dataesr/scientific-paragraphs-categorization huggingface dataset:
We also analysed two putative proteins from different species to determine whether this localization of the polymorphisms might be common to other ANK and TPR motifs. We chose the ANK and TPR proteins with the highest number of highly conserved ANK and TPR motifs, gi116208038 from Chaetomium globosum (PNP_UDP/ NACHT/ANK) and gi255934897 from Penicillium chrysogenum (UNK/AAA/TPR), with, respectively, 21 ANK repeats and 21 TPR motifs. By comparing the repeats and mapping the variable positions onto a homology model (PDB ID 4GPM for ANK and 3EDT for TPR), we found that polymorphisms map to the same positions in the a-helices of the concave surface of the TPR domain and to the inner helices and b-hairpin/loop region of the concave interface of the ANK domain (supplementary fig. S7 , Supplementary Material online).
Indeed, it seems that Berg and Burmeister frequently exchanged specimens (Roig, pers. comm. ). In addition, wing spans indicated in the original description (1-1. 2 inches) correspond to the specimens that we consider syntypes. Halesidota rectilinea Burmeister, 1878: 445 Fig. 8  Current identity. Biturix rectilinea  (Burmeister, 1878). Remarks. The label with "864" printed on it is the catalogue number in the database of the MACN. Halesidota trifasciata Burmeister, 1878: 446 Fig. 9  Current combination. Tessellota trifasciata trifasciata  (Burmeister, 1878). Material. Described from a single male from Buénos-Ayres [Buenos Aires]. Type locality. Buénos-Ayres [Buenos Aires]. MACN. In the Berg collection there is a male specimen with a label "Cumtypo/ comparat. " and another label representing the flag of Argentina without any indication.
Acknowledgements We wish to thank  Dr. Arturo Roig Alsina  and MACN for allowing the study of the specimens in the Burmeister and Berg collections, to  Lic. Hugo Castello  for the comments on the labels and his assistance with Burmeister's bibliography, to  Prof. Cecilia Saleme de Dip  ( Facultad de Filosofía y Letras ,  Universidad Nacional de Tucumán, Argentina ) for reading and correcting to the manuscript and to  Dr. Adriana Zapata  ( Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba ) and  Johanna Valeria Rodríguez Ramírez  for their help during the visit in MACN. Great thanks are due to the reviewers for valuable comments and many useful suggestions on the manuscript. This research was funded by  CONICET  ( Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina ), which awarded a doctoral grant to HMB.
Data sources The main indicator used to describe the annual incidence of pregnancy-related listeriosis is the rate of number of cases per number of live births in the French population. The number of live births is recorded every year by the French Statistical Office (Institut National de la Statistique et des Etudes Economiques; INSEE)  [10]. The number of cases was retrieved from different sources for the following periods: -1984-1991: studies by the French National Health Laboratory  [9, 11]. -1992-1998: National Listeria Reference Centre (NLRC) database. NLRC started ascertaining cases nationwide in 1992 because of a listeriosis outbreak  [12]. The number of cases related to that outbreak has not been considered for the calculation of the annual incidence rate. In 1997, the sensitivity estimation of case ascertainment was 76%  [9].
-1999-2011: mandatory notifications. Listeriosis has been listed for mandatory notification in France since 1999. Accordingly, each diagnosed case must be declared by clinicians and laboratories to the regional health agency. Sensitivity was estimated at 87% in 2001  [13]  and at 92% in 2006 (data not shown), using the capture-recapture method. The mandatory notification includes demographic, clinical, and laboratory information  [14]. Moreover, upon diagnosis, mothers are asked to complete a standard food questionnaire on their eating habits in the past two months. After validation of the content, the mandatory notifications and the food questionnaires are sent by the regional health agencies to the French Institute for Public Health Surveillance (InVS). The annual incidence rate was estimated from 1984 to 2011, considering the sensitivity of each data source.
The MONALISA study (Multicentric Observational National Analysis of LISteriosis and ListeriA; http://clinicaltrials. gov/show/ NCT01520597), a prospective study on listeriosis, will present detailed clinical, biological and microbiological data of all incident cases of listeriosis in France from the end of November 2009 until 2013, including pregnancy-related cases, and provide extensive information on the prognosis of newborns.
Acknowledgements We are indebted to the clinicians, microbiologists that isolate Listeria from patient samples and employees of the local health departments, to the  Institut Pasteur, particularly to Viviane Chenal-Francisque , the  Institut de Veille Sanitaire , particularly to  Veronique Vaillant , and the  Ministry of Health; Ministry of Agriculture and Ministry of Finance  who contributed to human listeriosis surveillance in France. This work was supported by the  National Institute of Health  which is funded by the  French Ministry of Health.
Experimental Study Experimental Chickens. Seventy 1-d-old conventional broiler chicks were obtained from a local hatchery  [18]. Chickens were housed in isolators  [19]  from d 1 until the end of the experiments. Virus Strains. Two different live vaccines were used: the commercial Massachusetts vaccine, H120 strain  [20] , and the commercial CR88 vaccine, 793B type  [21]. The vaccines were used as recommended by the manufacturers. The challenge IBV TN20/00 strain (laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur Tunis, Tunis, Tunisia; Gene Bank accession number: EF535998), a Tunisian pathogenic variant, was isolated at the Laboratory of Epidemiology and Veterinary Microbiology, Institute Pasteur Tunis, in 2000 from broilers with nephritis (from flock located in Tunis).
Acknowledgments We thank  Tolga Bozkurt ,  Yasin Dagdas ,  Kentaro Yoshida ,  John Rathjen ,  Kai P. Rinha , and  Silke Robatzek  for their suggestions. We are also grateful to those who contributed to a broadly diffused community email discussion, as well as those who commented on the Twitter and Scoop. itsocial networks, for helping to sharpen our thoughts. We apologize for limited literature coverage owing to space limitation.
g. "new species") or options (e. g. " species delineation" in TOPIC and not only in TITLE) led to a much higher number of articles (several thousands). From the resulting list of 666 articles, we removed 172 articles that did not fit the context of this review (i. e. methodological and theoretical articles, review studies that did not perform any species delimitation, studies that re-analyzed published data, and studies that focused on supra-or infra-species levels only). For the 494 remaining articles, we extracted data on the number of delimited species, the number of new species delimited, the number of new species described (and, when given, the reason(s) why new species were not described), and the studied taxon. We did not attempt to interpret published results ourselves, but recorded the number of species (delimited, new and described) as reported by the authors of each paper.
We also recorded the type of data and methods used to delimit species: molecular data, morphology (including anatomy, cytology…), ecology (including phenology, niche modelling…), cross tests, behavior (e. g. call songs) and other miscellaneous methods (e. g. caryology, chemical data, presence of endosymbionts, etc…). We considered the geographical distribution to be implicitly used in all articles. The resulting table is presented in Online Appendix 1. Contingency tables were analysed using Fisher's Exact Test, given the relatively small number of observations. We investigated journal editorial policies on including formal taxonomic descriptions into articles. As a proxy for editorial policies, we recorded whether journals that published articles in which new animals species were delimited also published formal descriptions, within three time periods  (1864-2004, 2005-2010, 2011-2013) , using the "Systematics Controlled Terms" feature in the Zoological Records database (Online Appendix 2).
7% of the total number of delimited species in the 494 studies (7205). Among the studies that delimited new species, 125 delimited but did not describe at least one new species and 139 described at least one new species (in 10 studies some new species were described and others not). The ratio of Described over Undescribed Species (hereon called the "DUS" ratio, more specifically calculated as the number of studies that delimited new species and described at least one new species divided by the number of studies that delimited new species and did not describe at least one new species) was approximately of 1. 11 for the whole dataset and did not change significantly from 2006 to 2013 (Fisher's Exact Test: p=0. 91). The DUS ratio varies non significantly among taxa: when considering only the taxa represented by more than five studies, the ratio varied from 0.
ACKNOWLEDGMENTS The authors thank  Jean-François Flot , organizer of the  Species Delimitation Symposium , and the  Society of Systematic Biologists , which funded the participation of NP to the 2013 Evolution meeting. This work beneficiated from the project  CONOTAX , funded by the  French ANR  ( ANR-13-JSV7-0013-01 ). Amélia Viricel ,  Philippe Bouchet  and  Sarah Samadi  are also thanked for their helpful comments.
FUNDING This work was partly supported by the project  CONOTAX , funded by the  French "Agence Nationale de la Recherche " (grant number  ANR-13-JSV7-0013-01 ). Salary for E. P. was covered by a grant to the Poitou-Charentes region (Contrat de Projet-État-Région 2007-2013) and by a grant from the  Fond Européen de Développement Régional.
0 mL. The injector temperature was set at 250 C and the detector temperature at 280 C. The oven temperature was initially set at 75 C for 3 min, then programmed to increase to 150 C at a rate of 37. 5 C min À1 , and then to 215 C at a rate of 3 C min À1  (Luna et al. , 2004). Qualitative fatty acid composition of the samples was determined by comparing the retention times of the peaks with those of standards 05632 and 189-19 (Sigma, Chemical Co. , St Louis, MO, USA). The Galaxie Chromatography Data System (Varian Chromatograph Systems) was used for identification and quantification of peaks. The relative content of FAME was calculated from the area of each peak, and expressed as a percentage of total FAME, according to the official method Ce 1-62  (AOCS, 2005). Results were grouped and expressed as g 100 g À1 of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA).
Acknowledgments The authors acknowledge  DuPont Danisco (Cotia, São Paulo, Brazil), Chr. Hansen (Valinhos, São Paulo, Brazil)  and  DSM Food Specialties (Jaguaré, São Paulo, Brazil)  for the donation of cultures,  Fundação de Amparo à Pesquisa (FAPESP, Brazil)  for the PhD fellowships of  Ana Carolina Rodrigues Florence  and  Conselho Nacional de Pesquisa (CNPq)  for financial support.
Above-ground symptoms of root rot disease were assessed visually at least every two days. We have adopted as a measure of incubation period the time interval between inoculation and detection of the first symptoms. In our statistical analyses, we ignore this censoring in the data as the censoring interval is small. For each host age, we infected at least 40 plants. Specifically, we obtained measures of the incubation period of 78,  52, 53, 49, 46, 49, 45, 46,   1 ). Two time scales are often used to measure processes in plant systems: calendar time in days, which is useful for practitioners, and time in degree-days, which incorporates temperature-dependence in plant and pathogen responses  [36]. In this work, we measure time in degree-days because temperature was a key abiotic variable that was not controlled during our experiments.
The parameters were evaluated using maximum-likelihood estimation and neglecting the censoring imposed by the two-day observation frequency, i. e. , assuming the data represent the actual time period between infection and first emergence of symptoms for each plant. We used the Akaike information criterion (AIC) metric to compare the goodness of fit of the alternative pdf models over all age groups and for each age group. For each plant age group, we also compared the survival function associated with each twoparameter distribution, Gamma, Weibull and Lognormal, against its non-parametric Kaplan-Meier estimator  [37]. We assessed the effect of the location of individuals in plots (south, middle and north) on the incubation period, by age, by using Cox proportional hazards regression. As we found this covariate to be nonsignificant, we did not include it in subsequent analyses.
The reason for this tractability is that an Erlang-distributed random variable with parameters k and l is the sum of k exponentially-distributed random variables with rate parameter l. Here, we consider this particular case of model (1a), i. e. , T,Erlang(k, l(t)), and compare age-varying distribution models for the incubation period where k is a free integer parameter. Note that k = 1 corresponds to the exponential distribution. The probability densities of the parameters k, a, b and c, were estimated from the experimental data using a Bayesian framework with a likelihood function based on (1), and non-informative prior distributions. Posterior densities were obtained via Markov Chain Monte Carlo (MCMC) parameter sampling run on OpenBUGS  [40] , whose outputs were analysed with R software  [38]  (see Appendix S3 for more details).
Acknowledgments We thank two anonymous reviewers for their helpful comments and suggestions for revision of the initial manuscript. We are very grateful to our missed colleague,  Doug Bailey , who was initially involved in this project; his deep insight and ideas were central to the development of this work. We thank  P. Farcy ,  E. Lemarchand ,  M. Prunier ,  P. Delarue  and  S. Carillo  for assistance with these experiments and  F. Monfort  for her active involvement in early part of this work.
The origin of modern sugarcane cultivars raises issues not only related to the extent and nature of the divergence of the sugarcane and sorghum genomes, but also about the relationships (meiosis and expression dosage) among hom(e)ologous loci. Equally importantly, deciphering the sugarcane genome is a major goal for improving genome wide assisted selection breeding opportunities worldwide. However, the hybrid polyploid nature of modern cultivars imposes limitations to breeders in understanding genotype to phenotype allelic variation and dosage. The present study was undertaken within the framework of a larger sequencing initiative to generate a comprehensive dataset, providing information on sugarcane genome structure and function as a basis for future functional genetic studies.
Two hundred and five BACs were assembled into one contig each and the remaining 112 BACs were assembled into an average of 3. 15 contigs. Although not all BACs were single contigs, all have a proposed scaffold and are a single-fasta file. To date, most of the gaps have repetitive sequences at the ends. The minimum, maximum, median, and average sizes of BAC assemblies were 12. 25, 259. 2, 115. 38 and 112. 34 Kb, respectively. A BLASTn search indicates that none of the sequences were derived from chloroplast or mitochondrial genomes. The repetitive content was estimated from BAC assemblies using the Repbase database [9] and a curated sugarcane Long Terminal Repeat (LTR) retrotransposon database  [10]. Fifty percent of the BAC sequences are repetitive, 49. 4% transposable elements (TEs) and 0.
Gene annotation and CDS validation BAC assemblies masked for repetitive sequences were analyzed by a combination of de novo gene prediction software programs and searches against databases to identify non-TE coding genes. For 14 BACs there were no predicted protein-coding genes identified. A total of 1,400 coding regions were predicted and annotated. An average of 3. 8 CDSs (Coding DNA Sequences) were found per 100 Kb, representing one protein-coding gene per 26. 12 Kb. RNA-seq data from the cultivar RB92-5345 and the sugarcane assembled EST sequences (SASs) from the SUCEST (sugarcane EST) Project  [8]  were used to validate CDSs. All CDSs mapped against at least one SAS and 1,218 mapped against at least one pair of RNA-seq reads (87% of the total). This may be because there was no detectable expression of these genes under the experimental conditions used, or high sequence divergence between the two cultivars (R570 and RB92-5345) for these specific loci, and/or false positive gene annotation.
Using Blast2GO, GO (gene ontology) terms were assigned to 1,081 of the 1,400 predicted protein-coding sequences (77. 8%). A total of 4,730 GO functional terms were assigned to the 1,081 sequences. GO terms were placed into three broad categories, Biological Process 1,884 (39. 8%), Molecular Function 1,502 (31. 7%) and Cellular Component 1,344 (28. 5%). The most abundant terms in the Biological Process category include cellular process and metabolic process and in the Molecular Function category, catalytic activity and binding. In the Cellular Component category, the most common terms were organelle, membrane and cell (Additional file 5: Figure  S2 ). BLASTp searches against the NCBI nr database  [11]  confirmed that most of the sugarcane protein sequences are most similar to those of sorghum (Additional file 6: Figure  S3 ).
Sucrose-6-phosphate phosphohydrolase (S6PP) catalyzes the reaction from sucrose-6P to sucrose. There is a tandem duplication of this gene, not previously published, but evidenced by genomic sequences in the Phytozome database [14], in sorghum (Sb09g003460. 1 and Sb09g003463. 1), Setaria italica (Si022142m and Si0 24709m) and Panicum virgatum (Pavirv00037112m and Pavir00037113m). However, the same duplication is not found in maize or any of the other grass genomes available. The BAC SHCRBa_104_G22 annotation suggests that s6pp is duplicated in the sugarcane genome. In order to better understand this region, which is important for sucrose synthesis, we examined the composition of the intergenic region between the two copies of s6pp in modern sugarcane cultivars, Saccharum species, sorghum and Miscanthus sp.
by sequencing a PCR amplified 1,539 bp fragment. One hundred and ninety amplicons were aligned against sorghum sequences and the R570 BAC (SHCRBa_104_G22). Overall nucleotide identity is high, 99. 988% (SD 0. 001). The sorghum sequence is the most divergent with an average 99. 935% (SD 0. 005) identity compared with all other sequences. S. spontaneum sequences are more divergent from the other sugarcane sequences (99. 985%, SD 0. 006). Neighbor-joining and maximum likelihood phylogenetic analyses resulted in unresolved evolutionary relationships (data not shown). Network analyses can be used to predict relationships amongst sequences with low diversity  [15]. Because of the low sequence diversity of the sugarcane s6pp duplication, a haplotype network was generated to describe the relationships of sugarcane species and cultivars.
sRNAs in sugarcane BACs A sRNA library from sugarcane leaf tissue  [10]  was mapped against the BACs to evaluate the sRNA landscape and to identify new microRNA (miRNA) genes (Additional file 11: Figure  S6 ). This library was derived from the hybrid SP80-3280, the main cultivar used to produce the SUCEST database  [8]. Most sRNAs from grasses are in the 24-nucleotide size range and therefore are most likely small interfering RNAs (siRNAs) or repeated-associated small interfering RNAs (rasiRNAs)  [17]. Sixty-one percent of the sRNAs in the SP80-3280 sRNA library were in the 23-25 nt range, and 48% of them mapped to TEs identified in the BACs. The 23-25 nt RNAs mapped to the TEs are 3 × more frequent than did the smaller 20-22 nt RNAs. This pattern is expected for rasiRNAs  [17]  and suggests that TEs are the origin of the 23-25 nt rasiRNAs, as well as the target for sRNA-mediated gene regulation.
Comparative genomics with sorghum A BLAST based pipeline against the sorghum genome and protein databases was used to determine the distribution of the BACs relative to the sorghum genome in order to examine synteny between genomes and to gain insights into the evolution of sugarcane genomic structure  [14]. A sorghum ortholog was assigned to 1,367 sugarcane predicted genes, with a redundancy of 31. 6%. After excluding redundant genes (i. e. those with the same sorghum ortholog), 935 genes were analysed. For 318 genes there was a single BLAST match against sorghum-annotated proteins [14] and orthologous relationships for the remaining 617 genes were inferred by high-throughput maximum-likelihood phylogenetic analysis  [23]. Using the chromosomal locations of the 935 sorghum-sugarcane orthologous, we were able to localize 265 sugarcane BACs onto sorghum chromosomal arms (Figure  4 ).
No structural variation between groups II and III was detected, apart from a variant region downstream from the sixth gene, which contained several copies of different LTR retrotransposons. The BACs selected using the rpa1a gene were also mapped against the SUCEST database (EST sequences) and the RNA-seq and sRNA libraries. Figure  5B  shows mapping for one BAC of each of the three phylogenetic groups (I, II and III) and the other two BACs (SHCRBa_035_B09 and SHCRBa_196_O13). While most of the mRNA transcripts mapped against the CDSs, some sRNAs also mapped against TE sequences or non-coding regions, as expected. Two expression patterns were of particular note. First, there was a common region in all BACs, downstream from a LTR retrotransposon, with peaks of mRNA sequences (Figure  5Bi ). Transcription of this region may be directed by promoter sequences in the 3′ LTR of the LTR retrotransposon.
For over 10 years directed genetic modification of sugarcane has been a reality in laboratories with field trials also being conducted  [44]. Genomics could also aid in traditional marker-based breeding, providing putative marker sequences derived from genes, TEs, intergenic or low complexity regions  [45] [46] [47]. Here we have sequenced and annotated 1,400 sugarcane protein-coding genes and several non-coding genes, including ribosomal and miRNA genes. The protein-coding genes code for enzymes in several metabolic pathways. For some of the genes that are clearly important in sugarcane breeding, for example, genes from the sucrose and starch metabolism, the complete CDSs are available in the transcriptome database, but no information about introns and intergenic regions have been previously published.
Other genes have not been previously sequenced in sugarcane, among them genes involved in the metabolic pathways not traditionally considered in sugarcane breeding, such as the carotenoid biosynthesis pathway. The sequencing of complete genes, including coding regions, UTRs, introns and promoters in genomic sequencing projects, instead of sequencing only transcribed sequences, as in transcriptome sequencing projects, provides a broader database for the design of transgene constructs. This work has shown that it is fundamental to combine genome and transcriptome sequencing approaches (sRNA and mRNA) to validate genome annotation and provide a broad understanding of functional genomics. The potential of the sequenced BAC collection was demonstrated by sequencing 16 genes related to the central enzymatic steps of carbon partitioning in source-sinkgrowth in plants.