dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments We are grateful to all those who helped with sample collection. This includes the  MEDITS survey programme  ( IEO Mallorca ) for Mediterranean samples. Portugal mainland samples were collected under the EU Data Collection Framework (DCF, PNAB). Azores specimens from the  Department of Oceanography and Fisheries (DOP) of the University of the Azores (UAc)  were collected under the project  DEMERSAIS ''Monitorizaca ˜o das especies demersais dos Acores '' financed by the  Azorean government , and the project  DEECON ''Unravelling population connectivity for sustainable fisheries in the Deep Sea '' project approved by the  European Science Foundation (ESF)  under the  EUROCORES programme  (proposal No  06-EuroDEEP-FP-008 & SFRH-EuroDEEP/0002/ 2007 ). This study was funded by the  UK Natural Environment Research Council  ( NERC) Oceans 2025 Strategic Research Programme Theme 6 (Science for Sustainable Marine Resources ).
REB was supported by the  Fisheries Society of the British Isles (FSBI) ,  BSP  was funded by the Fundaca ˜o para a Ciencia e a Tecnologia,  SFRH/BPD/72351/2010  and JL was supported by  The Alasdair Downes Marine Conservation Fund. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://crea tivecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Energy resources may also be limited, in which case the animal would use its lipid reserves, leading also to death if the animal's lipid content reached a minimum lipid value [equation (A19) in Appendix A]. On the other hand, if energy resources were available in excess, lipids were deposited as adipose tissue (equation (A17) in Appendix A). If an animal died, its data were replaced by mean values over the flock in order to mimic the purchase of a new sheep. The number of animal deaths was recorded.
We used the function 'morris' of the package 'sensitivity'  (Pujol et al. 2014)  of the software R (R: A Language and Environment for Statistical Computing, 2014), which implements the Morris elementary effects screening method  (Morris, 1991). We considered a design with 5 levels, and a grid jump of 2 to follow the Morris recommendation. Due to the large number of parameters included in our model, we chose r = 200 replications to ensure the number of combinations of parameters was sufficient. This resulted in a design with (p + 1) × 200 = 5600 combinations of parameters. For each combination, we evaluated our model and registered output traits of interest: life/death status at the end of the lamb period (i. e. on day 152) the value of which was either the day of death or 152 if the lamb was still alive, life/death status at the end of the simulation period (i.
Detailed sensitivity analysis. The parameters highlighted by the screening step are partly different for animal mortality and for WM. These were further studied in two more detailed sensitivity analyses with the same uncertainty domain. Other parameters were fixed to their nominal values. Latin hypercube sampling (LHS) was used to design 3000 and 4000 experiments with our model to respectively study sheep mortality and the level of infection. A Latin hypercube is the generalization of a Latin square to an arbitrary number of dimensions. This experimental design is often used in computer experiments as it ensures that the ensemble of random numbers is representative of the real variability (more uniformly). To do this, we used the function 'OptimLHS' of the R package 'lhs'  (Carnell, 2012).
The outputs observed were the same as those observed in the screening step, plus the FEC and the body weight at each key point of time, and the milk yield at three main points of the lactation period. Multivariate sensitivity analysis was carried with the R-package 'multisensi'  (Lamboni et al. 2009)  which ensures dynamic sensitivity analysis by computing sensitivity indices on each daily WM output. We also analysed single outputs by using a polynomial linear metamodel  (Faivre, 2013)  with the function 'PLMM' in the R-package 'mtk'  (Wang et al. 2014).
2%. Among queens declared pregnant, 8. 4% failed to maintain pregnancy. Globally, 78% of the mated females gave birth to 28,065 kittens within 7,075 L. Mean litter size was 4. 0 ± 1. 9 kittens among which 8. 5% were stillborn. Neonatal and paediatric mortality rate was 8. 2%. In total, 16. 0% of kittens born died before weaning. The results of this study are based on the largest feline database ever analysed. The figures collected can thus be used as reference to define average reproductive performances in numerous breeds for cat breeders. Further analysis will identify factors influencing reproductive performances and early mortality in the feline species.
| Data management Each line in the database corresponds to an oestrus with mating. Only purebred matings were registered. Variables included information on genitors, environment and litters. Corrections have been made to ensure the quality of the data. Every negative interval was considered as aberrant data (e. g. queening cannot occur before mating). Intervals of aberrant length according to literature lead to exclude the corresponding data: mating has to occur within 15 days after the onset of oestrus, pregnancy declaration, abortion and queening have to occur, respectively, between 15 and 80 days, 15 and 56 days, 50 and 80 days after mating  (Johnston, Kustritz, & Olson, 2001; Sparkes et al. , 2006). The status of the queen (pregnant, aborted or queening) as declared by breeders has been verified thanks to kitten's data (birth or not).
| Definitions of variables Variables used in the analysis were defined as follows: Age of the queen/tomcat at mating (year): mating date subtracted by the birth date of the queen/tomcat divided by 365. 25. Origin of the tomcat: housing to the declarant or not. The females were all considered as belonging to the cattery of the declarant, as external origin was marginal (<0. 01% (21/5303)). Pregnancy rate: number of pregnant females (as declared by the breeders) divided by the number of mated females (all the females included in the database were mated)*100.
| Statistical analysis Descriptive statistics were performed on gestation length, pregnancy rate, abortion rate, queening rate, pre-weaning mortality, stillbirth, neonatal and paediatric mortality rates thanks to Microsoft Excel software (Microsoft corporation) and SAS software (SAS-PC system, Version 9. 3 for Windows; SAS Institute, Cary, NC, USA) in the general population with 95% confidence intervals (calculated thanks to Exact binomial) and for each breed represented by a sufficient number of oestrus (n > 10).
| Reproductive performances Pregnancy rate was 85. 1% (n = 7,710). Among pregnant queens, 8. 2% (n = 637) failed to maintain pregnancy. Globally, 78. 1% (n = 7,075) of the mated females gave birth to 28,065 kittens within 7,075 L (Table  1 ). Sex ratio of born kittens (male:female) was 1:1. 1. Mean litter size was 4. 0 ± 1. 9 kittens. Most of the queens (58%, n = 4,126) delivered between three and four kittens and <10% (n = 586) delivered four kittens or more. Table  2  provides pregnancy and queening rates together with prolificacy for the 34 breeds represented by more than 10 oestrus in the dataset.
| DISCUSSION To our best knowledge, the database analysed in the present work is the largest ever analysed for the feline species in reproduction. The process of data registration, online, by breeders for the management of their own cattery, is much more powerful than any ret- Persian and British Shorthair with a difference of 4%) over the same period. Nevertheless, it may also be speculated that the breeders that did contribute to the dataset through the breeding management software were probably among the most motivated and progressive breeders. This may have slightly skewed the results, with better results with breeding and kitten survival than the total French feline population. Such a dataset allows to calculate key reproductive indexes for the different breeds, but offer limited opportunity to identify factors potentially impacting reproductive performances.
| Genitors and mating The mean young age at mating observed in our study (2. 7 years for females and 2. 9 years for males) is similar to published studies ranging from 2. 8  (Sparkes et al. , 2006)  to 3. 3 years  (Ström Holst & Frössling, 2009). As suggested by  Sparkes et al. (2006)  who reported a high proportion of primiparous females (39. 6%), this may be associated with a high rate of female turnover. However, in our dataset, some queens and tomcats were observed mated as old as 11. 6 and 18. 1 years, respectively; in 9. 4% of the matings, at least one partner was older than 6 years. The low number of queens per cattery and litters per queen registered over the 4 year study may indicate that reproduction is practised on a weak intensity, but parity and the following reproductive career of queens would be needed to conclude.
| Pregnancy Queens were considered as pregnant in our dataset based on the breeder's opinion without any information on the time of diagnosis (mid or late gestation or even at queening) as well as the method used (veterinary ultrasound examination, abdominal palpation by breeder or observation of queening). The proportion of queens undergoing a veterinary diagnosis is probably very limited  (Ström Holst & Frössling, 2009). So pregnancy and abortion rates have thus to be considered with caution, with our pregnancy rate being slightly higher (85%) than 73% in  Swanson, Roth, and Wildt (1994)   were ovariohysterectomized and examined for the presence and viability of embryos between 2 and 20 days of pregnancy.
| Queening The queening rate we observed (78. 1%) was similar to that of a Canadian study on 189 queens (from around 10 breeds) reporting 70%, ranging from 40% to 80% according to the breed  (Povey, 1978). Abortion and pregnancy rates were not documented. The queening rate of Persians markedly differs between our (76. 4%) and Povey's study (40%), either revealing a large individual variability or a positive evolution of the breeding management of Persian. Prolificacy was consistent with other studies, with a mean litter size ranging from three to five kittens  (Jemmett & Evans, 1977; Johnstone, 1987; Povey, 1978; Prescott, 1973; Root et al. , 1995; Sparkes et al. , 2006; Ström Holst & Frössling, 2009). While litter size did not exceed T A B L E 2 Reproductive performances and kitten mortality rates in the 34 most represented cat breeds (more than 10 oestrus in the database) Stillbirth rate (8.
5%) was consistent with other studies: from 4. 7% to 9. 7%  (Jemmett & Evans, 1977; Povey, 1978; Root et al. , 1995; Sparkes et al. , 2006; Ström Holst & Frössling, 2009). Nevertheless, the experimental designs of these studies (including this one) may lead to an underestimation of kitten mortality rates, especially for stillbirth. Indeed, registration of kittens born dead is of no interest for breeders, neither in national kennel club files (in some countries, breeders have to pay for the registration of each newborn), nor for their own internal cattery management (those kittens will obviously not be sold). Stillbirth rate increases with litter size  (Sparkes et al. , 2006). The higher proportion of stillbirths observed in this study might be explained by the number of large cats (Main Coon, Norwegian Forest cats) included in the database, with larger litters (Fournier).
| Neonatal and paediatric mortality The global kitten mortality rate in our dataset (15. 7%) was lower than the rate reported in the literature, ranging from 16. 3% to 29. 1%  (Jemmett & Evans, 1977; Povey, 1978; Root et al. , 1995; Sparkes et al. , 2006; Ström Holst & Frössling, 2009). Factors responsible for this high mortality rate, especially stillbirth, remain to be identified. The neonatal and paediatric mortality rates (7. 2%) are the lowest range reported in the literature  (Jemmett & Evans, 1977; Povey, 1978; Root et al. , 1995; Sparkes et al. , 2006; Ström Holst & Frössling, 2009). While infectious status of catteries and breeding management (indoor or outdoor) were unknown, low intensive reproduction in France and internal mating for the vast majority of queens reduce the risk of infectious diseases, maybe contributing to these low neonatal and paediatric mortality rates.
| CONCLUSION The database analysed in this study is the largest feline reproduction database ever surveyed. Due to the large number of contributing breeders, the figures provided are probably a good start to assess feline reproductive performances. As inter racial variations may exist in the domestic cats, performance indexes have to considered by breed. Further analysis will attempt to identify factors of significant influence on reproductive performances and early mortality. Management practices might then be adapted to improve feline breeding productivity. T A B L E 3 Kitten mortality rates (means and 95% confidence intervals (CI)) n = 7,075 L including 28,065 kittens from 5,303 queens of 45 cat breeds.
Primers and probes design The primers and probes were designed to amplify and detect specific regions for each of the four targeted pathogens. The targeted gene fragments were located on the 30 kDa RNA polymerase subunit (RPO30) gene for CaPV, the nucleoprotein (NP) gene for PPRV, the Kmt1 gene (alpha/beta hydrolase family protein) for PM and one helicase gene for Mccp. The fulllength sequences of the targeted genes of PPRV, CaPV and PM were retrieved from GenBank and were aligned individually for each pathogen using MEGA Version 5. 1. The target gene for Mccp was selected from the sequences generated by CIRAD, (Accession number: LM995445). Primers and probes were designed using the conserved regions of those genes using Allele ID1 software version 6 (Premier Biosoft International, Palo Alto, USA).
The one-step multiplex RT-qPCR was developed and evaluated on the CFX 96™ real time PCR machine (Bio-Rad) with cycling parameters as follows: 50°C for 20 min followed by 95°C for 5 min and 40 cycles of denaturation at 94°C for 10 sec, annealing at 56°C for 20 sec, and extension at 62°C for 20 sec. The data acquisition was performed during the annealing step on four different channels: green (FAM), yellow (HEX), orange (TEXAS RED) and red (CY5).
Analytical sensitivity of the assay The limit of detection of the multiplex assay was determined for each pathogen as follows: for CaPV and PM, plasmid dilutions of 20, 16, 12, 8 and 4 copies/reaction were assayed. For Mccp, the dilutions were: 80, 40, 16, 12, 8 and 4 copies/reaction and PPRV transcript dilutions were 200, 160, 120, 80 and 40 copies/reaction. The analytical sensitivity of the assay was determined by testing these diluted plasmids and PPRV transcripts for amplification in pentaplicate separately at three different intervals. The proportion of predictive positive results was determined by regression analysis using the STATGRAPHICS Centurion XV Version 15. 2. 12 software package (StatPoint Technologies, Warrenton, VA, USA).
Acknowledgments The authors duly acknowledge all the veterinarians and technicians involved in the collection and provision of samples used during the development and validation of the assay. The authors would also like to thank  Dr William Dundon ,  Dr Caroline Adombi  from  APHL  for providing PPRV samples;  Dr Jolanta Kolodziejek  and  Dr Norbert Nowotny ,  Vetmed University, Vienna  for providing parainfluenza 3 viral RNA used in this study. The authors would also like to acknowledge  Dr Jenna Achenbach  for language editing of the manuscript.
Identification, characterization and distribution of TNLs We carried out BLAST P analysis on the predicted peptides database for the peach genome v1. 0, with various relevant sequences as queries, to extract the putative peach TNL proteins. With this screening method, we retrieved 205 predicted TNL proteins from the predicted peptide dataset. The complete structure of all predicted TNLs was characterised and refined by retrieving the associated nucleotide sequences together with a 5 kb 5' extension and a 5 kb 3' extension. Analyses of these extended genomic sequences with relevant gene-predicting software suites revealed the presence of unidentified or mispredicted exons, thereby improving v1. 0 gene sequence predictions. Fgenesh  [35]  was the only program to predict the correct intron-exon structure of the Ma gene (Additional file 1).
The translated DNA coding sequences were then analysed with the InterProScan tool  [36] , to delineate the various domains in each TNL genes. These procedures made it possible to decrease the total number of TNL genes to 195. This set of TNL genes was also mapped onto the v2. 0 genome sequence. The full list of TNL-related genes, with their exon/domain structure, positions and accession numbers (used in both versions of the genome) are indicated in Additional file 2. In parallel, we developed a TNL-specific generic format file (gff3 file, see Additional file 3) to facilitate the comparison between our predictions and the v2. 0 genome annotation. We retained the accession numbers from v1. 0 of the genome, making it possible to relate the two accession glossaries directly. A comparison of the different types of structures among these TNL genes in the peach genome (Fig.
There seems to be a conserved general pattern with a few atypical structures resulting from exon duplication or deletion. Based on the complete data for the peach genome, we were able to define a typical TNL pattern (Fig. 2 ). Each single exon of a TNL gene corresponds to a single domain in the corresponding protein and the mean sizes of the TIR, NB and NLL exons were 523, 1038 and 286 bp, respectively. The exons corresponding to the LRR and PL domains had mean sizes of 906 and 578 bp, respectively. These domains displayed greater size variation than the N-terminal domains, consistent with their greater polymorphism and the difficulties encountered in their accurate prediction. The N, BS4 [GenBank:AAR21295] [37], and RPS4 [GenBank:CAB50708]  [38]  genes, used as reference TNLs, have a single exon encoding both the LRR and PL domains.
PL domains We initially defined the PL domains as sequences located in C-terminus of the TNL-related peptides and not matching any known protein domain. We extracted all the PL domain amino-acid sequences and added the corresponding PL domains from the reference TNLs, N, Ma, BS4, RPS4 and Gro1-4 [GenBank:AAP44390]  [13]. By combining expert annotation, alignment and size selection, we obtained a complete set of 124 PL domains that we considered reliable for use in subsequent motif detection. Through MEME analysis, we developed three specific signatures of the PL domain (Table  1 ), which were recovered in 95, 89, and 83 % of the PL sequences, Fig. 3  Location of the predicted TNL-related genes in the physical map of the peach genome v2. 0. The map position of the 195 total TNL-related proteins is depicted within the eight Prunus persica (Prupe) pseudo molecules (chromosomes).
Accession numbers are related to the genome glossaries of the v2. 0 and v1. 0 when available. Merged predicted peptides identified through corrected predictions are underlined and highlighted with brackets. The size of each scaffold (in Mb) and the respective number of TNL-related predicted peptides are shown above each scaffold. The Ma orthologue is indicated in red upper case. Unmapped genes in the v1. 0 and mapped in the v2. 0 are in green boxes. The red box shows re-localisation of TNL genes in the v2. 0. Predicted peptides that are not indicated anymore in the v2. 0 are labelled with an asterisk. Orange and yellow boxes highlight strand inversion of TNLs and unmapped TNLs, respectively respectively. When present, these motifs were always detected in the same order from the N-to the C-terminus of the protein.
0 sequence. A complete PL sequence was expressed for both genes, as demonstrated by the sequencing of PCR products (Additional file 6) (EMBL accession numbers LT555556 to LT555568). For each candidate, the alignment of the peach 'Nemared' and plum 'Myrabi' cDNA sequences (when available) with their genomic sequences and their sequences as predicted from mRNA revealed the correct location of the intron between the LRR and PL exons (Fig. 5b ). As expected, a lower level of polymorphism has been observed between the genome and the 'Nemared' peach sequence than between the genome and the 'Myrabi' plum sequence (Fig. 5b ).
These data highlight the correlation between the similarity and physical location of the PL domain sequences. This correlation made it possible to attribute the unmapped TNLs ppa026065m and ppa000640m from clade 3 to chromosome 8 and the unmapped TNL ppa021732m from clade 2 to chromosome 1. Similarly, the four unmapped TNLs from the same subclade unmapped in the v1. 0 sequence, ppa015313m, ppa025931m, ppa025473m and ppa000477m, were localised to the same cluster on chromosome 3 of the v2. 0 sequence (Additional file 4). Within the Ma gene cluster, the higher degree of conservation of the PL sequences between Ma [GenBank:-CAR94514] and its peach orthologue (ppa021441m) than between the Ma peach orthologue (ppa021441m) and its peach paralogue (ppa014815m), all belonging to clade 4, indicates that the separation of the peach and plum lineages occurred after the TNL duplication.
PL detection among genomes MAST and BLASTP analyses were conducted with the PL motifs and the Plant Genome Database, to determine the number of TNL-related protein genes that could be detected in ten reference genomes of various sizes. The P. persica dataset was used to assess the relevance of our approach, Using PL motifs, we were able to detect 72 % (94 of 130) of all peach TNLs with one or several PL domains (Table  2 ). Indeed, the automated prediction for v1. 0 did not detect PL domains for any of the 36 missing sequences that were later annotated as PL-carrying TNL genes. Nevertheless, a combination of the use of transcriptomic data and the reannotation of the v2. 0 genome sequence resolved most of the mispredicted PL domains. In dicots genomes, between 50 and 87 % (Table  2 ) of TNL sequences could be detected using PL signatures.
For example, in the P. trichocarpa genome  [5]  69 of the 91 TNL related-genes identified presented PL signatures. Thus, at least three quarters of the TNLs of this species carry a PL domain. The proportion of TNL genes with a PL domain was highest in the potato genome (87 %). By contrast, no PL domain sequences were detected in the three Poaceae species (O. sativa, S. bicolor and Z. mays), consistent with the almost total absence of TNLs in monocots. Moreover, no non-TNL sequences were found to have PL motifs with a consistent e-value (<0. 01), suggesting that these motifs are specific to TNLs. The detailed results of the BLASTP analysis are reported in Additional file 7. Furthermore, the use of our motifs led to the detection of particular PL domain repeats in peptide databases. We detected a few proteins with atypical structures in V.
Unmapped sequences are labelled in white. Predicted peptides marked with purple and orange stars are attributed to chromosomes 2 and 3 respectively in the v2. 0. The protein labels contain the genome predicted peptide identifier followed by the PL domain number. Bootstraps over 70 (out of 100) are shown were identified in any of the other plant genomes tested. An orthoMCL analysis on 31 plant genomes conducted with the protein orthologous to Ma in peach (ppa021441m) revealed an orthoMCL group (GRP18645) including the other three members of the ppa021441m cluster (ppa014815m, ppa020701m, ppa025905m) (Fig. 3 ) and six other members from the apple protein dataset (Malus domestica) [GDR:MDP0000267764, MDP0000176003, MDP0000272063, MDP0000158765, MDP0000264373, MDP0000143700]. MDP0000176003 is presumably the Ma apple orthologue (lacking the TIR domain), as it has a similar five-PL domain structure.