dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments We thank all the surviving patients who agreed to participate in the study. We thank the research staff at the  "Direction de la Recherche Clinique et de l'Innovation" of Nîmes University Hospital :  S. Clément ,  C. Meyzonnier ,  N. Best ,  A. Megzari ,  E. Dupeyron ,  S. Granier ,  B. Lafont ,  C. Masseguin ,  H. Obert ,  H. Léal ,  O. Albert ,  C. Suehs ,  P. Rataboul , and  M. P. Francheschi. We thank the staff at the  "Département de Biostatistique, Epidémiologie, Santé Publique et Information Médicale , BESPIM" at  Nîmes University Hospital ,  P. Fabbro-Peray  and  Thibault Mura. We also thank  Teresa Sawyers  for her expert editorial assistance.
In order to get a dimensionless loss, we use the normalization : J(ν 0 ) := L(F(ν 0 ), ν) := L SD (F(ν 0 ), ν)/L SD (F(ν), ν). ( 30 ) We recall that the desired prescribed target ν is the point source solution and the denominator cannot vanish as F(ν) = K ν (see remark 2). Figure  4  is a plot of the Loss value using a parametric family of point source target mixing two Gaussians with varying expectations: (t, t ) ∈ [0, 1] 2 → L(F(ν (t,t ) 0 ), F(ν ( 1 3 , 1 3 ) 0 ), (31) where ν (t,t ) 0 = N u(t), π 21 + N v(t ), π 24 , u(t) = 20π 16 + t 2π 16 , v(t ) = 26π 16 + t 2π 16. The graph is smooth and convex. The optimal transport computations were implemented using the Geomloss package  [21]. The desired illumination data ν is either discrete or sampled into a discrete empirical measure and the potentials are approximated through a finite number of Sinkhorn iterations  (22).
The differentiability with respect to ν F , the desired property, is discussed in detail in  [22]. The simplicity of the computational approach allows using the auto-differentiation algorithms embedded in modern software (we use Pytorch, for the full code see  [23] ). Remark 4 (On the differentiability of J). While the Sinkhorn-Divergence potential f SD is differentiable with respect to ν 0 , the definition of the forward map itself depends on proposition 2 and the convexity of the reflector. This is only established for the non-entropic ε = 0 reflector. In practice f SD (see  (25) ) is a good approximation of f 0 and we used the autodifferentiation and gradient based optimization methods of Pytorch without any difficulties.
Western Blotting Fibroblasts were lysed with 8 M urea/10% NP-40/0. 2 M EDTA/protease inhibitor cocktail/0. 5 M Na 2 HPO 4 pH 7. 5. Lysates were collected and pelleted by centrifugation (30,000× g). Salts and proteins were precipitated with 10% trichloroacetic acid, centrifuged, rinsed with acetone, pelleted, dried and suspended in RIPA buffer (50 mM Tris-HCl, pH 8. 0, 150 mM NaCl, 1% NP-40, 0. 5% sodium deoxycholate, 0. 1% SDS, 1 mM Na 3 VO 4 , protease cocktail inhibitor (Sigma-Aldrich, Saint Quentin Fallavier, France)). Protein concentrations were measured using the Pierce BCA method, as recommended by the manufacturer. Proteins were then loaded on polyacrylamide gels in Laemmli sample buffer. Membranes were blocked with 5% non-fatty milk after transfer and incubated with primary antibody FBN2 (HPA012853, Sigma-Aldrich, St Quentin Fallavier, France) and LOX  [38] , washed with 1X tris-buffered saline (TBS) with 0.
Statistical Analysis Statistical analyses were conducted with Graphpad Prism software. In all analyses n comprised between 3 and 8 per group as indicated in the corresponding figure legends. Different parametric statistical tests were applied depending on the data to be analyzed. Comparisons of two groups were made by single or multiple unpaired t tests, while ANOVA with Dunnett's multiple comparisons post hoc tests were performed when more than two groups were compared. Significance was indicated as follows: * p < 0. 05; ** p < 0. 01; *** p < 0. 001; **** p < 0. 0001.
Acknowledgments: We thank  UAR3444 SFR Biosciences  for the technical facilities,  Catherine Moali  for scientific advice concerning BMP-1 and  Nguyen Hong Phuc Pham  for expert technical contributions. Audrey Josset-Lamaugarny and Jocelyne Vial (Anexpeau)  are also thanked for their in vivo technical help and  Nicolas Gadot  for the Anipath facilities. The manuscript was reviewed by  Patricia Hulmes  (native English speaking).
We further probed this dataset to explore the degree to which serological data on diphtheria and pertussis might suggest different complete vaccination coverage amongst the districts, with a particular focus on numbers of diphtheria only seropositive children in each district, potentially indicating higher rates of natural infection (although a failure of the pertussis component of the vaccine is also possible). We found that although the estimated vaccination coverage bounds vary among the three districts (Antananarivo Renivohitra (45. 1%-49. 5%), Midongy Atsimo (35. 3%-38. 7%), Antsalova(22. 4%-24. 6%)), the number of diphtheria only seropositive children appears to be at a comparable level (Supplementary Table  S1 , Fig. 4c ). Reported administrative coverage levels for complete 3 dose vaccination in 2015-2016 averaged 74% for Antananarivo Renivohitra, 63.
5% for Midongy Atsimo and 48% for Antsalova. We did not conduct this analysis for the 8-15 year olds since the interpretation of seropositivity is complicated by antibody waning and boosting events (Supplementary Table  S2 ). Finally, we compared seropositivity to the administrative coverage data (i. e. , numbers of vaccine doses delivered divided by target population size) in our focal districts. Administrative coverage fluctuates considerably through time (Fig. 4a ). Given likely uncertainty in translation between administrative coverage and vaccine doses delivered  [38] , we take the median and the range across the 3 years available, and plot the median against the proportion of individuals seropositive for both pertussis and diphtheria, to compare this alternative window onto the proportion of individuals vaccinated (Fig.
Discussion Understanding gaps in immunity and shortfalls in vaccination coverage for vaccine-preventable infections is a key question in public health. Here, we measured serological data on diphtheria and leveraged it with previously acquired pertussis serological data to expand our understanding of the characteristics of the landscape of immunity, the footprint of diphtheria and DTP vaccination coverage in Madagascar. Since the DTP vaccine is among the earliest delivered, it is often considered a good proxy for health system functioning and has recently been associated with less severe COVID-19  [42]. These results therefore provide a broader window onto the functionality of the expanded programme on immunisation in Madagascar. First, since the vaccination series for diphtheria should be completed by 14 weeks, the proportion of children aged greater than 14 weeks that have no antibodies provides a lower bound on the number of children who have not been reached by the vaccination programme -as long as these children are young enough to ensure that seropositivity has not been lost  [43, 44].
Acknowledgements. We thank  Dr Mirella Malala RANDRIANARISOA  of  Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar , for helping us define the nutritional status of our participants. We also acknowledge  Mializay RALALANOMBANA  and  Hortensia Marcelle HERINIAINA  for their help in performing the laboratory manipulation. Financial support. AW and CJEM were supported by the  Wellcome Trust  ( 106866/Z/15/Z ). AW was also supported by a  Career Award at the Scientific Interface  by the  Burroughs Wellcome Fund.
All FVI were analysed using an automatic Matlab algorithm detailed elsewhere, and average Young moduli values given in this work were derived from all the force curves. a) ATR-FTIR spectroscopy ATR-FTIR spectra were recorded on a Bruker Tensor 27 spectrometer equipped with a KBr beam splitter and a DTGS detector. Spectra recording and data processing were performed using the Bruker OPUS 7. 5 software. The resolution of the single beam spectra was 4 cm -1. Two hundred scans were collected per spectrum corresponding to a 2-minutes accumulation time. All interferograms were Fourier processed using the Mertz phase correction and a Blackman-Harris three-term apodization function. A nine-reflection diamond ATR accessory (Durasampl IR TM , SensIR Technologies, incidence angle: 45°) was used for acquiring spectra.
Acknowledgments This work was supported by the  French PIA  project " Lorraine Université d'Excellence  " reference  ANR-15-IDEX-04-LUE. AM and HA thank the  CC3M  for the SEM and optical microscopy analysis. The CLSM was performed at the  UMS2008 Imaging Core Facility from Lorraine University , https://umsibslor. univ-lorraine. fr/en/facility/imaging. FQ, GF thank the  Spectroscopy and Microscopy Service Facility (SMI) of LCPME (Université de Lorraine-CNRS  -http://www. lcpme. cnrsnancy. fr ) where the ATR-FTIR and AFM experiments were performed.
Solution spectra were measured in CaF2 cells of various pathlengths (0. 5, 1 and 2 mm, according to the concentration) and were corrected for air, solvent and cell absorption. Spectra for solutions were reported in extinction molar coefficient (L. mol -1. cm -  ) as a function of the wavenumber. Films and gels were measured on KBr cells and corrected for air and cell absorption. Attenuated total reflectance (ATR) FT-IR spectra for solids were collected on a Bruker tensor 27 FT-IR spectrometer equipped with the ATR platinum module, with a detector RT-DLaTGS. The OPUSv5. 5 software (Bruker Optics, Germany) was set up with the following parameters: the spectral resolution was fixed to 4 cm -1 , the number of scans to 32 and the selected spectral range between 4000 and 400 cm -1. The main peaks were reported as m: medium or s: strong.
UV-Vis analyses: UV-Vis absorption spectra were performed on a Jasco J-1500 spectrometer equipped with a Peltier thermostated cell holder and a Xe laser. Data were recorded at 293 K in CHCl3 between 800 and 270 nm and extracted after correction of the absorption of air, solvent, and cell contribution at the same temperature. The pathlength of the cell was adapted as follows: 1 mm rectangular quartz cell for 0. 1 mM solution, 0. 1 mm Starna© cylindrical closed quartz cell for 2. 3 mM solution and 0. 05 mm Starna© cylindrical closed quartz cell for 11. 4 mM solution. Spectra were reported in extinction molar coefficient (L. mol -1. cm -  ) as a function of the wavelength. UV-Vis-NIR analyses: UV-Vis-NIR absorption spectra were measured on a Varian Cary 5000 spectrophotometer. Data were recorded with the following parameters: double beam mode, 600 nm.
min -1 sweep rate, 1 nm data pitch, 2 nm bandwidth, and between 1500 and 240 nm (for solutions) or between 1500 and 200 nm (for films) and automatically extracted after correction of the absorption of air, solvent, and cell contribution at the same temperature. Spectra are shown only between 1000 and 240 or 200 nm since no signals have been detected in the 1000─1500 nm region. [53] Spectra were corrected for the sudden change in intensity that occurs at 900 nm due to change of the light source. Spectra were reported in extinction molar coefficient (L. mol -1. cm -  ) as a function of the wavelength. Films and gels were measured on lamellar quartz cells and corrected for air and cell absorption. Small-angle neutron scattering (SANS) analyses: SANS measurements were made at the LLB (Saclay, France) on the PA20 instrument, at three distance-wavelength combinations to cover the 1.
72×10 -3 to 0. 30 Å q -1 range, where the scattering vector q is defined as usual, assuming elastic scattering, as q = (4π/λ)sin(θ/2), where θ is the angle between incident and scattered beam. Data were corrected for the empty cell signal and the solute and solvent incoherent background. A light water standard was used to normalize the scattered intensities to cm -1 units. The data was fitted with the DANSE software SasView with a form factor for flat objects of finite thickness and infinite lateral dimensions. The thickness obtained from the fit (54 Å) corresponds to roughly twice the diameter for extended TATA-C13 molecule (30 Å). [37]  Electron Paramagnetic Resonance (EPR) analyses: X-band EPR spectra were recorded in non-saturating conditions on a Bruker ELEXSYS 500 spectrometer at 293 K.
Acknowledgements The  French Agence Nationale de la Recherche  is acknowledged for funding the project  AbsoluCat  ( ANR-17-CE07-0002 , PDRA position of PA). Jacques Jestin (LLB, Saclay)  is acknowledged for assistance with SANS experiment and  Dr. J. -L. Cantin  from  INSP  ( UMR 7588 ,  CNRS -Sorbonne Université ) for access to the EPR spectrometer. Claire Troufflard  is acknowledged for assistance with NMR experiments.
In others words, associated variants fell primarily in non-coding intergenic or intronic sequences (Table  S2 ). To confirm that associations were not caused by confounding cryptic geographic structure in our dataset and to take into account putative dominance effects of wing-pattern loci, we also performed univariate associations using as covariates two genotype-dependent variables (for dominance effects) and the first ten principal components describing the whole-genome structure [for population stratification effects; see Methods and Figure  S5  ;  (46) ]. Because univariate analyses can only study a single variable at a time, they cannot identify variants that are associated with a phenotypic feature that would only be described by a combination of phenotypic principal components (in contrast to multivariate analyses).
For instance, some regions of the gene cortex were associated with changes in yellow features on the forewing whereas closely-linked regions of the same gene were associated with changes in black features on the hindwing (Fig. 3 4 , Table  S2 ). In contrast, several variants within the supergene were associated with similar variations of the wing pattern. The co-association of distant genomic region with similar phenotypic variation in Hn123 samples could be caused by the correlation of multiple phenotype features in our dataset -i. e. the non-uniform phenotypic variation among Hn123 samples (Figure  1c )-leading the genetic variants controlling these independent features to apparently have the same effect (as observed in a much stronger proportion in Hn0 samples). Co-association of closely-linked variants could be simply caused by their linkage disequilibrium, owing to our relatively reduced sample size.
This observation was confirmed by univariate association analyses taking into account dominance effect and populations stratifications. This lends support to the long-standing hypothesis that the supergene P coordinates the variation of multiple, independent sites each associated with specific elements of wing-pattern. Our results therefore support the « supergene model » or "beads-on-a-string" model  (12, 13, 49) , and are generally inconsistent with the alternative hypothesis that the supergene could involve a single master gene with pleiotropic effects  (50). Since our findings are based on genotype-phenotype correlations, we cannot exclude that only some of the loci associated with wing pattern variation in our dataset would be functionally involved in wing colouration. An association could result, for instance, from a correlation between wing pattern traits and certain unmeasured traits.
Sampling and sequencing Resequenced genome data from references  (29, 31)  were used and were completed by 62 new specimens. In total, 131 specimens belonging to 16 mimetic variant of H. numata and from five geographical origins: Peru (n=85), Ecuador (n=13), Colombia (n=10), French Guiana (n=6), Brazil (n=17) were used (Table  S1 ). Wings were preserved at room temperature and bodies were conserved in DMSO at -20 °C. DNA was extracted from thorax tissue using the Qiagen DNeasy blood and tissue extraction kit. Illumina Truseq paired-end libraries were prepared and sequenced in 2x100 base pair on an Illumina NovaSeq platform (Get Plage, INRA Toulouse). Reads were mapped on the H. melpomene (Hmel2) reference genome  (57)  with NextGenMap (58) with default parameters. Mapped reads were processed with GATK and SNP and indel detection was performed with the unified genotyper, following the procedure recommended by the authors  (59).
Before filtering for the G*E association, the dataset included 46,999,947 SNPs. SNPeff (v4. 3; ((60)) was used to annotate genetic variants based on H. melpomene reference genome annotation. Our reference genome Hmel2 turned out to contain an assembly error: a 45,853 bp contig considered to be on the chromosome 7 was in fact on chromosome 15 within the supergene. This explains the peak of association on chromosome 7 (Figure  2 ). The misplacement of the scaffold on chromosome 7 was determined by mapping this scaffold with blast on the NCBI database and by aligning this scaffold on an improved Heliconius melpomene genome published after the performance of the analyses presented here ((61); Figure  S14 ). Aligment was perform with mummer V4. 0 (62) with a 1000bp maximal gap between two adjacent matches and visualised with Circos (63).
Population genetic analyses Principal component analyses were computed on genetic data using SNPRelate (v. 3. 9; (64) ) with standard option. This was used to detect whole genome H. numata geographical structure (Figure  S5 ). To quantify the geographical structure observed with genomic PCA, we performed Fst scans using scripts from https://github. com/simonhmartin/genomics_general, using 5000 bp windows with at least 500 SNPs per window, using all SNPs. The pairwise level of disequilibrum (R2) was measured with plink v1. 90b6. 6 (45) between all biallelic SNP at the P region (n=762,526, including the three inversions and flanking regions), keeping only sites with minor allele frequency > 0. 2 and with R2 > 0. 2 to reduce computing time. Because populations from the Atlantic forest of Brazil were shown to be substantially differentiated from other H.
Gene expression analyses RNAseq data from (47) were reanalysed using the EdgeR R package [v3. 16. 5; (48)  ]. Gene expression in early pupal (24h) wings discs from silvana individuals (Hn0/Hn0, n=3) was compared to gene expression in both tarapotensis and aurora individuals (Hn123/Hn123, n=7). Gene expression in prepupae wings discs from bicoloratus individuals (Hn1/Hn1, n=3) was compared to gene expression in both tarapotensis and aurora individuals (Hn123/Hn123, n=8). The data was normalized with the calcNormFactors function. The dispersion was estimated with the estimateDisp function. Data was fitted with a quasi-likelihood negative binomial generalized log-linear model with the glmQLFTest function and p-values were ajusted using the Benjamini & Hochberg correction for false discovery rate.
In order to study the evolutionary history of the supergene and determine whether recombination occur at the supergene, we computed sliding window phylogenies along the supergene, using 10 kb windows with RaxML  (67). Only sample homozygous for the inversions or for their absence were used (Hn0/Hn0, Hn1/Hn1, Hn123/Hn123). Moreover, based on PCR genotyping  (29)  and breeding experiment results (data not shown), we removed samples that might be heterozygous for two supergene allele belonging to the same allelic class. For instance, considering that different Hn123 haplotypes encode the morphs aurora and tarapotensis, respectively, a Hn123/Hn123 individuals might have an aurora/tarapotensis genotype, which could confound phylogenetic analysis studying the evolution of these two haplotypes. Because haplotypes of the same allelic class recombine and because there are likely many neutral polymorphisms segregating in each classes, phylogeny topology were highly variable along the supergene.
Univariate association studies with covariates. To verify that the wing-pattern associated regions we found with multivariate analyses were not false positives due to a geographic structure in our dataset, we repeated our analyses but using a single phenotype and multiple geographical covariates with PLINK v1. 90b6. 24 (45). We used the first 10 principal components of whole-genome PCA (see the Population genetic analyses sections and Figure  S5 ) as covariates in these analyses (computed only with Hn123 or Hn0 samples). To analyse wing pattern variation in as much detail as possible with univariate analyses, in addition to the associations performed using as phenotype the principal components summarising the variation of hind and forewing together (as done in multivariate analyses), we also performed associations using as phenotype the principal components of PCA focusing on more specific aspect of wing variation: variation found on hindwings only, variation found on forewings, variation in yellow patterning, variation in the forewing tip, variation in the forewing middle part and variation in the forewing base.
Acknowledgments We are very grateful to  Oscar Puebla ,  Floriane Coulmance , and to the  Puebla lab  for their careful review and useful comments on this manuscript. We thank the  Peruvian government  for providing the necessary research permits ( 236-2012-AG-DGFFS-DGEFFS ,  201-2013-MINAGRI-DGFFS/DGEFFS  and  002-2015-SERFOR-DGGSPFFS ). This research was supported by  Agence Nationale de la Recherche (ANR)  grants  ANR-12-JSV7-0005  and  ANR-18-CE02-0019-01  and  European Research Council  grant  ERC-StG-243179  to MJ. This project benefited from the  Montpellier Bioinformatics Biodiversity  platform supported by the  LabEx CeMEB ,  ANR  " Investissements d'avenir" programme   ANR-10-LABX-04-01.
oriTs are frequent in plasmids of E. coli and S. aureus To unveil the mechanisms of mobilization of the many plasmids lacking a relaxase, we searched for oriTs. To do so, we collected 51 oriT from the 'oriT database'  31  and added 40 new ones from the literature (Table  S3 ). Most of these 91 experimentally validated oriTs (mean size ~131 bp) were originally identified and verified in plasmids of γ-Proteobacteria (n=44) and Bacilli (n=22) (Fig  S2 ). We used it to search for origins of transfer in the 1,585 E. coli and 581 S. aureus genomes by sequence similarity (see Methods). We identified 2,831 putative oriTs in 2,626 plasmids, almost the totality of which locate in intergenic regions (Fig  S3 ). Even if E. coli has more diverse plasmids and more types of oriTs (n=37) than S. aureus (n=7), oriTs were found at similar frequencies in the plasmids of the two species (ca.
These results show that plasmids lacking relaxases can be split in two categories, where those with an oriT have an important role in the spread of antibiotic resistance. pOriTs exploit either conjugative or mobilizable plasmids. The identification of homologous oriTs allows to test functional dependencies between plasmids. We have previously proposed that relaxases of pMOB evolve to interact with multiple types of MPF encoded in pCONJ, whereas those of pCONJ co-evolve with the MPF to optimize their mutual interaction  32, 33. These differences might require the presence of different oriTs in pMOB and pCONJ, as previously suggested  26. In our dataset, many families of oriTs are present in either pCONJ or pMOB, but few are present in both (Fig  4A ). The exceptions tend to correspond to "pCONJ-like oriTs" (oriTs typical of pCONJ) that were found in large pMOB plasmids.
Mobilization explains patterns of plasmid co-existence The dependence of certain plasmids, e. g. pOriT, on others, notably pCONJ, for conjugative transfer means that the type of mobility of plasmids may affect the patterns of their co-occurrence in cells. We can now test this hypothesis by analyzing which plasmids tend to co-occur with others. The number of plasmids per genome is much more variable (and on average higher) in E. coli than in S. aureus. Hence, we concentrated on the E. coli data for this analysis. We identified the most common patterns of occurrence among the 1,207 plasmid-bearing E. coli genomes, focusing on pCONJ, pMOB, pOriT and pNT (Fig  8A ). The most common pattern is the presence of only conjugative plasmids in the cell. The second and fourth most frequent patterns are a pair of pCONJ-pMOB and the triplet pCONJ-pMOB-pOriT.