNTR-4 bis and VNTR-Lb5, the genotypes of 17 out of 42 (40. 5%) DNA samples were identified. These 17 Leptospira DNA samples exhibited the same genotype, which was consistent with the strains L. interrogans sv. Copenhageni or Icterohaemorrhagiae. Using VNTR-4 bis and VNTR-Lb5, the genotype determination was 100% when the Ct was 30 cycles (8250 copies/ml, data not shown) and 28. 5% (10/35) when the Ct was >30. We then evaluated the integrity of three genotypable DNAs and three non-genotypable DNAs by performing a standard PCR targeting the secY gene.
MLVA has been previously proposed for typing the L. interrogans, L. borgpetersenii, and L. kirschneri strains  [40, 13]. In our study, the HRM analysis of the VNTR sequences was performed using ScreenClust HRM software. To the best of our knowledge, our study signifies the first time that Leptospira strains have been genotyped using VNTR primers. Using our method, we obtained a high Hunter-Gaston's discriminatory index (0. 98) compared to a serological classification of all the reference strains tested. This high index (> 0. 95) shows the genetic polymorphism within each tested species and validates the high sensitivity and specificity of auto-calling genotypes from HRM data using ScreenClust software. The discriminatory index was relatively lower for L. kirschneri (0. 87), which is potentially due to the decreased polymorphism of this species.
This is consistent with the earlier finding that spontaneous fadeout occurred in 66% of runs, either in the first 2 yr (43% of runs) or subsequently (23% of runs;  Marcé et al. , 2011a). Spontaneous fadeout is assumed to occur as a consequence of insufficient within-herd transmission to establish infection, highlighting the importance of continual high standards of animal husbandry and management in minimizing the likelihood of infection when it is unknowingly introduced. In the current study, we only included those assays with published Se and Sp figures at each stage of infection. For this reason, pooled culture and PCR were not included; however, the model can be easily extended as additional test data become available. As an example, it is anticipated that serum and milk ELISA will be used in series with PCR, rather than fecal culture, once robust estimates of the Se and Sp of PCR are available for each stage of infection.
ACKNOWLEDGMENTS This research was supported by  Animal Health Ireland. Financial support for the Marcé model was provided by  INRA (Paris, France) ,  IRSTEA  ( Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture, Antony, France ), and  Basse-Normandie, Bretagne, Pays de la Loire and Poitou-Charentes Regional Councils (in Caen ,  Rennes ,  Nantes , and Poitiers, respectively) under SANCRE (Santé animale, sécurité de l'aliment et compétitivité des filières animales régionales) project, in the framework of " For and About Regional Development " programs. Funding was also provided by the  French research agency, program Investments for the Future , project  MIHMES   ANR-10-BINF-07. We thank  Laurence Shalloo  ( Teagasc, Moorepark, Fermoy, Co. Cork, Ireland ) and  Luke O'Grady  ( UCD Veterinary Medicine, University College Dublin, Ireland ) for helpful discussions relating to the economics of premature culling.
The env gene of the prototypic Pan troglodytes verus SFVpvr. SFV7 strain (52) was amplified from SFVpvr. SFV7-infected BHK-21 cells (a gift from A. Rethwilm) using primers CPZENVF1 and CPZENVR2b (Table  1 ) with an annealing temperature of 57°C and an extension time of 3 min 30 s. PCR products were directly sequenced by MWG Operon (Ebersberg, Germany). Both sense and antisense sequences were obtained for each fragment and were found to be identical. To obtain complete env sequences, the different env fragments were concatenated (the overlapping regions were identical in all samples). Phylogenetic analyses. Multiple-sequence alignments of previously known (Table  2 ) and newly generated sequences were performed by using the DAMBE program (v4. 2. 13 [http://dambe. bio. uottawa. ca]). Modeltest v3.
6 was used to select the most appropriate nucleotide substitution model, based on the Akaike information criterion (AIC). Generalized time reversible (GTR) was found to be the best-fitting model. Phylogenetic trees were constructed by using the neighbor-joining method, and bootstrap values were calculated with 1,000 replicates. Phylogenetic tree topologies were confirmed by using the maximum likelihood method with the PAUP program (v4. 0 [http://www. paup. csit. fsu. edu]). Percent identity was calculated by CLC software (CLC DNA Workbench 6; CLCbio) on the alignment obtained with DAMBE. By definition, a clade is a monophyletic group supported by a strong bootstrap value. Here, we used "group" as a host-specific clade and "subgroup" as a clade defined based on the central region of env. Recombinant analyses.
To search for potential recombination events, similarity plot and bootscanning analyses were performed with Simplot software (v3. 5. 1; J. R. Simplot Co. ). These analyses were performed with default parameters, except for the bootscan repetitions (set to 1,000) and the evolution model (Kimura two parameter). The similarity plot depicts a similarity score between a group of interest (query) and other groups (defined based on the phylogenetic tree) over a 200-bp-long region, and the overall env gene was analyzed in 20-bp-long steps. The bootscan analysis reflects the phylogenetic relationship (bootstrap value) between a group of interest (query) and the other groups (window, 200 bp; step, 20 bp). The Recombination Detection Program (RDP4)  (53)  was also used to investigate putative recombination.
Unlike Simplot-derived studies, the RDP method looks for recombination by analyzing every possible sequence triplet (instead of considering groups). A window is moved along the genome, and a percentage of identity between each of the three possible pairs is calculated at each position. A P value is calculated to determine the likelihood that the potential recombination event is due to chance. Protein analysis. Percent identity was calculated by using CLC software (CLC DNA Workbench 6) on the alignment obtained with DAMBE after translation of the sequences into amino acids. Putative glycosylation sites were identified by the NetGlyc 1. 0 program and consisted of NXS/T  Nucleotide sequence accession numbers. All complete and partial env sequences generated in this work were submitted to GenBank.
1 ). In addition, we also obtained complete env sequences from four wild-born NHPs living in the same region as the infected individuals (one gorilla and three chimpanzees), and we sequenced the env gene of a prototypic Pan troglodytes verus strain, SFVpvr. SFV7 (Table  4 ). All newly obtained sequences contained an open reading frame of 2,958 to 2,970 bp and were unique. Complete env sequences define host-specific SFV groups. We analyzed phylogenetically the complete env sequences by using the neighbor-joining (Fig. 2 ) and maximum likelihood (data not shown) methods. The newly generated complete env sequences were included together with the SFV env sequences available in GenBank (Table  2 ). The topologies of both phylogenetic trees were comparable. Host-specific groups (gorilla, chimpanzee, cercopithecus, and macaque) were identifiable and supported by strong bootstrap values (Ͼ90).
ACKNOWLEDGMENTS We thank the  Institut de Recherche pour le Développement (IRD)  and the  Centre Pasteur du Cameroun  for collaborating with us concerning the field work in Cameroon. We thank  Axel Rethwilm  for providing SFV7infected BHK cells and  Arifa Khan  for helpful discussions about foamy virus taxonomy. L. R. was personally supported by the  Bourse de l'Ecole Normale Supérieure, Faculté Paris Diderot. E. B. was supported by the  Virus Cancer Prevention Association  and by the  Institut National pour le Cancer. This.
Alignment and cross-checking of the sequences were performed with CLC Main Workbench 5. 7 software (CLC bio) and a consensus sequence of 1816 bp was obtained by combining the two overlapping fragments. The nearly complete sequence (1816 bp) of the 18S ssrRNA gene recovered from the original archived material of Hemolivia stellata was deposited in GenBank under Accession Number KP881349. Our new sequence of H. stellata and 179 sequences of adeleid parasites (Table  2 ) were aligned using a Muscle algorithm  [19]. Molecular phylogeny was performed by the Maximum Likelihood (ML) method with a GTR + C + I model, using PhyML 3. 0 software  [23]. Nodal robustness of the tree was evaluated by non-parametric bootstrapping (1000 replicates). Garnham, 1954 [20]  and we will only provide a general outline: (i) in the haemocoelom: large immature oocysts with peripheral nuclei (Figs.
Molecular data of Hemolivia The molecular data deposited under the name Hemolivia into the databanks reaches 21 sequences of the 18S ribosomal RNA gene: (i) The sequence JN211118 deposited by  Barta et al. (2012)   [3]  as Hemolivia mariae Smallridge & Paperna, 1997  [67]  was isolated from dried blood films containing gamonts from an experimentally infected Tiliqua rugosa Gray, 1825 from Australia. This sequence is not included into our tree (Fig. 2 ) because of its shortness and of poor overlap with the rest of the sequences. However, it clusters with the Hemolivia sequences that are long enough to overlap (data not shown). In  Barta et al. (2012)   [3] , it also clusters with the sequence ''Hepatozoon'' sp. EU430236 that belongs to the Hemolivia clade in Kvic ˇerová et al. (2014)  [34]  and in our analyses (Fig.
2 ). (ii) The sequence HQ224961 also deposited by  Barta et al. (2012)   [3]  as Hemolivia mariae Smallridge and Paperna, 1997  [67]  is mistakenly referenced in GenBank while it is clearly stated in the text of the article that it is a sequence of Babesiosoma stableri  Schmittner & McGhee, 1961 [62]  obtained from Rana septentrionalis Baird, 1854 collected by hand from Lake Sasajewun, Algonquin Provincial Park, Ontario, Canada. As reported  [3, 34] , this sequence also clusters in our analysis (Fig. 2 ) with the related Dactylosoma ranarum Labbé, 1894  [35]. (iii) The sequence KC512766 deposited as Hemolivia sp. by  Harris et al. (2013)   [27]  was isolated from Hyalomma aegyptium Linnaeus, 1758 collected on Testudo graeca Linnaeus, 1758 in Algeria, the original host and locality of H. mauritanica.
1A  in  Herbert et al. , 2010 [29]  and Fig. 9  in Desser, 1978  [16] ) considered by Laird to be merozoites. Herbert et al. 2010 described oocysts and sporocysts in the haemocoel of the tick. However, as there is no description of the initial stages (pairing and fertilisation) and the partial sequence (233 bp) is too small, the parasite's identity cannot be ascertained and the sequence was not included. The majority of sequences in the phylogenetic tree fall into one of the four groups defined below and correspond to a different genus characterised by its cycle, hosts and vectors. However, a few sequences appear in a group which does not correspond to the life history supposed by their authors. The risk of errors, when classifying a haemogregarine according to molecular data only, is that, when indispensable information on their life cycle is lacking, many species with sequences deposited in the databanks are not identified correctly at the generic level.
List of the sequences used in the phylogenetic construction. The different columns give respectively the accession numbers of the sequences, the name of the parasites to which they are assigned, their vertebrate hosts, their isolation source, the country in which they have been found and the number of the associated reference in the references list. Unpub. : unpublished data only deposited in GenBank; a: experimentally fed on a naturally infected host; b: experimentally infected; c: collected from naturally infected wild host; d: Amblyrhynchus cristatus DNA detected in the last blood meal; n. a. : not available.
The need to bridge between the unstructured data on the Document Web and the structured data on the Web of Data has led to the development of a considerable number of annotation tools. However, these tools are currently still hard to compare since the published evaluation results are calculated on diverse datasets and evaluated based on different measures. We present GERBIL, an evaluation framework for semantic entity annotation. The rationale behind our framework is to provide developers, end users and researchers with easy-to-use interfaces that allow for the agile, fine-grained and uniform evaluation of annotation tools on multiple datasets. By these means, we aim to ensure that both tool developers and end users can derive meaningful insights pertaining to the extension, integration and use of annotation applications.
In particular, GERBIL provides comparable results to tool developers so as to allow them to easily discover the strengths and weaknesses of their implementations with respect to the state of the art. With the permanent experiment URIs provided by our framework, we ensure the reproducibility and archiving of evaluation results. Moreover, the framework generates data in machineprocessable format, allowing for the efficient querying and post-processing of evaluation results. Finally, the tool diagnostics provided by GERBIL allows deriving insights pertaining to the areas in which tools should be further refined, thus allowing developers to create an informed agenda for extensions and end users to detect the right tools for their purposes. GERBIL aims to become a focal point for the state of the art, driving the research agenda of the community by presenting comparable objective evaluation results.
INTRODUCTION The implementation of the original vision behind the Semantic Web demands the development of approaches and frameworks for the seamless extraction of structured data from * Further co-authors can be found at the end of the article. text. While manifold annotation tools have been developed over the last years to address (some of) the subtasks related to the extraction of structured data from unstructured data  [13, 17, 24, 25, 27, 32, 35, 41, 44] , the provision of comparable results for these tools remains a tedious problem. The issue of comparability of results is not to be regarded as being intrinsic to the annotation task. Indeed, it is now well established that scientists spend between 60 and 80% of their time preparing data for experiments  [14, 18, 31]. Data preparation being such a tedious problem in the annotation domain is mostly due to the different formats of the gold standards as well as the different data representations across reference datasets.