dataesr/scientific-paragraphs-categorization huggingface dataset:
The dataset also featured 140 negative cases among which 16 samples presented a large number of blood cells consecutive to a traumatic lumbar puncture. The remainder included 12 cases (6%) of which the diagnosis was not deemed definitive at the time of the study. Lens-free microscopy acquisitions were performed at three different wavelengths in order quickly and efficiently to reconstruct the image of the cells with a resolution sufficient to obtain size and position information (Fig. 1 ). An optical signature for every cell was obtained by propagating the reconstructed complex image of the cell along the optical axis at different distances Z from the sensor plane (Fig. 2 ). Based on this optical signature, we then developed an algorithm for counting CSF leukocytes and erythrocytes in CSF samples, to establish an early diagnosis of meningitis.
On the basis of this first CSF dataset, we established an algorithm to detect CSF specimens with a leukocyte concentration > 10 cells/μ L, i. e. the limit used for the biological definition of meningitis. Cell counting by microscopic counting, with the reading done by an operator, was performed for comparison. Figure  3  shows the receiver operating characteristic (ROC) curves obtained with different lens-free classification algorithms. The first lens-free classification algorithm performs a gating on the measured cell diameter to count the leukocytes and test the limit of 10 leukocytes/μ L. The results are not convincing, as they are close to the threshold of non-discrimination. Accordingly, the reconstructed module image presented an insufficient resolution to distinguish the different blood cells based on size criteria, i.
In a third step, we measured the performance of lens-free microscopy and an algorithm for the diagnosis of infectious meningitis. In a blind assay, we prospectively compared lens-free microscopy on 116 CSF clinical specimens with the diagnosis actually determined for every patient. The results for meningitis/non-meningitis categories using a 10 leukocyte/μ L cut-off allow one to establish the sensitivity and specificity of lens-free microscopy. The dataset of 116 CSF clinical specimens included six cases of microbiology-confirmed infectious meningitis, and 20 cases of non-infectious meningitis, including four cases of carcinomatous meningitis, 12 cases of hemorrhages, and four cases of autoimmune diseases. The dataset also featured 90 negative cases, among which 31 samples presented a large number of blood cells consecutive to a traumatic lumbar puncture.
(b) Scatterplot of the automatic lens-free count of leukocytes and erythrocytes resulting from the analysis of the first datasets featuring 116 clinical specimen used in the proof-of-concept study. We counted in total 31 positive samples corresponding to six true positive of infectious meningitis and 25 false positives cases. Eight false positives diagnosed are further discarded by applying additional criteria on the on the number of erythrocytes. As a result, lens-free microscopy achieved a sensitivity of 100% and a specificity of 79% for the diagnosis of infectious meningitis.
We estimated the average recombination rate of Lacaune sheep at 1. 5 cM/Mb, identified 50,000 crossover hotspots on the genome, and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting interindividual variation in recombination rate in Lacaune, including the RNF212 and HEI10 genes and possibly two other loci of smaller effects including the KCNJ15 and FSHR genes. The comparison of these new results to those obtained previously in a distantly related population of domestic sheep (the Soay) revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome. The two data sets were thus combined to create more precise male meiotic recombination maps in Sheep. However, despite their similar recombination maps, Soay and Lacaune males were found to exhibit different heritabilities and QTL effects for interindividual variation in genome-wide recombination rates.
Study population and genotype data In this work, we exploited two different data sets of sheep from the Lacaune breed: a pedigree data set of 8085 related animals genotyped with the medium-density Illumina Ovine Beadchip including 54,241 SNPs, and a diversity data set of 70 unrelated Lacaune individuals selected as to represent population genetic diversity, genotyped with the high-density Illumina Ovine Infinium HD SNP Beadchip  (Moreno-Romieux et al. 2017; Rochus et al. 2017). Standard data cleaning procedures were carried out on the pedigree data set using plink 1. 9  (Chang et al. 2015)  excluding animals with call rates below 95% and SNPs with call frequency , 98%. After quality controls, we exploited genotypes at 46,813 SNPs and 5940 meioses. For these animals, we only selected the sires that had their own sire known and at least two offspring and the sires that did not have their own sire known but at least four offspring.
Specifically, a mixture of Gaussian distribution was fitted to the genome-wide distribution of log 10 ðl j Þ using the mclust R package  (Fraley and Raftery 2002; Fraley et al. 2012) , considering that the major component of the mixture modeled the background distribution of l j in nonhotspot intervals. From this background distribution, a P-value was computed for each interval that corresponded to the null hypothesis that it does not harbor a hotspot. Finally, hotspot-harboring intervals were defined as those for which false discovery rate (FDR) (l j ) , 5%, estimating FDR with the  Storey and Tibshirani (2003)  method, implemented in the R qvalue package. This procedure is illustrated in  Figure S2 in File S11. Combination of meiotic and historical recombination rates and construction of a high-resolution recombination map: To construct a meiotic recombination map of the HD SNP array requires that the historical recombination rate estimates be scaled by four times the effective population size.
After having corrected for the chromosome effect, the GC content effect and for windows farther than 4 Mb of the chromosome end, we fitted a linear regression model to estimate the effect of hotspot density on the meiotic recombination rate. Comparison with Soay sheep recombination maps and integration of the two data sets to produce new male recombination maps in sheep: To compare the recombination maps in Lacaune with the previously established maps in Soay sheep  (Johnston et al. 2016) , we downloaded the raw data from the dryad data repository (doi: 10. 5061/dryad. pf4b7) and the additional information available on https:// github. com/susjoh/GENETICS_2015_185553. As the approach used in  Johnston et al. (2016)  to establish recombination maps differs from the one used here, we chose to apply the method of this study to the Soay data to perform a comparison that would not be affected by differences in the methods.
As the Lacaune data consist only of male meioses, we also only considered male meioses in the Soay data. The final Soay data set used consisted of 3445 individuals, among which were 299 male FIDs, defined as in the Lacaune analysis. After detecting crossovers with LINKPHASE, one FID exhibited a very high average number of crossover per meiosis (. 100) and was not considered in the analyses (Soay individual ID: RE4844), leaving 298 FIDs. The final data set consisted of 88,683 crossovers in 2609 male meiosis and was used to estimated meiotic recombination maps using the exact same approach as described above, both on intervals of 1 Mb and on the same intervals as the ones considered in the Lacaune meiotic maps on the medium-density SNP array. Note that the Soay sheep are not necessarily polymorphic for the same markers as the Lacaune, but that our method is flexible and can nonetheless estimate recombination rates in intervals bordered by monomorphic markers: in such a case adjacent intervals will have the same estimated recombination rate.
Single-and multi-QTL GWAS on GRR We first tested association of individual estimated breeding values e u s (EBVs) with mean genotypes at 503,784 single SNPs imputed with BimBam. We tested these associations using the univariate mixed model approach implemented in the Genome-wide Efficient Mixed Model Association (Gemma) software  (Zhou and Stephens 2012). To account for polygenic effects on the trait, the centered genomic relationship matrix calculated from the mean genotypes was used. The P-values reported in the results correspond to the Wald test. To go beyond single SNP association tests, we also estimated a Bayesian sparse linear mixed model  (Zhou et al. 2013)  as implemented in Gemma. This method allows the consideration of multiple QTL in the model, together with polygenic effects at all SNPs.
Given that the average physical distance between SNPs on the high-density SNP array is 5 kb, this procedure interrogates the probability of the presence of a QTL in overlapping windows of 250 kb. For the univariate analysis, the FDR was estimated using the ash package  (Stephens 2017) , and SNPs corresponding to an FDR , 10% were deemed significant and annotated. For the multivariate analysis, regions where the rolling sum of PIPs were. 0. 15 were further annotated. The annotation of the QTL regions consisted of extracting all genes from the Ensembl annotation v87 along with their Gene Ontology (GO) annotations and interrogating for their possible involvement in recombination. Variant discovery and additional genotyping in RNF212: identification and assignation of the RNF212 sheep genome sequence The RNF212 gene was not annotated on the Ovis aries v3.
Variant discovery in RNF212 in the Lacaune population Based on the genomic sequence and structure of the RNF212 gene annotated in O. orientalis (NCBI accession NW_011943327), a large set of primers were designed using PRIMER3 software (Table  S1  in File S11) for amplification of each annotated exon and some intron parts corresponding to exonic regions annotated in Capra hircus (Chir_v1. 0). PCR amplification (GoTaq; Promega, Madison, WI) with each primer pair was realized on 50 ng of genomic DNA from four selected homozygous Lacaune animals exhibiting the GG and AA (nonimputed) genotypes at the most significant SNP of the medium-density SNP array of the chromosome 6 QTL (rs418933055, P-value 2. 56e217). Each PCR product was sequenced via the BigDye Terminator v3. 1 Cycle Sequencing kit and analyzed on an ABI3730 sequencing machine (Applied Biosystems, Foster City, CA).
Data availability Genotype data and pedigree information on Lacaune individuals after quality controls are deposited on Zenodo  (Astruc et al. 2017)  as well as high-density genotypes of 70 unrelated Lacaune individuals (Moreno-Romieux et al. 2017). Computer code and scripts needed to reproduce all results are available on Github (https://github. com/BertrandServin/ sheep-recombination) and described in supporting material File S10. Additional data, including output from PHASE, LINKPHASE, BimBam, and Gemma, are provided on the Zenodo repository (DOI: 10. 5281/zenodo. 821569) (Petit et al. 2017).
In highly recombining chromosomes, recombination rates were globally higher on chromosome 14, while chromosome 11 exhibited two very high-recombination windows between 7 and 8 Mb and between 53 and 54 Mb. In addition, we found, consistent with the literature, that GC content was quite significantly positively correlated with recombination rate both in medium SNP array intervals (P-value , 10 216 , r = 0. 20) and in 1 Mb intervals (P-value , 10 216 , r = 0. 28). Estimation of historical recombination rates and identification of crossover hotspots: We used a different data set, with 51 unrelated individuals from the same Lacaune population genotyped for the Illumina HD SNP array (600K) comprising 527,823 autosomal SNPs after quality controls. Using a multipoint model for LD patterns  (Li and Stephens 2003) , we estimated, for each marker interval of the HD SNP array, historical recombination rates r (see Materials and Methods).
For each interval between two adjacent SNPs of the density array, we (i) extracted the number of significant historical hotspots and (ii) calculated the historical hotspot density (in number of hotspots per unit of physical distance). We found both covariates to be highly associated with meiotic recombination rate estimated on family data [r = 0. 15 with hotspot density (P , 10 216 ) and r = 0. 19 with the number of hotspots (P , 10 216 )]. These correlations hold after correcting for chromosome and GC content effects [respectively, r = 0. 14 (P , 10 216 ) and r = 0. 18 (P , 10 216 )]. Figure  2  illustrates this finding in two 1-Mb intervals from chromosome 24: one that exhibits a very high recombination rate (7. 08 cM/Mb) and the second a low one (0. 46 cM/Mb). In this comparison, the highly recombining window carries 36 recombination hotspots while the low recombinant one exhibits none.
Improved male recombination maps by combining Lacaune and Soay sheep data: Recently, recombination maps have been estimated in another sheep population, the Soay  (Johnston et al. 2016). Soay is a feral population of ancestral domestic sheep living on an island located northwest of Scotland. The Lacaune and Soay populations are genetically very distant, their genome-wide Fst, calculated using the sheep HapMap data  (Kijas et al. 2012) , being 0. 4. Combining our results with results from the Soay offered a rare opportunity to study the evolution of recombination over a relatively short timescale as the two populations can be considered to have been separated at most dating back to domestication, 10,000 years ago. The methods used in the Soay study are different from those used here, but the two data sets are similar, although the Soay data has fewer male meioses (2604 vs.
5940 in the present study). To perform a comparison that would not be affected by differences in estimation methods, we ran the method developed for the Lacaune data to estimate recombination maps on the Soay data. As the Soay study showed a clear effect of sex on recombination rates, we estimated recombination maps on male meioses only. Figure  4  presents the comparison of recombination rates between the two populations in marker intervals of the medium-density SNP array. The left panel shows that the two populations exhibit very similar recombination rates (r = 0. 82, P , 10 216 ), although Soay recombination rates appear higher for low recombining intervals (c , 1. 5 cM/Mb in gray on the figure). We explain this by the shrinkage effect of the prior, which is more pronounced in the Soay as the data set is smaller: the right panel on Figure  4  shows that the posterior variance of the recombination rates are clearly higher in Soays for low recombining intervals while they are similar for more recombining intervals.
(2013)  led to estimate that, together, QTL explain 40% of the additive genetic variance for GRR, with a 95% credible interval ranging from 28 to 53%. The most significant region was located on the distal end of chromosome 6 and corresponded to a locus frequently associated with variation in recombination rate. In our study, the significant region contained 10 genes: CTBP1, IDUA, DGKQ, GAK, CPLX1, UVSSA, MFSD7, PDE6B, PIGG, and RNF212. For each of these genes except RNF212, which was not annotated on the genome (see below), we extracted their gene GO of the Ensembl v87 database, but none was clearly annotated as potentially involved in recombination. However, two genes were already reported as having a statistical association with recombination rate: CPLX1 and GAK  (Kong et al. 2014 ). CPLX1 has no known function that can be linked to recombination  (Kong et al.
It matched an association signal on GRR in Soay sheep  (Johnston et al. 2016). Consistent with our finding, in the Soay sheep study, this association was only found using regional heritability mapping and not using single SNP associations with the medium-density SNP array. This locus could match previous findings in cattle (association on chromosome 10 at 20 Mb on assembly btau3. 1); however, the candidate genes mentioned in this species (REC8 and RNF212B) were located 2 and 1. 5 Mb away from our strongest association signal, respectively. In addition, none of the SNPs located around these two candidate genes in cattle were significant in our analysis. Eleven genes were present in the region: OR10G2, OR10G3, TRAV5, TRAV4, SALL2, METTL3, TOX4, RAB2B, CHD8, SUPT16H, and RPGRIP1. The study of their GO, extracted from the Ensembl v87 database, revealed that none of them were associated with recombination, although SUPT16H could be involved in mitotic DSB repair  (Kari et al.
Discussion In this work, we studied the distribution of recombination along the sheep genome and its relationship to historical recombination rates. We showed that contemporary patterns of recombination are highly correlated to the presence of historical hotspots. We showed that the recombination patterns along the genome are conserved between distantly related sheep populations but that their genetic determinism of genome-wide recombination rates differ. In particular, we showed that polymorphisms within the RNF212 gene are strongly associated to male recombination in Lacaune, whereas this genomic region shows no association in Soay males. Hence, combining three data sets, two pedigree data sets in distantly related domestic sheep populations and a densely genotyped sample of unrelated animals, revealed that recombination rate and its genetic determinism can evolve at short timescales, as we discuss below.
2014 ) and bovids  (Ruiz-Herrera et al. 2017). Furthermore, the variations at the major mammal recombination loci (RNF212, CPLX1, and REC8 or the Human inversion 17q21. 31) explain only 3 to 11%  (Ritz et al. 2017)  of the phenotypic variance among individuals. Elucidating the genetic determinism of these different processes would thus require much larger sample sizes or different experimental approaches  (Baier et al. 2014; Ruiz-Herrera et al. 2017). The combination of data sets from the Lacaune population and one from the recent study of recombination in Soay sheep  (Johnston et al. 2016 ) allowed us to study the evolution of recombination at relatively short timescales. One of the most striking differences between our two studies is that the two QTL that were detected to be in common had no effect in Soay males, whereas they had strong effects in Lacaune males.
Acknowledgments Numerical analyses were performed on the genotoul bioinformatics platform  Toulouse Midi-Pyrenees  ( Bioinfo Genotoul ). We are thankful to  Tom Druet ,  Laurent Duret ,  Alain Pinton ,  Pierre Sourdille ,  Susan Johnston , and an anonymous reviewer for their helpful comments on an earlier version of the manuscript. Institut de l'Elevage  (J. M. A. ) and breed organizations (Ovitest and  Confédération de Roquefort)  provided the SNP genotypes and pedigree information. This work was partially funded by the  BoDeliRe  grant of the  Institut National de la Recherche Agronomique Selgen Metaprogram  and by  Région Midi-Pyrénées.
EU401923) and conserved C-terminus (aa: 281-350; Sal-1 sequence, accession no. GU339059) (Fig. 1C ). For the second construct, (named after CS712 based on the number and the tandem of motif repeats; accession no. KY548404), both N-and C-terminals were the same as the first designed construct. However, the arrangement of the repeats in CS712 was four of ANGAGNQPG and three of ANGAGDQPG repeats of VK247 (totally, 7 repeat types of VK247), followed by six of each VK210 (GDRA[A/D]GQPA) (totally, 12 repeat types of VK210) (Fig. 1D ). To design both constructs, Sal-1 and PNG reference sequences were retrieved from the GenBank and aligned with ClustalW software (http://www. ebi. ac. uk/Tools/msa/clustalw2/)  (Thompson et al. , 1994)  to define conserved and non-conserved regions. Then the both genes were synthesized based on E.
Three dimentional structure validation analyses Visualization of 3D structure was carried out by PyMOL software version 1. 7. 2  (DeLano, 2002; Pedretti and Vistoli, 2004). Ramachandran plots were calculated by RAMPAGE server (http://mordred. bioc. cam. ac. uk/~rapper/rampage. php)  (Laskowski et al. , 1993). Moreover, the molecular docking approach was used to model the interaction between a small molecule of heparan sulphate binding and both chimeric proteins at the atomic level. The results could characterize the behaviour of ligand in the binding site of target chimeric constructs as well as elucidate fundamental biochemical processes  (Morris and Lim-Wilby, 2008). Docking analysis was performed by Hex Protein Docking  (Ghoorah et al. , 2013). For docking analysis, the PDB files of both tertiary structures of chimeric proteins predicted by I-TASSER and PDB files of ligand (PDB ID: 1HPN) were used.
Statistical analysis A database was generated with SPSS 16. 0 for windows (SPSS Inc. , USA). As the antibody levels were not normally distributed, non-parametric tests were used. Chi-square comparison of proportions and McNemar's test were applied to assess the differences in the proportions of IgG-positive subjects. Wilcoxon Signed Ranks test was also used to analyze differences between the mean absorbance of chimeric antigens. P values < 0. 05 were considered statistically significant in all tests.
Chimeric gene optimization The amino acids of both constructs were back translated to nucleotide sequence based on E. coli codon usage and both synthetic chimeras were analyzed for codon bias and GC content. An online database (http://www. jcat. de/) for gene optimization was used to predict the expression of the chimeric gene in E. coli. The synthetic constructs were further confirmed by the Codon Adaptation Index (CAI), which is a measurement of the relative adaptiveness of the codon usage of a gene compared with the codon usage of highly expressed genes in E. coli. The overall GC content, considered as a measure value for transcriptional and translational efficiency, was improved to 63. 22% for both constructs in comparison with the reference sequences (Sal-1, accession no. GU339059 for VK210: GC 50% and PNG, accession no.
It seems that the better expression level in the case of CS712 could be explained with the difference in the energy in these regions (-9. 8 for CS712 in comparison to -6. 9 for CS127). Furthermore, the higher yield of CS712 signifies that this construct can provide tremendous flexibility in terms of scaling-up and cost in large-scale vaccine production by fomenters. The analysis of physico-chemical parameters of CS127 and CS712 chimeric genes by ProtParam software; showed the acidic nature of both chimeric proteins (pI value = 5. 49), the same as natural CSP. High extinction coefficient was predicted for both chimeric proteins at 280 nm, which was confirmed by the high yield of protein expression. ExPASy ProtParam classifies both recombinant CS127 and CS712 chimeric structures as stable on the basis of instability index, which is necessary for chimeric recombinant structures.
One of the most significant obstacles in designing a recombinant chimeric protein is to have functional properties that are highly dependent on the 3D structure of the designed sequences. This concern is usually solved by the analysis of the predicted 3D structures of the designed protein. Ab-initio I-TASSER software, a reliable analysis tool, predicts precisely the CS127 and CS712 proteins folds and creates a good high-resolution model for these chimeric proteins. However, the theoretical predicted 3D structures of both constructs are slightly different, which is in the consequence of different positions of VK210 and VK247 repeats in both constructs. Despite these discrepancies, they showed similar biological activity using heparan sulphate and hepatoma cell line HepG2binding assay. This finding suggests that, the arrangement of repeat types can change the 3D structure of proteins though; no significant biological activity was identified.