dataesr/scientific-paragraphs-categorization huggingface dataset:
Description of the Experiment in the Shopping Mall. ULISS was held in hand by three pedestrians (M1, W1, and M2) over a 1 km walk in a shopping mall at comfortable speed (Figure  14 ). W1 and M2 carried ULISS in a texting mode for the 1st half of the track set and in a swinging mode for the 2nd half. M1 was walking in a texting mode for the entire walk. The reference solution is computed using a geodetic GNSS receiver carried in a backpack whose data are postprocessed in a differential mode with RTKLIB software. The decimetrelevel accurate DGPS solution is available outdoors at the entrance of the shopping mall and at the middle of the walk (500 m). Inside, main corridor directions are used to assess the accuracy of the position estimates. Figures 15, 16, and 17  show in red/blue the PDR trajectory estimates for three persons and the DGPS reference positions in green.
Performance Assessment of the Postprocessed PDR Trajectories. In Figures  16  and 17 , the pedestrian's trajectory is divided into two parts, shown in red and blue. They correspond to    the texting carrying mode and the swinging carrying mode, respectively, for the test subjects M2 and W1. The distinction is made because a different statistical GMM (see  (2) ) is constructed for each carrying mode for the same person. Although GPS signal is available at the beginning, the middle, and the end of the experiments, it is not used to compute the PDR trajectories but only to assess the PDR positioning performances. It is observed that the pedestrians remain in the corridors inside the shopping mall. The error on the walking direction estimation for all three datasets varies between 1. 4 ∘ and 15.
Long Outdoor/Indoor Walk in the Research Facility Site. A longer experimentation has been conducted in IFSTTAR's facilities in order to test the proposed pedestrian positioning methods and system in another environment. This environment is a mixed indoor and outdoor space. During the data collection, ULISS was held in hand in a swinging mode during a 2 km walk. Similar to the tests conducted in the shopping mall, GPS signals have only been used to compute the first initial location's coordinates. Similar performances are obtained for this new dataset. The footpath computed with the proposed PDR algorithms is depicted in blue in Figures  18  and 19. The magenta tracks correspond to the GPS-only positions computed in differential mode. Figure  19  focused on the indoor parts, where no GPS solution is available.
| Statistical analysis Positive responses of the ELISPOT assay were determined using a statistical method called DFR(eq) (Distribution Free Resampling), proposed by Moodie's laboratory, 2006. 17 It is based on a permutation resampling method adjusted for multiple comparisons. The aim of this method is to compare the antigen and negative control using permutation resampling. For continuous variables, a nonparametric Wilcoxon-Mann-Whitney test was performed to compare variable distribution between two groups, and a Kruskal-Wallis test was used for at least three groups. Fisher's exact test was performed to test the independence between modalities of two categorical variables. Analyses were conducted using SAS ® 9. 4. Tests were performed at the level of 5%.
| DISCUSSION HBV chronic infection can be controlled but is rarely cured with firstline treatment regimens. Restoration of host antiviral immunity against HBV is considered an important strategy in the currently developed novel therapeutic approaches. Recently, a novel active targeted immunotherapeutic (therapeutic vaccine) TG1050 has been developed (Phase I clinical trial, NCT02428400). In preclinical study, TG1050 displayed a number of immunological features similar to those found in HBV spontaneous resolvers together with the capacity to exert antiviral activity in an HBV-persistent murine model. CHB patients with control of viral replication)  12  that are currently not considered by the guidelines for antiviral therapy. 26, 27 Here, we increased the size of the cohorts studied and extended analysis to two major viral proteins, the Core and Polymerase.
Peptide libraries were composed of 15-mers overlapping by 11 aa covering the TG1050-encoded HBV Core and Polymerase domains derived from a genotype D sequence (GenBank No. Y07587) synthesized by Chinese Peptides company (Hangzhou, China). For HBV-specific T-cell expansion, large panels of peptides were pooled in 4 mixtures: Core (43 peptides), Pol1 (69 peptides), Pol2 (69 peptides) and Pol3 (68 peptides).
Immunofluorescent assays were performed on acetone-fixed cells with rabbit anti-human-E-Cadherin, Vimentin and Fibronectin as primary antibodies, and Alexa Fluor-conjugated donkey anti-mouse-IgG and anti-rabbit-IgG antibodies (Invitrogen, Carlsbad, CA, USA) as secondary antibodies. Nuclei were stained by DAPI. The protein expression levels were scored based on staining intensity (SI) and distribution using the immunoreactive score (IRS). Briefly, IRS = SI × PA (positive area). The intensity of immunohistochemical and immunofluorescence staining was measured by the Image-Pro Plus 6. 0 image analysis software (Media Cybernetics, Inc. , Silver Spring, USA)  29. PCR gene Array. TGF-β PCR gene Array (SABiosciences/Qiagen, Frederick, MD, USA) was performed by 7500HT Fast Real-time PCR system according to the manufacturer's instructions.
The cDNA fragments went through an end repair process, the addition of a single ' A' base, and ligation of the adapters. The products were purified and enriched with PCR to create the final cDNA library. The clusters of the cDNA library were generated on the flow cell using TruSeq PE Cluster kit and HiSeq PE flow cell. The clusters were finally sequenced on HiSeq. 2000 system using TruSeq SBS kit. Cloning and plasmid construction in Zebrafish. Adult zebrafish (Danio rerio) were raised following established protocols. Zebrafish jam-1 gene was identified according to homology to human JAM-A. The specific primers were designed based on genomic sequence in the UCSC data base (University of California, Santa Cruz) to amplify part of jam-1 gene. The plasmid was constructed by GENECHEM, Shanghai, China.
Acknowledgements This study was supported, in part, by research funding from the  National Natural Science Foundation of China  ( 81325003 ,  81520108003 ,  81670716  and  81201863 ), the  Shanghai Commission of Science and Technology  ( 14430723400 ,  14140903100  and  16JC1405800 ), The  National Key Research and Development Program  ( 2016YFC0902800 ),  Shanghai Municipal Education Commission Gaofeng Clinical Medicine Grant Support  ( 20152206  and  20152208 ), Multi-center clinical research project by  Shanghai Jiao Tong University School of Medicine  ( DLY201601 ),  SMC-Chen Xing Scholars Program ,  Chang Jiang Scholars Program ,  Innovation Fund Projects of Shanghai Jiao Tong University  ( BXJ201607 ),  Collaborative Innovation Center of Systems Biomedicine  and the  Samuel Waxman Cancer Research Foundation.
In asynchronous cells, using equal low amounts of FLAG-Fbw7α expression plasmids, Fbw7α-S18E was reproducibly expressed in slightly higher amounts than Fbw7α-wt or Fbw7α-S18A (Fig 5D ), suggesting that the phospho-mimetic mutant is the most stable mutant form. Indeed, the were treated with nocodazole and probed for cyclin B to monitor progression into M phase. D. HeLa cells were transfected or not (-) with Flag-Fbw7α-wt, -S18A or -S18E, and Fbw7α levels were analyzed by immunoblotting from asynchronous (AS). E. HeLa cells were transfected with FLAG-Fbw7α-S18A or FLAG-Fbw7α-S18E, treated with cycloheximide (CHX) for the time indicated and analyzed by immunoblotting (upper panel). Fbw7 protein levels of two independent experiments were quantified with ImageJ software and normalized to tubulin.
Fbw7 protein levels of two independent experiments were quantified with ImageJ software and normalized to tubulin. The results were plotted as the relative Fbw7 levels compared to those at the time 0 of CHX treatment (lower panel). F. HeLa cells were transfected as in D and treated with nocodazole (+ noco). G. Extracts from HeLa cells, transfected and treated with nocodazole as in F were supplemented with MG132 and phosphatase inhibitors to be subjected to immunoprecipitations with anti-FLAG and control antibodies (IPc) and analyzed by immunoblotting to detect the presence of ubiquitin and pS18-Fbw7α. H. HeLa cells, co-transfected or not (-) with FLAG-Fbw7α-S18E and HA-Fbw7α-S18A, were synchronized in G1/S or arrested in prometaphase and recovered by shake-off. Cell extracts were analyzed by immunoblotting to detect the presence of Fbw7α.
Acknowledgments We are grateful to  D. Fesquet  and  S. Boulon  and to the past members of the  Coux laboratory  for their advice and suggestions. We thank  D. Joubert  for the gift of GFP-PKC constructs,  S. Reed  for the gift of pCMVFLAG-hCdc4α,  P. Richard  from the animal facility for the production of rabbit polyclonal antibodies,  Y. Boublik  for baculovirus production, the  Montpellier Ressources Imagerie (MRI)  facility for assistance with immunofluorescence microscopy and  J. Hutchins  for checking the scientific English of the manuscript. S. Z. was supported by studentships from the  Agence Universitaire de la Francophonie  and the  Ligue Nationale Contre le Cancer. Dr. Catherine Papin  passed away before the submission of the final manuscript. Dr. Catherine Bonne-Andrea  accepts responsibility for the integrity and validity of the data collected and analyzed by  Dr.
, Hampshire, UK), using a protocol similar to the one described in  [35]. In this study, the samples were rotated within a laser beam with the full rotation scan mode (Fig. 2 ), on 5 equidistant slices along the palm fibre sample. The UvWin 3. 40 Software gives the mean cross-section. After dimensional assessment, the samples were tensile tested using a TEST108 2kN universal testing machine (GT-TEST, France), equipped with pneumatic side action grips (1kN, Instron) and the Testwinner software (Testwell®) in a climatic chamber (20°C; 55% RH). The displacement rate was set at 10 mm/min and the test was considered successful when failure occurred in the gauge length; 33 samples satisfied this criterion.
Acknowledgements The authors thank  Miguel Pernes , and  Francois Gaudard  from  INRA  for their technical assistance,. Dr Johnny Beaugrand  is thankful for the support provided by the MATRICE state-to-country ( Région Alsace Champagne-Ardenne Lorraine) program ,  France. Dr Darshil Shah  and  Dr Michael Ramage  were supported by a  Leverhulme Trust Grant. Dr Alain Bourmaud  thanks  Region Bretagne and OSEO  for the FIABILIN programme funding.
In silico Analysis Primer sequence was designed using the Primer3 software  (Untergasser et al. , 2012). The REBASE database  (Roberts et al. , 2015)  was used to identify a putative Dam methyltransferase, M. PluTDamP (REBASE Enzyme Number 7410), in the P. luminescens TT01 genome. Alignments between Dam from various organism were performed using the Multalin tool  (Corpet et al. , 1998).
35% agar and inoculated using 5 µL of cells grown in exponential phase (OD 540 nm = 0. 8), as previously described  (Givaudan et al. , 1995). The diameter of the halo size of swimming motility was measured 24 h and 30 h after incubation. Data from 3 independent experiments (with 10 plates used in each condition) were analyzed using Wilcoxon test. Growth of P. luminescens was monitored with a TECAN automated turbidimetric system (Infinite M200 TECAN R ). Estimation of maximum specific growth rate (µ max ) was performed on 4 independent biological replicates for each strain, using serial dilution of the inoculum as previously described  (Augustin et al. , 1999). The P. luminescens biofilm formation was determined as follows. Five milliliters of LB medium in glass tubes were inoculated at 10% with an overnight culture and incubated for 12 days at 28 • C in static conditions.
The tubes were then rinsed with PBS before the addition of 7 mL of Crystal violet solution at 0. 01% (in PBS) to stain the biofilms during 15 min. Biofilms were rinsed with PBS and then dissolved 3 h in 7 mL ethanol. The OD 570 nm measurement allowed the quantification of the biofilmassociated crystal violet. Data from 3 independent experiments with replicates (totalizing 17 tubes for each strain) were analyzed using Wilcoxon test. The P. luminescens spontaneous mutation rate was assessed by quantifying the emergence of rifampicin-resistant CFUs as follows. P. luminescens was grown overnight in 100 mL of LB medium supplemented with gentamycin (for plasmid maintenance) before plating on LB and LB with rifampicin. The mutation rate was calculated as the rifampicin-resistant population divided by the total population.
Altogether, the survival rate of 80-100 larvae for each bacterial strain were analyzed. The CFU of bacteria were determined by plating dilutions on LB agar. Insect death was monitored over time for up to 60 h. The time for killing 50% of the insect larvae (LT 50 ) was calculated. Statistical analysis (Wilcoxon test) was performed as previously described  (Givaudan and Lanois, 2000; Brillard et al. , 2002)  using SPSS version 14. 0 (SPSS, Inc. , Chicago, IL) to compare the mortality state.
RNA Sequencing The RNA-sequencing was performed as previously described  (Mouammine et al. , 2017)  with the following changes. Equal amounts of total RNA from three independent samples per strain were pooled together to generate one final biological RNA sample per strain. Thus, from the initial nine independent RNA samples per strain, three final RNA samples were generated for each strain and subsequently treated as follows prior sequencing. Ribo-Zero rRNA Removal Kit Bacteria (illumina, San Diego, CA) was used to remove ribosomal RNA from 4 µg of total RNA. For each sample, 100 ng of rRNA-depleted RNA was used to construct sequencing libraries using Illumina's TruSeq Stranded mRNA Sample Prep Kit (Low throughput). The mRNA was chemically fragmented. The first cDNA strand was generated by reverse transcription with random hexamer primers, SuperScript IV Reverse Transcriptase (Life Technologies), Actinomycine D.
The Second strand cDNA was synthesized by replacing dTTP with dUTP. A single "A" nucleotide was added to the 3 ′ end and ligation was carried out with Illumina's indexed adapters. After 15 cycles of PCR, libraries were validated on a Fragment Analyzer (AATI, Ankeny, IA) and quantified with a KAPA qPCR kit. On a sequencing lane of a flowcell V4, nine libraries were pooled in equal proportions, denatured with NaOH and diluted to 8 pM before clustering. Clustering and 50 nt single read sequencing were performed according to the manufacturer's instructions. Cluster formation, primer hybridisation and single end-read 50 cycles sequencing were performed on cBot and HiSeq2500 (Illumina, San Diego, CA), respectively. Image analyses and basecalling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
RNA-Seq Analysis High-throughput transcriptomic sequencing data were processed with a bioinformatic pipeline implemented at the Microscope platform  (Vallenet et al. , 2013). The reads were mapped onto the P. luminescens subsp. laumondi TT01 genome sequence (EMBL accession number: BX470251) with BWA software (v. 0. 7. 4)  (Li and Durbin, 2009). We then used SAMtools (v. 0. 1. 12) (Lister et al. , 2009)  to lower the false-positive discovery rate and to extract reliable alignments from BAM-formatted files. The number of reads matching each genomic object harbored by the reference genome was then calculated with the Bioconductor-GenomicFeatures package  (Lawrence et al. , 2013). For reads matching several genomic objects, the count number was weighted so as to keep the total number of reads constant.
Finally, we used the Bioconductor-DESeq package  (Anders and Huber, 2010)  with default parameters to analyze raw count data, to normalize the samples to the reliable reads and to evaluate differential expression between conditions, as previously described  (Jubelin et al. , 2013). Between 14 and 19 million Illumina sequences (50-base reads) were obtained for each sample and between 80 and 93% of high-quality sequences mapped to at least one site in the reference genome. The complete dataset from this study has been deposited in NCBI's Gene Expression Omnibus (GEO) database, under accession number GSE100650.
ACKNOWLEDGMENTS The authors thank  N. Ginibre ,  S. Pagès , and  W. Levrat  for technical assistance and  Philippe Clair  from the  Montpellier GenomiX facility  for assistance with real-time PCR. They are grateful to  Anders Løbner-Olesen  for gift of E. coli strains. The authors thank  INRA Plant Health and Environment (SPE) division  for financial support ( SPE2015-65359 ) and GAIA doctoral school # 584  for supporting AP's PhD.
Virus Samples We analyzed a total of 82 nearly complete genome sequences from EBLV-1 isolates, collected in nine countries between 1968 and 2015. Details of these isolates are provided in supplementary table  S1 , Supplementary Material online. Except for two, all genomes were generated in this study based on 35 EBLV-1 samples from the archives of the World Health Organization Collaborative Centre for Reference and Research on Rabies, or from the National Reference Centre for Rabies, both located at Institut Pasteur, Paris, France and 45 EBLV-1 samples from ANSES's Nancy Laboratory for Rabies and Wildlife, EU and OIE reference laboratory for rabies located in Malzeville, France. These data were combined with two full-length genome sequences extracted from GenBank (KF155003 and KP241939) selected to be representative of the overall phylogenetic diversity of EBLV-1 in bats.
The majority nucleotide (>50%) at each position with generally a minimum coverage of 200 was used to generate the consensus sequence. All consensus sequences generated were manually inspected for accuracy, such as the presence of intact open reading frames, using BioEdit (http://www. mbio. ncsu. edu/bio edit/bioedit. html). A multiple sequence alignment of the 80 newly sequenced genomes combined with the two complete genome sequences from GenBank (KF155003 and KP241939) was constructed using ClustalW2 with default parameters  (Larkin et al. 2007 ) (http://www. ebi. ac. uk/Tools/msa/clus talw2) implemented in Galaxy and manually adjusted when necessary. All the nearly full-length genome sequences generated in the present study have been submitted to GenBank (supplementary table S1, Supplementary Material online).
2008 ). In our partitioning scheme, we allowed for a different relative substitution rate for each gene; the product of the relative rate and the overall substitution rate provides evolutionary rate estimates for each gene in units time per site. We ran three independent MCMC analyses for 50 million steps sampling every 10,000 states. We used the BEAGLE high-performance computational library  (Suchard and Rambaut 2009)  in conjunction with BEAST to speed up the calculations. The log and tree files of each MCMC chain were combined using LogCombiner v1. 8. 2 (http://tree. bio. ed. ac. uk/ software/beast/), with a burn-in of 10%. We assessed convergence of each parameter in this combined file using TRACER v1. 6 (http://tree. bio. ed. ac. uk/software/tracer/) based on effective sample size (ESS) >200.
The degree of statistical uncertainty in each parameter estimate was given by the 95% highest posterior density (HPD) values. A Maximum Clade Credibility (MCC) tree was summarized using TreeAnnotator v1. 8. 2 (http://tree. bio. ed. ac. uk/software/ beast/) and visualized in FigTree v1. 4. 2 (http://tree. bio. ed. ac. uk/software/figtree/).
All PCR products were visualized on a 1. 5% agarose gel containing ethidium bromide. Further, PCR products were diluted and mixed into two sets according to their size and dyes (supplementary table  S3 , Supplementary Material online) and run on an ABI Prism 3730 genetic analyzer (Applied Biosystems) with Genescan Rox 500 size standard (Applied Biosystems). Microsatellite alleles were sized using GeneMapper 4. 0 software (Applied Biosystems).
Microsatellite Data Analyses To estimate the genetic variability in the microsatellite data set, we first assessed the size range of PCR products and the number of alleles. The observed (Ho) and unbiased expected heterozygosity (He) for each locus were calculated using GENETIX 4. 05. 2  (Belkhir et al. 2004). We then used microsatellite data to analyze the population genetic structure of Eptesicus serotinus with two different clustering algorithms: the methods implemented in STRUCTURE 2. 3  (Pritchard et al. 2000)  and GENELAND 4. 5. 0  (Guillot et al. 2005). STRUCTURE proposes a Bayesian algorithm to identify clusters of individuals respecting the Hardy-Weinberg/linkage equilibrium. With this first method, we estimated the number of clusters (K) with ten independent runs of K ¼ 1-10 carried out with 10 6 MCMC iterations after a burn-in period of 10 5 iterations, using the model with correlated allele frequencies and assuming admixture.
The most probable number of clusters was identified based on the loglikelihood values (and their convergence) associated with each K and visualized with STRUCTURE HARVESTER  (Earl and VonHoldt 2012). GENELAND also implements a Bayesian clustering model, but also considers the sampling coordinates of each individual when inferring population genetic structure. With GENELAND, the number of genetic clusters was determined by running the algorithm 10 times, allowing K to vary from 1 to 10, with the following parameters: 10 6 MCMC iterations with a thinning of 1,000, maximum rate of the Poisson process fixed to 100, and maximum number of nuclei in the Poisson-Voronoi tessellation fixed to 300. Finally, we estimated Bray-Curtis dissimilarities (BCD)  (Bray and Curtis 1957)  as interindividual distances based on microsatellite data, as well as F ST  (Weir and Cockerham 1984)  distances estimated with the R package "hierfstat"  (Goudet 2005)  between defined groups of individuals.
Mitochondrial DNA Sequence Analyses Alignments obtained for the two mitochondrial gene fragments CytB and D-loop were concatenated in a single alignment (1,488 bp) for subsequent analyses. Median-joining networks  (Bandelt et al. 1999)  were inferred for the concatenated alignment using the software NETWORK 4. 6. 6 (available at http://www. fluxus-engineering. com). We used the program SPADS 1. 0  (Dellicour and Mardulyn 2014)  to compute interindividual distances (IID, number of mismatches divided by the sequences length), and the pairwise distance U ST  (Excoffier et al. 1992 ) among the same groups of individuals defined above: 1) the group of E. serotinus individuals tested negative for EBLV-1 versus the group of individuals tested positive for EBLV-1, and 2) the group of individuals tested positive for EBLV-1 subtype a versus the group of individuals tested positive for EBLV-1 subtype b.
Geographic distances were computed as great circle geographic distances (i. e. , distances on the surface of the earth, measured in kilometers) with the R package "fields" (https://cran. r-project. org/web/packages/fields/in dex. html). In the second case, "mirror" data sets were first generated to only contain genetic data corresponding to host individuals for which viral sequence, host mtDNA sequences and microsatellite data are available. This resulted in matrices of viral/host sequences and viral sequences/host microsatellite data with 25 entries. The different Mantel tests  (Mantel 1967)  were performed with the R package "vegan" (https://cran. rproject. org/web/packages/vegan/index. html) and based on 10,000 permutations.