dataesr/scientific-paragraphs-categorization huggingface dataset:
Extension to other databases The EWET-DB contains data about human and animal hosts. For this reason the database can be linked to other information systems such as the EurEchino database (http://cnr-echinoalveolaire-ccoms. univ-fcomte. fr) for epidemiological and medical data about alveolar echinococcosis patients  [36] , and to a database on small mammal intermediate host communities in France, China and Kyrgyzstan, developed by the authors [FR, University of Bourgogne Franche-Comte, France]. For the specimens studied on additional genetic markers, the Gen-Bank access number could be available in the EWET-DB. With the advent of new generation sequencing, additional genetic data and metadata could be linked to the specimens included in the EWET-DB in the future. Moreover, in the item named "more about", additional information can be found about each specimen.
Conclusion Collecting, organizing and sharing data is fundamental in science, but it is only possible if data are managed and stored efficiently and metadata are made available. Centralizing data is a key step towards valorizing the data generated, and for promoting international collaborative projects. The EWET-DB is dedicated to sharing genetic data about E. multilocularis focused on the EmsB microsatellite, a powerful marker for genetic studies of the parasite, as well as genetic data associated with information on the parasite host and geographical coordinates. The available online dataset allows researchers to perform genetic and spatial analyses on the reference collection and their own data. The quality control of the EmsB analysis will improve thanks to the calibrator. EmsB data integrated in a database will be in a secure environment, with accurate and controlled information from sampling to genetic treatment.
Crystallization of the FIV CA Protein Screening of crystallization conditions was performed in 96-well plates using a mosquito nanopipette and commercial crystallization screening kits (Hampton Research, Aliso Viejo, CA, USA and Qiagen) with the sitting drop procedure. The FIV CA protein at 7 mg/mL in HEPES/NaCl buffer crystallized in the presence of an equal volume of 0. 2 M magnesium sulfate, 20% PEG 4000, 10% glycerol (condition E11 of the Qiagen PEGs II Suite) supplemented with 10% DMSO final. Using these conditions with the hanging drop technique and drops of 1 µL of protein with 1 µL of crystallization conditions, plate-shaped crystals grew within 15 days. Due to the presence of 10% glycerol in the crystallization solution, the cryoprotection step was dispensable and crystals were directly flash frozen in liquid nitrogen prior to data collection.
X-ray Data Collection and Structure Determination X-ray data were collected at best to 1. 67 Å resolution at the European Synchrotron Research Facility (ESRF) beamline ID30-B (Grenoble, France) at 100 K with a wavelength of 0. 99187 Å and a PILATUS 6M-F detector. Crystals belonged to a monoclinic space group C2 with cell dimensions a = 122. 2 Å, b = 74. 6 Å, c = 77. 0 Å, α = γ = 90. 0 • , β = 128. 7 •. Indexation and scaling were performed using XDS and XSCALE programs  [35]. The structure of FIV CA protein was determined by molecular replacement using the program MrBUMP  [36]  of the CCP4 program suite  [37]  and the structures of RELIK (Rabbit Endogenous Lentivirus) CA NTD fragment (PDB ID: 2XGU)  [38]  and FIV CA CTD fragment (PDB ID: 5DCK)  [33]  as search models. One solution was found with two monomers in the asymmetric unit and an R-factor of 48%.
The crystallographic refinement was performed with PHENIX (version 1. 12-2829)  [39]. A few residues in the β-hairpin, the cyclophilin binding loop and the C-terminal end were built manually using WinCOOT  [40]  and six molecules of glycerol were positioned in the electron density maps. The structure was refined to a final R work of 19. 7% and R free of 24. 1%, respectively, and statistics of the X-ray data are showed in Table  1. It showed a good geometry with 98. 6% in preferred regions, 1. 4% in allowed regions, and no Ramachandran outliers. The omit map around the cis-peptide of the CypBL loop was generated using the PHENIX software with the annealing method on residues 88-92 from chain B. Figures were generated using PyMol (Schrödinger, New York, NY, USA)  [41].
Asymmetric Unit and Crystal Packing The 1. 67 Å crystal structure of FIV CA was determined in the monoclinic space group C2 with two monomers in the asymmetric unit. The two chains (chains A and B) are quasi equivalent in structure and can be superposed with a root-mean-square deviation (RMSD) of 0. 63 Å on all Cα pairs. The FIV CA appears to be organized as a dimer of dimers in the crystal (Figure  1a ), which assembly is predicted to be stable in solution according to the PISA server for detection of biological oligomers  [42]. The A-B dimer (Figure  1b ) of the asymmetric unit is related with its symmetrical counterpart A -B via a 2-fold crystallographic axis to form a tetramer A-B-A -B (Figure  1a ). Dimeric CA interfaces have been described for other lentiviruses: for EIAV (PDB ID: 2EIA)  [22] , the CA NTD from one monomer is interacting with the CA NTD from the second monomer in a head-to-tail orientation, resulting in free CA CTDs in opposite directions in the dimer.
Regarding HIV-1 (PDB ID: 3NTE)  [43] , the CA NTD from one monomer (helices α1 and α2) is interacting with the CA CTD from the other monomer (helices 3 10 and α9), also resulting in a head-to-tail dimer. The A-B dimer of the asymmetric unit contains the two CA monomers in a head-to-tail orientation (Figure  1b ) in this FIV CA structure. The FIV CA NTD of one monomer interacts through loop L4 (between α3 and α4, Figure  2 ) with the loop L12 (between α10 and α11) of the CA CTD of the other monomer. The average buried surface area in this dimer is ~1100 Å 2 per monomer, with a calculated ∆G of -21. 1 kcal/mol. This interface is further stabilized through interactions between the tips of α1 of each FIV CA NTD (Figure  1b ). Intriguingly, the two monomers in the asymmetric unit are covalently linked by a disulfide bridge between the Cys61 of each CA monomer (Figure  1b ).
Acknowledgments: We thank the staff of the  Protein Science Facility (PSF) of the UMS BioSciences Gerland-Lyon Sud  and especially  Isabelle Zanella-Cléon  for Mass-Spectrometry analyzes. We also thank the staff at the ID30A-3 beamline of  European Synchrotron Radiation Facility  ( ESRF, Grenoble, France ). Finally, we would like to thank  L. Ballut  and  L. Carrique  for the data collection at the  ESRF. C. Folio  benefits from a fellowship from the  Ministère de l'Enseignement Supérieur et de la Recherche  and  M. Dujardin  from a fellowship from  Agence Nationale de la Recherche (ANR). This work is supported by the  ECOS-Sud program  (action  U14S01 ).
Collection of data The data used in this study were collected from September 2014 to September 2015. The monitoring of animals was carried out on a weekly basis (all the batches slaughtered on Monday) in an abattoir in Emilia Romagna (Società Cooperativa Agricola OPAS -Organizzazione Prodotto Allevatori Suini) which slaughters about 4,500 fatteners per day. Pigs (around 165 kg live body weight and 9 months of age) were delivered to the abattoir by trucks in batches of about 135 (minimum 130; maximum 140) animals derived from the same holding; all the pigs belonging to the same batch were consecutively slaughtered on the same day  (Merialdi et al. , 2012). In each batch, about 100 animals (minimum 95; maximum 105) were selected for the pluck evaluation, omitting carcasses at the beginning and end of each batch in order to avoid any risk of accidentally including pigs belonging to the previous or the next batch.
Pluck inspection Speed of the slaughter line was 480 animals per hour and inspection of the pluck was performed directly during the slaughtering process, from a platform immediately after the evisceration area. The examination of the pluck of each animal was conducted by two veterinarians, trained to assign a score for each lesion (Table  1 ), who alternately worked side by side the government official veterinarians, but using different protocols of evaluation. The involvement of two veterinarians who alternately collected data on the platform guaranteed a good standard for attention in scoring across many batches throughout the day. To standardize the definition of the lesions across the inspectors, once in each season the two veterinarians underwent a refresher day where the same pigs were assessed on the abattoir line by both the assessors.
Examination of the pluck was conducted by visual inspection and manual palpation of the organs, without any incision. Scores were registered using a voice recorder placed in the upper pocket of the overalls, and were transcribed in an Excel file for analysis during intervals between work shifts. Statistical methods All the statistical analyses were performed in SAS (Inst. Inc. , Cary, NC). For each batch, the average value for the lesion score of each organ was calculated, as well as the frequency of binary variables. Descriptive statistics of frequency of different scores for lesions were carried out (PROC UNIVARIATE). Data were analysed for their distributions. For normally distributed data an ANOVA was carried out with season as the fixed effect and farm as a random effect (PROC MIXED).
Correlation between different lesions and redundancy of parameters The correlations between different lesion parameters are shown in Table  3. Many correlations were statistically significant, although the absolute r values were low, as a consequence of the large dataset processed. A cluster analysis (Figure  1 ) was used to identify possible redundancy within the measures reported. In this specific case, cluster analysis was used to determine the autocorrelation among variables. The similarity decreases along the y axis. When the variables are grouped near to a similarity equal to 1, they are strongly correlated (e. g. % pleura severe lesions and pleura APP index) and very similar (redundant). Therefore the assessment of one of the two variables reflects the same information of the other.
Acknowledgements The authors thank the abattoir  Società Cooperativa Agricola OPAS (Organizzazione Prodotto Allevatori Suini, Carpi, Modena, Italy)  for the availability to host the research team; Chemifarma S. p. A. and  Merial Italia S. p. A. for helping in funding; and  University of Padova  for supporting the research activity in collaboration with  Prof Sandra Edwards  through the call "Visiting Scientist 2016".
, 2014). Among molecular alterations associated with EMT, pathway analysis revealed association between high EMT score and high expression of several immune checkpoints including PD1, PD-L1, PD-L2, B7-H3, OX40, OX40L, CD137, TIM3, LAG3, and CTLA4  (Mak et al. , 2016). Lou et al. (2016)  confirmed these observations in three independent datasets of lung cancer patients with early or advanced NSCLC adenocarcinomas. Additional reports suggested an association between PD-L1 expression and EMT in NSCLC and HNSCC  (Kim et al. , 2016; Ock et al. , 2016b). In their study, Lou et al. further found that tumors harboring high Mes content were associated with increased infiltration by TILs and Treg cells, and increased expression of costimulatory molecules (CD80, CD86). Furthermore, they showed elevated endogenous immune activation in these tumors, as revealed by a higher expression of IFN-c, IFN-c-inducible CXCL10 and IDO, among many other upregulated genes  (Lou et al.
, 2016). By investigating the Epi marker ESRP1 into The Cancer Genome Atlas dataset,  Yao et al. (2016)  identified a link between enhanced Mes features in ESRP1-low melanoma and high infiltrating lymphocyte activity, as assessed by a two-gene signature (PRF1 encoding for perforin and GZMA encoding for granzyme A). The ESRP1-low/Mes high group further showed better overall survival compared to groups expressing full-length or truncated forms of ESRP1. The authors suggested this subgroup of melanoma patients as well suited for immunotherapy intervention. In this regard, in the recent study of  Hugo et al. (2016)  analyzing biopsies of anti-PD1-treated advanced melanoma patients, EMT signatures and Mes-related genes were found to be upregulated among nonresponding relative to responding patients, thus suggesting that the Mes features of the primary tumor may be associated with innate anti-PD-1 resistance.
Lactic acid and tyramine quantification Lactic acid metabolism has been linked to virulence in E. faecalis  [23]  so this parameter was quantified. Figure  4a  shows the lactic acid production normalized to control. Exposure of E. faecalis V583 to SP led to an increase of lactic acid production but the pH was not modified despite the acid production (data not shown). Tyramine was also overproduced when the bacteria were treated with SP (Fig. 4b ). This may explain the absence of acidification. In order to evaluate the pathogenicity of E. faecalis V583 after treatment with SP, in vitro assay were then conducted using Caco-2/TC7 intestinal epithelial cells.
Imaging of fly abdomens Cuticle preparations were imaged with a binocular equipped with Leica DC480 digital camera using the Leica IM50 Image Manager software. An annular lamp was used to ensure homogeneous lighting. All pictures were taken in the same session and identical settings were used throughout the session. Pigmentation was quantified in A5, A6, and A7 hemisegments as the mean intensity using ImageJ software as previously reported  [33]. For this, the hemisegments were delimited by hand and the function "measure" of ImageJ used. The obtained values were subtracted from 255 to get values comprised between 0 (white) and 255 (black).
Immunofluorescence assay and confocal microscopy Rabbit anti-IL2Rγc (Biolegend), rabbit anti-synaptopodin (Santa Cruz) and rabbit anti-nephrin (LifeSpan BioSciences Inc. ) antibodies were incubated overnight on frozen kidney slides after blocking with PBS containing 5% BSA. Kidney sections or human tissues were then incubated with anti-rat Alexa Fluor 488, or anti-rabbit Alexa Fluor 546 conjugated secondary antibodies (Invitrogen). The nuclei were stained using DAPI (Invitrogen). Images from mice tissues were obtained with laser scanning confocal microscopy (TCS SP2 AOBS, Leica, Wetzlar, Germany). Acquisition software used was Leica Confocal Software and images (x630) were processed using Image J®. Images from human tissues were obtained with a wide-field light microscope (IX83, Olympus) and processed using Image J®.
Quantitative RT-PCR RNA was extracted from whole kidneys using TRIzol solution (Life Technologies). Residual genomic DNA was removed by DNase I treatment (Fermentas). RNA samples (1 µg) were reverse-transcribed using a Revert Aid H minus First Strand DNA Synthesis kit (Fermentas). Beta-Glucuronidase (Gusb) and Hypoxanthine-guanine phosphoribosyltransferase (Hprt1) genes were used as endogenous reference housekeeping genes. The specific PCR primer sequences used are listed in Supplemental Table  2. Normalization of the quantitative PCR (qPCR) data PCR analysis obtained using a LightCycler 480 (Roche Diagnostics) was performed using the Roche LightCycler 2. 0 software (Roche Diagnostics). Data were expressed as 2 -DCp, where Cp corresponds to the cycle threshold number.
Western blot analysis from cultured primary podocytes After extraction from podocytes with lysis buffer, samples were fractionated by SDS-PAGE NuPAGE 4/12% gels (Invitrogen) under reducing conditions and then transferred to a polyvinylidene difloride membrane. Membranes were incubated with the appropriate primary antibodies: anti-phosphorylated JAK1 (Cell Signaling), JAK3 (Cell Signaling), SYK (Novus Biologicals), anti-IL15Rα (Novus Biologicals), anti-IL2Rβ (Novus Biologicals). Protein loading was monitored by using the rabbit anti-GAPDH antibody (Sigma). Secondary antibody was horseradish peroxidase-conjugated goat anti-rabbit or anti-rat IgG (Amersham). Antigens were revealed with enhanced chemiluminescence (ECL)-plus (Amersham) on autoradiography films (Fuji). Relative quantification was made using Image J® software.
Data alignment and analysis were performed using the GobyWeb interface and examined visually at the Il2rg locus in the Integrative Genomic Viewer (http://www. broadinstitute. org/igv/) respective of Ensembl Annotation (Ensembl version 55). Values are means ± SEM from 6 mice in each condition tested. In D to F no significant differences were observed between groups. Bone marrow (BM) cells from 10-week-old wild type (WT) or Rag2 -/-mice (WT BM or Rag2 -/- BM, respectively) were transferred into sub-lethally irradiated 10-week-old WT (WT BM => WT, Rag2 -/-BM => WT) or into Rag2 -/-Il2rg -/-mice (WT BM => Rag2 -/-Il2rg -/-, Rag2 -/-BM => Rag2 -/-Il2rg -/-mice). Il2rg were not shared by other proxy genes, such as Gm20489-001 (red on the left in A), excluding any kidney-specific variants with an Il2rg similarity.
Acknowledgments This work was supported by  Inserm  and also in part by the  Faculté de Médecine Pierre et Marie Curie (Sorbonne Universités ,  UPMC Univ Paris 06 ). Y. L. is a recipient of  Fonds d'Etudes et de Recherche du Corps Médical  ( Assistance Publique des Hôpitaux de Paris ),  Société Française de Bienfaisance et d'Enseignement de San Sebastian-Donostia, Espagne and Société de Néphrologie  grants. D. C. is a recipient of a  European Renal Association -European Dialysis and Transplant Association (ERA -EDTA)  grant and the support from  Agence Nationale de la Recherche (ANR) of France. We thank  Edith Bouget ,  Chloe Cakin  and  Miftah Madi  for their technical assistance,  Benedita Rocha  and  Sophie Ezine  ( Inserm U1020, Hôpital Necker, Paris, France ) for providing.
In this study, we provide compelling evidence supporting a crucial role for CXXC5 in the regulation of DNA methylation and IFN response in pDCs, thereby demonstrating an additional layer of regulation integral to pDC function and antiviral defense. resuLts cXXc5 plays a critical role in pdc-elicited IFn response In the past decade, resources generated by immune cell gene profiling have led to the identification of lineage-specific regulators and the elucidation of principles governing immune cell specification. By searching these databases, we found that the putative epigenetic regulator CXXC5 is preferentially expressed in human and mouse pDCs  (Robbins et al. , 2008; Ghosh et al. , 2010; Miller et al. , 2012). Moreover, CXXC5, along with MAVS/IPS-1/VISA, has been previously linked to IFN response through a cDNA library screening  (Kawai et al.
The relative expression of Cxxc5 over Gapdh was measured by real-time PCR, and the data are presented as mean ± SD. This experiment was conducted twice with similar results. (B) Whole-cell lysates were prepared from Flt3L-pDCs, GM-CSF-cDCs, BMDMs, MEFs, splenic T cells, and B cells, and Western blotting was conducted with anti-CXXC5 antibody. This experiment was conducted twice with similar results. (C) Percentage of cDCs (CD11c hi , gated on B220 -CD3 -cells) and pDCs (B220 + PDCA1 + CD11c int ) in spleens was analyzed by flow cytometry, and total numbers of cDCs and pDCs were counted. This experiment was repeated three times, and similar results were obtained. The data are presented as mean ± SD. (D) Splenic pDCs (10 6 cells/ml) purified from WT and CXXC5 -/-mice (n = 4) were infected with HSV-1 for 24 h.
Production of IFNα/β was measured by ELI SA. This experiment was repeated twice, and representative data (mean ± SD) are shown (*, P < 0. 05, analyzed by Student's t test). (E) WT and CXXC5 -/-mice (n = 6) were either uninfected or i. v. infected with HSV-1 (5 × 10 6 pfu/mouse) for 9 h, and splenocytes were sorted by FACS. Total mRNA was prepared from 10 5 pDCs (CD11c int B220 + /PDCA1 + / Siglec-H hi ) and quantified by real-time PCR. This experiment was repeated twice, and representative data are shown (***, P < 0. 001, analyzed by Student's t test). (F) WT and CXXC5 -/-mice (n = 3) were either untreated or treated with i. v. injection of 20 µg CpG-A (complexed with 30 µg DOT AP) for 6 h, and sera were collected for ELI SA. This experiment was performed three times with similar results (*, P < 0.
To this end, we validated that (A-D) Flt3L-pDCs (10 6 /ml), splenic B cells (10 7 /ml, purified by anti-CD19 microbeads), GM-CSF-BMDCs (cDCs, 10 6 /ml), and BMDMs (10 6 /ml) were stimulated by CpG-B (100 nM) for 24 h, and supernatants (n = 3) were collected for ELI SA. These experiments were conducted three times, and the data are presented as mean ± SD (*, P < 0. 05; ***, P < 0. 001, by Student's t test). (E) Splenic B cells (10 7 /ml) were either untreated (UT) or treated with LPS (5 µg/ml) for 48 h, and secreted cytokines were measured by ELI SA. This experiment was conducted twice with similar results, and the data are presented as mean ± SD (**, P < 0. 01; ***, P < 0. 001, by Student's t test). (F) BMDCs Irf7, along with other CGI-containing genes Fos, Cxcl2, and Tnfα, were indeed down-regulated in steady-state CXXC5 -/- pDCs; however, some non-CGI genes such as Tlr7/9 and Tcf4 (which encodes E2-2) were normally expressed in these cells (Fig.
(G) Flt3L-differentiated pDCs from WT and CXXC5 -/-mice were stimulated with CpG-B (100 nM) for various times. Cell lysates were resolved by 10% SDS-PAGE and probed with the indicated antibodies. This experiment was repeated twice. (H and I) Flt3L-pDCs were stimulated with CpG-B (100 nM) for 2 h, and splenic B cells were treated with LPS (5 µg/ml) or CpG-B (150 nM) for 2 h. After cross-linking and FACS sorting, cell lysates were prepared and immunoprecipitated with 2 µg anti-p65. Immunoprecipitated promoters of proinflammatory genes were measured by real-time PCR and quantified over respective inputs (n = 4). These experiments were repeated twice, and representative data (mean ± SD) are shown (*, P < 0. 05; **, P < 0. 01; ***, P < 0. 001, analyzed by Student's t test). Besides Irf7, we observed decreased 5hmCs in CGIs of Cxcl2 and Tnfα in Tet2 -/-pDCs (Fig.
This experiment was repeated once. (B) Whole-cell lysates from Flt3L-differentiated WT and CXXC5 -/-(KO) pDCs were cross-linked and immunoprecipitated by control IgG or anti-Tet2. Enrichment of Tet2 on various regions of Irf7 promoter was determined by real-time PCR (n = 3). This experiment was repeated three times, and data (mean ± SD) were analyzed by Student's t test (**, P < 0. 01). (C) Genomic DNA from WT and Tet2 -/-Flt3L-pDCs were treated with sodium bisulfite, and the CGI region of Irf7 (500-1,000) was amplified by PCR and sequenced (n = 10). This experiment was conducted twice. (D and E) Flt3L-differentiated pDCs were cross-linked and subjected to ChIP with the indicated antibodies. Histone modifications (D) and enrichment of Ezh2 and Sin3a (E) in Irf7 CGI (500-1,000) were quantified by real-time PCR (n = 3).
These experiments were repeated twice, and data were analyzed by Student's t test and are presented as mean ± SD (*, P < 0. 05; ***, P < 0. 001). (F) Whole-cell lysates from Flt3L-differentiated WT and Tet2 -/-pDCs were resolved by 10% SDS-PAGE and probed with anti-IRF7 and anti-Tet2, respectively. This experiment was repeated once with similar results. (G and H) Flt3L-differentiated pDCs were cross-linked and sonicated, and chromatin fragments were immunoprecipitated with the indicated antibodies. 5hmC levels (G) and pol II enrichment (H) at the promoter regions of Irf7, Cxcl2, and Tnfα were quantified by real-time PCR (n = 3). These experiments were repeated twice with similar results (*, P < 0. 05; **, P < 0. 01; ***, P < 0. 001, analyzed by Student's t test and are presented as mean ± SD).