dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank all EQA participants:  Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria; Center for Virology, Medical University of Vienna, Vienna, Austria; Institute of Tropical Medicine; Central Laboratory for Clinical Biology, Antwerp, Belgium; Viral diseases, Scientific Public Health Institute, Brussels, Belgium; Microbiology department, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria; Research unit, University Hospital for Infectious Diseases "Dr. Fran Mihaljevic", Zagreb; Microbiology, CNPHI, Zagreb, Croatia; Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Dept. of molecular biology, Institute of Public Health, Ostrava, the Czech Republic; Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark; Virology Department, National Institute for Health Development, Tallinn, Lithuania; University of Helsinki and Helsinki University Hospital, Department of Virology and Immunology, Helsinki, Finland; Centre for Biological Threats and Special Pathogens, ZBS1 Highly Pathogenic Viruses, Robert Koch Institute, Berlin, Germany; Charité -Universitätsmedizin Berlin, Institute of Virology, Berlin, Germany; Bundeswehr Institute of Microbiology; Central Diagnostic Unit, Munich, Germany; Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany; Public health Laboratories, Hellenic Pasteur Institute, Athens, Greece; National Public Health Institute, Budapest, Hungary; National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland; Az.
National Center for Zoonotic Viruses, Central Virology Laboratory Public Health Services, Israel Ministry of Health Chaim Sheba Medical Center Tel -Hashomer, Israel; Federal Budget Institution of Science "Central Research Institute of Epidemiology", Moscow, Russia; Federal Office for Civil Protection, Spiez Laboratory, Spiez, Switzerland. Funding: This work was supported by the  European Centre for Disease Prevention and Control (ECDC)  under specific contract no. 3-ECD. 8456for implementation of the framework contract  ECDC/2016/002. Several virus strains were provided by the  European Virus Archive goes Global (EVAg)  project that has received funding from the  European Union 's  Horizon 2020 research and innovation program  under grant agreement No  653316.
Treponema pallidum subsp. pallidum is the causative agent of syphilis, a sexually transmitted disease with worldwide prevalence. Several different molecular typing schemes are currently available for this pathogen. To enable population biology studies of the syphilis agent and for epidemiological surveillance at the global scale, a harmonized typing tool needs to be introduced. Recently, we published a new multi-locus sequence typing (MLST) with the potential to significantly enhance the epidemiological data in several aspects (e. g. , distinguishing genetically different clades of syphilis, subtyping inside these clades, and finally, distinguishing different subspecies of non-cultivable pathogenic treponemes). In this short report, we introduce the PubMLST database for treponemal DNA data storage and for assignments of allelic profiles and sequencing types.
p. pallidum clades (TP0136, TP0548)  (Nechvátal et al. , 2014) , and can be used for differentiation of strains within each of these clades (TP0136 for the Nichols clade, and TP0705 for the SS14 clade). The purpose of this short report is to establish a single universal MLST scheme applicable to T. p. pallidum  (Grillová et al. , 2018a)  and introduce the PubMLST database for treponemal DNA data storage and ST assignments.
Treponema pallidum subsp. pallidum database hosted at PubMLST We have created a T. p. pallidum database hosted at PubMLST. PubMLST uses the BIGSdb platform for the storage and analysis of sequence data from bacterial isolates. The input format can be fasta files, which contain small contigs assembled from dideoxy chain termination sequencing of the typing loci, or complete or multiple contigs generated from next-generation sequencing platforms. When the new sequences are submitted to BIGSdb, the BLAST algorithm incorporated into BIGSdb identifies already known sequence variants or marks an unknown variant for curator verification. After verification by a curator, a novel allele number is assigned  (Maiden et al. , 2013). Metadata of the patients may be submitted to the database as well, and includes some important characteristics of isolates, for example, isolate identification name/number; country where the strain was isolated; biological source of sample; year of isolation; and resistance to macrolide antibiotics.
However, we encourage the researchers to upload as much information about patients and samples as available (e. g. , age, sex and sexual orientation of the patients, stage of the disease, serological results etc. ). The database can be accessed at https://pubmlst. org/tpallidum/. The database is primarily designed to be used as a tool for automatic ST assignments; for determination of new alleles; for storage of sample metadata; for identification of new associations between genetic types and metadata using various tools; and for user-friendly visualization of molecular typing data, particularly using GrapeTree  (Zhou et al. , 2018)  and Microreact  (Argimón et al. , 2016)  plugins. These plugins enable, for example, visualization of genomic epidemiology and phylogeography by showing the correlation of the STs and geographical areas in real time and visualization of phylogenetic data together with patient metadata.
Sequences submitted to PubMLST All published whole genome and draft genome sequences of T. p. pallidum  (Pětrošová et al. , 2012 (Pětrošová et al. , , 2013;; Giacani et al. , 2010 Giacani et al. , , 2014;; Zobaníková et al. , 2012; Tong et al. , 2017; Arora et al. , 2016; Sun et al. , 2016; Pinto et al. , 2016; Strouhal et al. , 2018; Grillová et al. , 2018b) , data available at GenBank, as well as sequences obtained by MLST  (Grillová et al. , 2018a; Pospíšilová et al. , 2018)  were submitted to the database.
Treponema pallidum subsp. pallidum database At the time of writing (September 2018), the databases contain 358 T. p. pallidum strains, mostly isolated from Europe (70. 87%), followed by North America (26. 33%), Asia (2. 52%) and South America (0. 28%) (Table  1 ). More than 90% of samples were clinically acquired and 31 strains were propagated in rabbits. A total of 71 samples represented whole/draft genomes and 287 samples were typed using MLST and yielded sequences only in typing loci. The samples were collected from 1912 to 2017. There were 272 samples collected from males (183 samples were collected from Men who have sex with men; MSM) and only four samples from females. Most of the samples were isolated from patients diagnosed with primary syphilis, followed by secondary syphilis, patients in the border of primary and secondary stage, and there were also three cases of congenital syphilis.
p. pallidum isolates obtained directly from patients belong to the SS14-like group  (Šmajs et al. , 2016). We encourage researchers and public health communities to use MLST, which is able to distinguish these two clonal complexes. Moreover, we recommend submitting the sequencing data to PubMLST along with the metadata (including data from the serological tests). The expansion of the sample set in the PubMLST with syphilis isolates from different geographical areas can lead to a better understanding of the epidemiology of the two genetically distinct groups of syphilis treponemes.
CONCLUSIONS Here, we present the PubMLST BIGSdb database of T. p. pallidum, which represents the first publicly available data storage of T. p. pallidum sequences connected to metadata of patients. The database identifies specific regions of uploaded sequencing data and their genetic variation in order to reveal the sequencing types of T. p. pallidum isolates based on the newly developed MLST  (Grillová et al. , 2018a). We hope that this tool will open new opportunities in epidemiology of syphilis thereby allowing studies of sequencing types in different locations, tracking of syphilis infections and finding the association of particular strains with specific groups of patients. All these data should improve our understanding of syphilis epidemiology.
Moreover, there are several hurdles for the development of effective anti-HCV vaccine, namely hyper-variability of HCV genome, existence of multiple viral subtypes and quasispecies  [34]  and most importantly the absence of small animal model that provides statistically meaningful data upon challenging with the viral infection. The known adjuvants in several studies also displayed weak response in presenting the HCV epitopes. In the current study, we designed 6 peptides derived from the most conserved regions of gpE1 (one peptide), gpE2 (2 peptides), NS4B (one peptide), NS5A (one peptide) and NS5B (one peptide). The amino acid sequences of the synthetic peptides were derived from HCV genotype 4 (ED43: GenBank accession no. Y11604)  [35] , the most prevalent genotype in Egypt (> 93%)  [36, 37].
Peptide design and synthesis The three peptides derived from the envelope proteins gpE1 and gpE2 have been shown to possess B cell function as described previously in the epitope maps reported by  Yusim, K. et al. (2005)   [38]  and by our laboratory  [11, 25]. Whereas the 3 peptides derived from the nonstructural proteins (NS4B, NS5A, NS5B) have been shown to trigger HCV-specific CD4+ T cell response in subjects who spontaneously cleared the infection  [13]. The peptides were synthesized by using the 9-fluorenylmethoxy carbonyl method. Each peptide was made up of an 8-branch multiple antigenic peptide (MAP) form where the arms are bound via a lysine backbone with 90% purity (Anaspec, Fremont, California, USA). The amino acid sequences in each peptide were aligned with viral isolates in HCV database to record the degree of sequence identity with HCV subtypes.
The six peptide sequences used in the current study were derived from HCV genotype 4a (EG. ED43. Y11604). The alignment was done by using Clustal W multiple sequence alignment program at http:// align. genome. jp/. Peptide sequences and alignments are summarized in Table  1. All lyophilized peptides were dsissolved in DMSO (Sigma, Germany) at a concentration of 10 μg/μL and stored at -20 °C. Prior to immunization, peptides were diluted to the desired dose concentration and were kept at 4 °C.
Viral neutralization by the generated murine antibodies The genotype 2a virus used in this study was based on the JFH1 isolate (genotype 2a; GenBank accession number AB237837)  [42] , kindly provided by T. Wakita (National Institute of Infectious Diseases, Tokyo, Japan). This virus contains mutations at the C terminus of the core protein leading to amino acid changes F172C and P173S, which have been shown to increase viral titers  [43]. Furthermore, the N-terminal E1 sequence encoding residues 196 TSSSYMVTNDC has been modified to reconstitute the A4 epitope (SSGLYHVTNDC), as described previously  [44]. In addition, neutralization experiments were also performed with a chimeric virus (ED43/JFH1), kindly provided by J. Bukh (Copenhagen University Hospital, Denmark), which is based on a JFH1 recombinant expressing core-NS2 of genotype 4a ED43 strain  [45].
Both primary and secondary antibody incubations were carried out in PBS containing 10% goat serum or 10% horse serum respectively for 30 min at room temperature. For quantification of infection levels, images of randomly picked areas from each well were recorded and processed using Image J software. For each condition 12 pictures were counted, as we took 4 non-overlapping pictures per well working in triplicates. Cells labeled with anti-E1 mAb A4 or anti-NS5A were counted as infected cells. The total number of cells was obtained from DAPI-labeled nuclei. The infections were scored as the ratio of infected cells to total cells. Each experiment was performed 3 times in triplicates. Percentage neutralization was calculated in relation to the mean of non-immunized BALB/c mice serum/virus mix controls.
The 50% Inhibitory concentration (IC50) was determined against JFH-1 by performing serial dilutions of our antibodies in a similar manner to the inhibition assays. The percent neutralization was calculated as the percent reduction in Focus Forming Unit (FFU) normalized to virus incubated with non-immunized BALB/c mice sera. Data transformation and four-parameter nonlinear regression analysis were performed using GraphPad Prism software.
, prior to inoculation onto Huh7 cells that were pre-seeded in 96 well plates. Cells were fixed and immunostained with A4 MAb at 30 h post infection, and counted by FFU-reduction assay. Each assay was performed in triplicates and data are shown as mean of three experiments. For each antibody, dose-dependent neutralization was measured to determine the concentration that resulted in a 50% reduction in FFU (IC50). For diluted IgG from mice immunized with 800 ng, 1600 ng and 16μg IC50 was calculated by nonlinear regression as a dilution of 004714, 0,004187 and 0,001185 respectively On the other hand, peptides containing epitopes derived from the gpE1 and gpE2 glycoproteins have been shown to generate neutralizing antibodies  [53]. Esumi et al. [54]  reported that immunization with recombinant proteins derived from gpE1 and gpE2 together with HVR1 peptides derived from different isolates can confer a complete protection of chimpanzee challenged with the same isolate  [54].
Crush injury also raised levels of granzyme B in the sciatic nerve (Figure  S5D ). Using two-photon imaging of the sciatic nerve in vivo 3 days after crush injury, we observed NKp46-YFP cells ''rolling'' along the wall of intra-neural blood vessels (Video S5). Within the sciatic nerve itself, NK cells were highly motile and displayed multipolar morphology (Video S6), reminiscent of stimulated NK cells in vitro. No YFP + cells were observed by two-photon imaging in the nerves of sham injured mice (data not shown). Endogenous NK Response Attenuates Post-injury Sensitivity Depletion of NK cells by DTx treatment in NKp46-DTR mice (Figure  S5E ) reduced NKp46 + cell infiltration (Figures  S5F  and S5G ) and granzyme B content in the crushed nerves (Figure  S5H ). Control (PBS-treated) NKp46-DTR mice were almost completely insensitive to pinprick stimulation of the hind paw until a relatively rapid heel-to-toe pattern of recovery beginning in the second week after injury (Figures  S5I  and S5J , PBS) consistent with axon regeneration through the foot  (Latremoliere et al.
Flow cytometry For surface labeling cell suspensions were transferred to 5 mL round bottom tubes and Fc receptors were blocked with unconjugated rat anti-mouse CD16/CD32 (clone 2. 4G2) monoclonal antibody (1:100; BD Biosciences, cat no. 553142. RRID:AB_394657) for 15 min at 4 C and labeled with a combination of fluorescently-conjugated anti-mouse primary antibodies for 30 min at 4 C. After washing with FACS buffer cell suspensions were run on a four-color flow cytometer (FACSCalibur, BD Biosciences) and gated populations analyzed with Cell Quest software (BD Biosciences). Lymphocytes were initially gated according to the FSC-SSC scatter profile; cell populations were identified by fluorescence gating compared to unlabeled or IgG controls. Antibodies used were PE rat antimouse NKp46 (clone 29A1.
0 were considered acceptable) and nucleotide content on a spectrophotometer. Equal amounts of RNA (150-250 ng from whole DRG, 500ng from cell cultures) was reversed-transcribed using M-MLV (200 U/rxn), dNTPs and oligo(dT) 12-18 primers (Invitrogen) in a 20 ml reaction volume according to the manufacturer's instructions. PCR reactions (25 ml) using Go Taq Flexi DNA polymerase (Promega) were then performed from cDNA on a thermal cycler (MJ Mini, BioRad) with the following primer pairs: Raet1a-e universal primers (Raet1 alpha, GenBank: NM_009016. 1; Raet1 beta, GenBank: NM_009017. 1; Raet1 gamma, GenBank: NM_009018. 1; Raet1 delta, GenBank: NM_020030. 2; Raet1 epsilon, GenBank: NM_198193. 2) (270bp), (forward*) 5 0 -GCTGTTGCCACAGTCA CATC-3 0 , (reverse) 5 0 -CCTGGGTCACCTGAAGTCAT-3 0 ; NK1. 1 (Klrb1c v1, GenBank: NM_001159904.
1; Klrb1c v2, GenBank: NM_008527. 2) (277bp), (forward*) 5 0 -GGAACAGAGCAGAGCATTCA-3 0 , (reverse*) 5 0 -CCAATCAGGGTCAGGACAAG-3 0 ; Advillin (NM_009635. 3) (332bp), (forward*) 5 0 -GCTACATCGTCCTCTCGACC-3 0 , (reverse*) 5 0 -CATTTCCACCTCCGTGGCTT-3 0 ; Gapdh (Gapdh v1, GenBank: NM_001289726. 1; Gapdh v2, GenBank: NM_008084. 3) (230bp), (forward*) 5 0 -AACAGCAACTCCCA CTCTTC-3 0 , (reverse*) 5 0 -TGGGTGCAGCGAACTTTAT-3 0. Asterisk (*) indicates primers which cross an exon-exon boundary. The PCR conditions were 95 C (2 min), cycled 35 times from 95 C (30 s) to 60 C (30 s) to 72 C (30 s), 72 C (5 min), 4 C (forever). Reactions performed without cDNA served as negative control. PCR products were run on an agarose (1. 5%) gel containing a DNA staining reagent (SafePinky, GenDepot, USA) and visualized on a UV transilluminator.
Quantitative real-time PCR Gene expression was analysis performed on cDNA from DRG using a Power SYBR Green PCR Master Mix (Applied Biosystems) and pairs of target-specific primers (500nM) in MicroAmp optical tubes (20ml reaction volume) on a 7500 Real-Time PCR system (Applied Biosystems). The PCR conditions were 50 C (2 min), 95 C (10 min), and cycled 40 times at 95 C (15 s) to 60 C (1 min). Samples were run in triplicate. Data were analyzed using the built-in 7500 software (v2. 0. 4, Life Technologies) and expression was determined relative to a reference gene (Gapdh) in adult DRG for cultures or contralateral DRG for nerve injury experiments using the comparative C t method. Primers were designed using Primer-BLAST software (NIH). Primers were selected based on specificity to the desired target gene upon BLAST search, overlap of the exon-exon boundary, lack of potential hairpin-forming or self-priming regions, single peak in the dissociation curve (single band PCR product) and equivalent amplification efficiency (linear shift in C t value upon serial dilution of cDNA).
QUANTIFICATION AND STATISTICAL ANALYSIS Laser scanning confocal imaging and analysis For analysis of neurite density in microfluidic co-cultures, single z section low magnification (x10) confocal images at 0. 5 zoom (LSM700, Zeiss) were acquired of b-tubulin III immunofluorescence (647nm emission) along the full length of the neurite compartment. Gamma high channel images were exported as an unaltered TIFF using Zeiss imaging software  (v8. 1, ZEN 2012 SP1, Zeiss). Images were converted to b/w by adjusting to a set threshold, scale calibrated and horizontal pixel density was measured using the Plot Profile function in  ImageJ (v1. 46r, NIH). The distance to 50% neurite density was calculated from the normalized cumulative pixel density. 6-8 images per were acquired per microfluidic device, n = 3 devices per group.
For analysis of b-tubulin III and STMN2 labeling in sciatic nerve tissue, a composite of the full length nerve was created from individual z section images acquired at x10 magnification and 0. 5 zoom along the length of the nerve (LSM700, Zeiss). Images containing crush site, as well as proximal and distal regions (±1-2 mm from the crush site) were exported to ImageJ, scale calibrated (0. 8 pixels/mm) and brightness threshold set in b/w mode. The mean pixel density from a 9000 mm 2 selection of the nerve mid-image was recorded from 3-4 images per nerve region, per mouse, per treatment. Co-localized regions of RAE1 double-labeling with b-tubulin III and STMN2 were exported using the co-localization function on the Zen 2012 software after setting for threshold image intensity in both fluorescence channels (1000 units per channel).
ROI selections were then applied to the red channel (in situ), which was converted to an 8-bit black/white image with threshold set at 1-255. The number of particles per NeuN+ ROI (larger than 1 mm 2 to eliminate background spots) were counted using the Particles Analysis function in ImageJ and exported to a spreadsheet (Microsoft Excel). A total of n = 2138 NeuN+ ROI from ipsilateral DRG and n = 1565 NeuN+ ROI from contralateral DRG were included; n = 3 mice, n = 3 sections per DRG per mouse. Data are presented as a frequency distribution of the number of in situ spots per neuron (NeuN+ ROI), and versus neuronal cell size (mm 2 ).
Statistical Analysis Comparisons between two groups of data were made with Student's t test (paired or unpaired) or Mann-Whitney test for non-normal distributions (confirmed with Kolmogorov-Smirnov test). Comparisons between three or more groups of data were made with One-way ANOVA. All tests are two-sided unless indicated. Two-way ANOVA tests were used to compare the effects of treatments on molecular, cellular and behavioral assays over time. Data are presented as mean ± standard error of the mean (SEM) unless otherwise stated. ns, not significant. Analyses were performed using GraphPad Prism version 5. 00 for Windows, GraphPad Software, San Diego California USA, https://www. graphpad. com/. No statistical methods were used to predetermine sample sizes, which were based on previous literature and availability of animals.
ACKNOWLEDGMENTS We thank  Daniel Bullock ,  Yildirim Han Ozdemir ,  Jina Won , and  Nadia Yessaad  for technical assistance and  Dr. Steve West  for help with ImageJ macro programming. We also thank  Dr. Eric Vivier  and  Dr. Lewis Lanier  for generously providing the Ncr1 icre and  Rosa26 raet1e  mice, respectively,  Dr. Noo Li Jeon  and  Dr. Sang Cheol Kim  for the kind gift of microfluidic chambers, and  Dr. David Bennett  and  Teodora Trendafilova  for assistance with in situ hybridization. We are especially grateful to  Dr. Susan E. Lewis  for editing the manuscript. Finally, thank you to all the staff at the  Seoul National University Dental Research Institute core facilities  for their support. This work was supported by the  Korean Government MEST Basic Science Research Program  ( NRF-2012R1A1A2040338  to A.
J. D. ) and by  National Research Foundation of Korea  grants ( NRF-2016M3A9B6021209 ,  NRF-2017M3C7A1025602 , and  NRF-2018R1A5A2024418  to S. B. O. and  NRF-2017R1A2B3004828  to K. -M. L. ). M. C. was supported by  NIH  grant  NS074430. S. R. is supported by an  MRC   Clinician Scientist Fellowship  ( MR/P008399/1 ). R. G. -C. was supported by  Alfonso Martin Escudero Fellowship. The laboratory of S. U. received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program , under grant agreement no. 648768  from the  Agence Nationnale de la Recherche (ANR ; no. ANR-14-CE14-0009-01 ), and from the  ARC foundation  (no. PGA120140200817 ) and is supported by institutional grants from  INSERM ,  CNRS , and  Aix-Marseille University  to the CIML.
These data warrant evaluation of BI 836826 in CLL and other mature B-cell malignancies. Here, we report a phase 1 first-in-human, open-label, dose-escalation study to evaluate the maximum tolerated dose (MTD), safety and efficacy of BI 836826 in relapsed/refractory CLL (NCT01296932). Eligible patients had relapsed/refractory CLL according to the International Workshop on Chronic Lymphocytic Leukemia (IWCLL) definition  [5] , and had received ≥2 prior treatment regimens (Supplementary Patients and Methods). The study was conducted in accordance with the Declaration of Helsinki and Good Clinical Practice guidelines, and the protocol approved by the relevant institutional review boards. Patients provided written informed consent. BI 836826 was administered at a starting dose of 1 mg (Supplementary Patients and Methods; Suppl.