dataesr/scientific-paragraphs-categorization huggingface dataset:
Polymorphism analysis on genic regions and BAC clones For variant analysis on the BAC clones, the short shot-gun library genomic reads were mapped to the BAC clones individually. GATK was then used to call variants. For variant analysis on the genic regions, transcript sequences used to generate the canonical proteome dataset were first aligned to the genome assembly. Genome alignments of less than 30 base pairs were discarded. The possible genome alignments were sorted based on number of mismatches with the top alignment having the least amount of mismatches. For each transcript, the top two genome aligments were used to call potential variants. Trascripts or parts of transcripts where there were more than five genomic mapping loci were discarded as potentially highly conserved domains or repetitive regions.
Polymorphisms in Parhyale developmental genes Parhyale genes (nucleotide sequences) were downloaded from GenBank. Each gene was used as a query for blastn against the Parhyale genome using the Geneious software  (Kearse et al. , 2012). In each case two reference contig hits were observed where both had E values of close to zero. A new sequence called geneX_snp was created and this sequence was annotated with the snps and/or indels present in the alternative genomic contigs. To determine the occurrence of synonymous and non-synonymous substitutions, the original query and the newly created sequence (with polymorphisms annotated) were in silico translated into protein sequences followed by pairwise alignment. Regions showing amino acid changes were annotated as non-synonymous substitutions. Five random genes from the catalogue were selected for PCR, cloning and Sanger sequencing to confirm genomic polymorphisms and assess further polymorphism in the lab popultaion.
Evolutionary analyses of orthologous groups Evolutionary analyses and comparative genomics were performed with 16 species: D. melanogaster,  A. gambiae, D. pulex, L. salmonis, S. maritima, S. mimosarum, M. martensii, I. scapularis, H. dujardini, C. elegans, B. malayi, T. spiralis, M. musculus, H. sapiens, and B. floridae. For orthologous group analyses, gene families were identified using OrthoFinder  (Emms and Kelly, 2015). The canonical proteome was used as a query in BlastP against proteomes from 16 species to generate a distance matrix for OrthoFinder to normalize and then cluster with MCL. Detailed methods are described in Source code 5. For the comparative BLAST analysis, five additional transcriptome datasets were used from the following crustacean species: Litopenaeus vannamei, Echinogammarus veneris, Eucyclops serrulatus, Calanus finmarchicus, Speleonectes tulumensis.
Cross species identification of GH family genes and immune-related genes The identification of GH family genes was done by obtaining Pfam annotations  (Finn et al. , 2006)  for the Parhyale canonical proteome. Pfam domains were classified into different GH families based on the CAZy database  (Cantarel et al. , 2009). For immune-related genes, best-reciprocal blast was performed with ImmunoDB genes  (Waterhouse et al. , 2007).
Bisulfite sequencing Libraries for DNA methylation analysis by bisulfite sequencing were constructed from 100ng of genomic DNA extracted from one Parhyale male individual, using the Illumina Truseq DNA methylation kit according to manufacturers instructions. Alignments to the Parhyale genome were generated using the core Bismark module from the program Bismark  (Krueger and Andrews, 2011) , having first artificially joined the Parhyale contigs to generate 10 pseudo-contigs as the program is limited as to the number of separate contigs it can analyse. We then generated genome-wide cytosine coverage maps using the bismark_methylation_extraction module with the parameter 'CX specified to generate annotations of CG, CHH and CHG sites. In order to analyse genome-wide methylation patterns only cytosines with more than a 10 read depth of coverage were selected.
Overall methylation levels at CG, CHH and CHG sites were generated using a custom Perl script. To analyse which regions were methylated we mapped back from the joined contigs to the original contigs and assigned these to functional regions based on RepeatMasker  (Smit et al. , 2013)  and transcript annotations of repeats and genes respectively. To generate overall plots of methylation levels in different features we averaged over all sites mapping to particular features, focusing on CG methylation and measuring the% methylation at each site as the number of reads showing methylation divided by the total number of reads covering the site. Meta gene plots over particular features were generated similarly except that sites mapping within a series of 100 bp wide bins from 1000 bp upstream of the feature start site and onward were collated.
Identification of non-protein-coding RNAs Parhyale non-protein-coding RNAs were identified using two independent approaches. Infernal 1. 1. 1 (Nawrocki and Eddy, 2013)  was used with the RFAM 12. 0 database  (Nawrocki et al. , 2015)  to scan the genome to identify potential non-coding RNAs. Additionally, MiRPara  (Wu et al. , 2011)  was used to scan the genome for potential miRNA precursors. These potential precursors were further filtered using small RNA read mapping and miRBase mapping (Griffiths-  Jones et al. , 2008). Putative lncRNAs were identified from the transcriptome by applying filtering criteria including removal of known and predicted coding RNAs. Detailed methods are available in Supplementary Data 11.
Identity of the protein was confirmed using two different specific antibodies; no bands were detected if the primary antibody was incubated with specific blocking peptide (SRD5A1 (A-18) peptide sc-20396 P) or in controls lacking the primary antibodies. In all cases loading control was goat anti-actin (Santa-Cruz biotech sc-1616; predicted molecular weight 43 kDa). Membranes were incubated with species-specific fluorescent-conjugated secondary antibodies and visualised using the Licor Odyssey system (Licor). Protein bands detected by Western blot were quantified by performing densitometry analysis using ImageJ (NIH. gov). Data were normalised to Actin and expressed as fold-change relative to control treatment. Immunofluorescence. Immunofluorescence was carried out on ESC grown on chamber slides (BD Biosciences) incubated with control media or DM to identify the localisation of the proteins within the cell and as numbers of primary cells were limited only one time point was selected (4 days).
Acknowledgements We thank  Dr Alistair Williams  for histological evaluations of endometrial tissue,  Catherine Murray  and  Sharon McPherson  for patient recruitment. We thank  Ronnie Grant  for preparation of figures and  Professor J. Ian Mason  and  Professor Evan Simpson  for helpful discussion. Studies undertaken in the author's laboratory were supported by  MRC  Programme Grant  G1100356/1  to PTKS. The authors have no conflicts of interest to disclose.
Acknowledgements We acknowledge the participationo ft he late  Luis Serrano-AndrØsi  nt he first stage of this work. L. B. and A. V. a cknowledge financial support from the  SpanishM inistry of Economy  ( CTQ2011-26573 ,  CTQ2015-69363-P ) and the  Generalitat de Catalunya (  2014SGR-1202 ) and the use of computer time at the  Consorci de ServeisU niversitaris de Catalunya. Q. L. acknowledgest he  National Natural Science Foundation of China  ( 21303007 ). M. G. acknowledges support by the  European Research Council Advanced  Grant  STRATUS (ERC-2011-AdG No. 291198 )a nd the  AgenceN ationale de la Recherche  for the 2015 project  FEMTO-2DNA  ( Spectroscopie 2DUV:u nn ouvel outil pour l'Øtude de biomolØcules ,  ANR-15-CE29-0010 ). D. R. -S. acknowledges support from the  Generalitat Valenciana  ( GV2015-057 ) and the  Spanish Ministryo fE conomy ( project  CTQ2014-58624-P  and grant  JCI-2012-13431 ).
CALIBAN is a metallic critical assembly managed by the Criticality, Neutron Science and Measurement Department located on the French CEA Center of Valduc. The reactor is extensively used for benchmark experiments dedicated to the evaluation of nuclear data, for electronic hardening or to study the effect of the neutrons on various materials. Therefore CALIBAN irradiation characteristics and especially its central cavity neutron spectrum have to be very accurately evaluated. In order to strengthen our knowledge of this spectrum, several adjustment methods based on activation foils measurements are being studied for a few years in the laboratory. Firstly two codes included in the UMG package have been tested and compared: MAXED and GRAVEL. More recently, the CALIBAN cavity spectrum has been studied using CALMAR, a new adjustment tool currently under development at the CEA Center of Cadarache.
Introduction The Criticality, Neutron Science and Measurement Department located on the French CEA Research Center of Valduc operates several experimental facilities mainly devoted to the production of neutron and gamma mixed fluxes. Two of these facilities, the metallic core reactors CALIBAN and PROSPERO are currently unique in Europe. Initially designed for electronic hardening studies, they are now used for different types of studies, from nuclear data evaluation to radiation shielding. To allow the analysis of these experiments, neutron spectra of the reactors have been studied since the beginning of their operation in the 70's, combining simulation calculations and activations measurements. In 2008, a benchmark of CALIBAN was published  [1] , providing a highly accurate description of the reactor.
This work allowed the enhancement of the quality of the reactor simulation calculations and was used to test new spectrum adjustment techniques and tools. First, MAXED and GRAVEL, two codes from the UMG package  [2]  developed by the German PTB were evaluated and results obtained with this software were compared with calculation from the neutron transport code TRIPOLI-4  [3]  and from the activation code FISPACT  [4]. More recently, CALMAR  [5] , a new adjustment code currently under development at the CEA Center of Cadarache, was tested to study CALIBAN cavity neutron spectrum.
Nuclear Data Evaluation The benchmark of CALIBAN provides an accurate description of the reactor, which allows the modelling of experiments carried out using the core and the analysis of achieved experimental results. Especially, this benchmark has been used recently to design and analyse experimental programs devoted to integral measurements carried out to test evaluated nuclear databases. As a first example, experiments performed using CALIBAN in the seventies and early eighties provided measurements of many fission product yields for fission neutron induced reactions on uranium 235, uranium 233 and plutonium 239. The results of these experiments, analyzed and published recently for the first time  [6, 7] , have been compared with evaluated data and are in good agreement for reactions on uranium 233 and uranium 235.
Nuclear Data Evaluation The Radiation Metrology Laboratory of the Criticality, Neutron Science and Measurement Department allows the measurement of activation foils used for neutron flux evaluation for experiments using CALIBAN. The laboratory uses the following types of measurement equipment: -three gamma spectrometry devices equipped with N-type semiconductor germanium detectors (HPGe). These detectors work on energy fields ranging from 60 keV to 2 MeV. The minimum detectable activity is about few tenths of Becquerel for samples with long halflives; 07005-p. 4 -one gamma spectrometry device equipped with a broad-energy germanium detector and dedicated to low level gamma spectrometry. This detector is built with materials selected to generate low background. A Plexiglas device located on the detector allows the placement of the sample at several vertical heights ranging from contact to a maximum of 10 cm, with high accuracy and repeatability.
All the detectors are placed in shielding castles with graded liners of high purity copper with a thickness of 2 mm. One of the castles is an ultra-low background shield, made up of a series of several layers (low and ultra low background lead, cadmium, copper, and Perspex). The efficiency calibrations of the gamma spectrometry devices are calculated with the CANBERRA software LABSOCS. Several software tools are used to evaluate correction factors for self-absorption, geometry, and peak sums. For intense photo-peak and low background measurements, the total uncertainty of activity measurements is about 1. 5%  (1 ). The Radiation Metrology Laboratory uses also fission chamber detectors specially designed for radiation measurements and thermo-luminescent gamma ray dosimeters. In 2013, the Radiation Metrology Laboratory took part in the EWGRD Round Robin measurement exercise  [9].
UMG Adjustments UMG is a software developed by the German PTB Research Center. It is composed of two programs, MAXED and GRAVEL, which can be used to provide a 'best fit' of a neutron flux spectrum from a set of activation foil measurements. The MAXED program is based on the maximum entropy principle. The solution is obtained by the maximization of the entropy of the system, taking into account constraints imposed by the measurements. MAXED needs a prior spectrum as input data. The GRAVEL program is based on an iterative least square method, using a modified SANDII algorithm. A prior spectrum is needed as input data. It is modified at each calculation step so that the solution fits better the activation measurements. MAXED and GRAVEL have been applied on a set of activation foil and fission chamber measurements carried out in the CALIBAN.
In comparison with STAYSL, a least square adjustment code included in CALMAR package, the level adjustment adds new correlations between the energy groups, whereas the shape adjustment lowers the correlations. This new version of the code has been applied to the set of activation foils measurements given in Table  1 , using the IRDFF 1. 03 nuclear database. The prior spectrum was calculated by TRIPOLI-4, using the JEFF3. 1 nuclear database, following a 150 energy group structure ranging from 10 keV to 20 MeV. The correlation initial matrices were built using the ASTM E721 data. Figure  5  displays the correlation added by CALMAR between the initial and the unfolded flux correlation matrices. Activation reactions rate for each foil of the set have been computed with CALMAR and are compared with the results given by MAXED and GRAVEL in Table  2.
We sent out an introduction letter containing a link (Internet address) to the online questionnaire that was unique to each participating member. Two reminders were sent (January 2014 and March 2014) and all the respondents were given 90 days to reply. The data were recorded in SPSS for Windows v. 22. Analyses of the difference in frequencies across groups were performed with the Pearson Chi-squared test and a p value ≤0. 05 was considered significant. Cramer's V was used for the evaluation of the strength of statistically significant associations.
Most of those participants pointed out "less than 5 years" as being the lower limit of age and "more than 70 years" as being the upper limit of age (Fig. 8 ). Pruritus (72 %), exacerbation of the primary local reactions (29 %) and erythroderma (12 %) were listed as the main adverse reactions. The professionals who perform more than 1 PT per week observed more often adverse reactions than those who did less than 1 patch test per week (86. 7 vs 13. 3 %, χ2 = 6. 416, p = 0. 04, V = 0. 214). Out of 142 replies, 30 % of members asked for a consent form before conducting the PT and 78 % provided an allergen information document or an allergy passport in case of positive result. The results of PT were recorded into the own database by 53 % of respondents, while 29 % stored the results into the Hospital database.
The SSU and LSU genes of TOSAG39-1 have introns. The SSU intron (440 bp) is at the same position as in RCC1105, but is only 91% similar. The LSU intron (435 bp) is only present in TOSAG39-1. The internal transcribed spacers (ITS) are different between the two TOSAG39-1 and the RCC1105 assemblies (82% and 86% for ITS1 and ITS2, respectively) but closer to those of two Bathycoccus oceanic strains from the Indian Ocean (RCC715 and RCC716) (Supplementary Figure  S4 ) and of a metagenome from the Atlantic Ocean DCM  40. We also looked at the plastid 16 S marker gene  41  and to the PRP8 intein gene that has been proposed as markers for Bathycoccus  10. The plastid 16 S sequences of the two Bathycoccus genomes share 92% identical nucleotides, and PRP8 is lacking from the TOSAG39-1 assembly. We were able to determine the affiliation of three metagenomes  23, 40  containing Bathycoccus and two Bathycoccus transcriptomes of the MMETSP database  42  (Supplementary Figures S5).
Metatranscriptomic data was used to select genes having an expression signal in at least six samples. Using these stringent criteria, we detected about one hundred dispensable genes for each genome (Supplementary Tables 1,4 and 5). Half of the RCC1105 dispensable genes (50/108) are located on chromosome 19, representing 70% of the genes on this chromosome. These genes have shorter coding and intronic regions than other genes (Supplementary Table  1 ), which is a property of the genes predicted on outlier chromosome 19  22. Dispensable genes on regular chromosomes also tend to be shorter. Additionally, the distribution of dispensable genes on the genome is not random. Among the 72 genes of chromosome 19, 47 out the 50 dispensable genes are grouped into two long blocks at the chromosome end, leaving the first part of chromosome 19 almost free of dispensable genes (Supplementary Figure  S11 ).
The former corresponds to the B1 clade and the latter to the B2 clade as, defined recently  11. Orthologous proteins of these two genomes share only 78% identity, which is similar to the 74% of amino-acid identity shared by the two sequenced Ostreococcus isolates which belong to different clades  52. A previous study 11 estimated a lower genetic distance (82% of identical nucleotides) between the two Bathycoccus using metagenomic data. This difference is probably as expected because of the reduced dataset of highly conserved and single copy genes (1 104 genes) considered in the latter analysis. The evolutionary distance that separates the protein coding genes of these two Bathycoccus is slightly smaller than the one between two vertebrate lineages separated by more than 400 million years (mammal and fish share 72% of identity  53  ) and larger than the one reported between many model organisms (for example, human and mouse share 85% of identity  54, 55  ).
We also used a public protein databank  76  and the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) collection of marine protist transcriptomes  42. In addition, we performed direct ab initio prediction by calibrating and running the Markov model implemented in snap  77. Integrating and combining all this evidence provided a final set of genes, using a process based on Gmorse software rationale  78. We evaluated the relative genomic abundance of each genome for two sampled depths (surface and DCM) at the 76 Tara Oceans stations (122 samples in total, Supplementary Figure  S13 ) by recruiting metagenomic reads  24. We mapped metagenomic reads directly from 0. 8-5 μ m organism-size fraction samples onto genome assemblies, and estimated the relative contribution of each Bathycoccus genome in the metagenomes.
Acknowledgements We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche  GDR3280 ),  European Molecular Biology Laboratory  (EMBL),  Genoscope/ CEA , the  French Governement 'Investissement d' Avenir' programs Oceanomics  ( ANR-11-BTBR-0008 ) and  FRANCE GENOMIQUE  ( ANR-10-INBS-09 ),  Fund for Scientific Research -Flanders ,  VIB ,  Stazione Zoologica Anton Dohrn, UNIMIB ,  ANR  ( projects POSEIDON/ANR-09-BLAN-0348 ,  PROMETHEUS/ANR-09-PCS-GENM-217 ,  TARA-GIRUS/ANR-09-PCS-GENM-218 ),  EU   FP7 MicroB3 /No. 287589 , US NSF  grant  DEB-1031049  to MES,  FWO ,  BIO5 , Biosphere 2, Agnès b. , the  Veolia Environment Foundation ,  Region Bretagne ,  World Courier ,  Illumina, Cap L'Orient , the  EDF Foundation EDF Diversiterre, FRB , the  Prince Albert II de Monaco Foundation ,  Etienne Bourgois , and not least, the Tara schooner and its captain and crew.
GN-1 Finally, to investigate the potential of 'real-time' viral genome sequencing, we considered the degree to which the findings could have been obtained at the height of the epidemic, had sequences been available shortly after samples were taken (see Methods for details). For the factors associated with EBOV dispersal the results were extremely comparable with those for the full dataset with the same five factors being strongly supported and having similar effect sizes (Figure  5 ). For the data set constructed from EBOV genome sequences derived from samples taken up until October 2014 (blue), the same 5 spatial EBOV movement predictors were given categorical support (inclusion probabilities = 1. 0) as for the full data set (red). Likewise, the coefficients for these predictors are consistent in their sign and magnitude.
Methods Sequence data. We compiled a data set of 1,610 publicly available full Ebola virus (EBOV) genomes sampled between 17 March 2014 and 24 October 2015 (see https: //github/ebov/space-time/data/ for full list and metadata). The number of sequences and the proportion of cases sequenced varies with country; our data set contains 209 sequences from Liberia (3. 8% of known and suspected cases), 982 from Sierra Leone (8. 0%) and 368 from Guinea (9. 2%) (Supplementary Table  1 ). Most (N =1,100) genomes are of high quality, with ambiguous sites and gaps comprising less than 1% of total alignment length, followed by sequences with between 1% and 2% of sites comprised of ambiguous bases or gaps (N =266), 98 sequences with 2-5%, 120 sequences with 5-10% and 26 sequences with more than 10% of sites that are ambiguous or are gaps.
We ran an additional analysis with a subset of data (787 sequences collected up to November 2014 -the peak of case numbers in Sierra Leone) to test the robustness of inference if they had been performed mid-epidemic. Geographic history reconstruction. The level of administrative regions within each country was chosen so that population sizes between regions are comparable. For each country the appropriate administrative regions were: prefecture for Guinea (administrative subdivision level 2), county for Liberia (level 1) and district for Sierra Leone (level 2). We refer to them as regions (63 in total but only 56 are recorded to have had EVD cases) and each sequence, where available, was assigned the region where the patient was recorded to have been infected as a discrete trait. When the region within a country was unknown (N =223), we inferred the sequence location as a latent variable with equal prior probability over all available regions within that country.
Within-location generalized linear models. Ebola virus disease (EVD) case numbers are reported by the WHO for every country division (region) at the appropriate administrative level, split by epidemiological week. For every region and for each epidemiological week four numbers are reported: new cases in the patient and situation report databases as well as whether the new cases are confirmed or probable. At the height of the epidemic many cases went unconfirmed, even though they were likely to have been genuine EVD. As such, we treat probable EVD cases in WHO reports as confirmed and combine them with lab-confirmed EVD case numbers. Following this we take the higher combined case number of situation report and patient databases. The latest situation report in our data goes up to the epidemiological week spanning 8 to 14 February 2016, with all case numbers being downloaded on 22 February 2016.