dataesr/scientific-paragraphs-categorization huggingface dataset:
d TBK1 -/-MEFs reconstituted with WT TBK1 or mutants were either left untreated (MOCK) or transfected with HMW poly(I:C) (5 μg/mL) for 4 h (trPoly(I:C)). TBK1 aggregation was then assessed by immunofluorescence staining and counting of the aggregates. The data shown are means ± SD from three independent experiments (300 cells were counted per condition). **0. 001 < P < 0. 01 versus MEFs reconstituted with WT TBK1 (Student's t test). e The reconstituted MEFs described in (c) and the initial TBK1 -/-MEFs were transfected with HMW poly(I:C) (5 μg/mL) for 0, 2, and 4 h (trPoly(I:C)). IFNB1 mRNA levels were then assessed by RT-qPCR with normalization against GAPDH. The data shown are means ± SD from three independent experiments (analysis of variance and comparison with WT TBK1-reconstituted MEFs in Student's t test).
* Indicates a non-specific band. f-i WT or OPTN KO HeLa cells were infected with SeV for the indicated times. IFNB1 and IL-6 mRNA levels were then assessed by RT-qPCR with normalization against GAPDH (f, g), or the production of IFNβ and IL-6 was analyzed by ELISA in the cell supernatant (h, i). The data shown are means ± SD from three independent experiments (analysis of variance and comparison with WT HeLa cells in Student's t test). ns, not significant; AU, arbitrary unit. j HEK293T cells stably expressing TLR3 (HEK293-TLR3) were either left unstimulated or stimulated with poly(I:C) (10 μg/mL) for 30 or 60 minutes. Cell lysates (Lys. ) were subjected to immunoprecipitation (IP) with an antibody against OPTN. Samples were then analyzed by immunoblotting with antibodies against the indicated proteins.
°Corresponds to TBK1 detection from a previous immunoblot. k HEK293-TLR3 cells were transfected with a control non-specific siRNA (NS) or with two individual OPTN-specific siRNAs (OPTN A and OPTN B) or a NEMO-specific siRNA. The cells were then transfected, 48 h later, with an IFNβ promoter reporter or with a NF-κB reporter and the Renilla luciferase gene as an internal control. Then, 24 h after transfection, cells were either left unstimulated (Unstim) or stimulated with poly(I:C) (10 μg/mL) for 7 h. Luciferase assays were performed and the results were normalized against Renilla luciferase activity. The data shown are means ± SD from three independent experiments (analysis of variance and comparison with the NS siRNA-transfected cells in Student's t test). ns, not significant. l HEK293-TLR3 cells were transfected as in (k).
Cell lysates were then analyzed by immunoblotting with antibodies against the indicated proteins. h-k BMDM isolated from WT or OPTN 470T mice were stimulated with poly(I:C) (1 μg/mL) for the indicated times. IFNB1 and IL-6 mRNA levels were then assessed by RT-qPCR with normalization against GAPDH (h, i), or the production of IFNβ and IL-6 was analyzed by ELISA in the cell supernatant (j, k). The data shown are means ± SD from three independent experiments (analysis of variance and comparison with WT BMDM in Student's t test). ns, not significant; AU, arbitrary unit confirming its ability to neutralize the activity of OPTN (Fig. 7f  ). Thus, the fact that OPTN is targeted by a viral protein to dampen type I IFN signaling reinforces our findings that OPTN is an important effector in TBK1 activation.
In parallel, the cells were also transfected with a plasmid encoding GFP or NS3-GFP. Then, 16 h after transfection, cells were either left unstimulated (Unstim) or infected with Sendai virus (+ SeV) for 7 h. Luciferase assays were then performed and the results were normalized against Renilla luciferase activity. The data shown are means ± SD from three independent experiments (analysis of variance and comparison with GFP-transfected cells in Student's t test). RLU, relative luminescence units. c HEK293T cells were transfected with a plasmid encoding GFP or NS3-GFP. Then, 16 h after transfection, cells were infected with SeV for the indicated times. Cell lysates were analyzed by immunoblotting with antibodies against the indicated proteins. d HEK293T cells were transfected with a plasmid encoding OPTN and a plasmid encoding GFP or NS3-GFP.
Statistical analysis We carried out t tests with Tukey's post hoc analysis to assess the statistical significance of differences (Prism GraphPad Software), and the P values obtained are indicated in the figure legends. Differences were considered to be significant if P < 0. 05. ****P < 0. 0001, ***P < 0. 001, **0. 001 < P < 0. 01, *0. 01 < P < 0. 05. ns, not significant. The data shown in each histogram are the means ± SD from three independent experiments.
Acknowledgements We would like to thank  Drs G. N. Barber ,  J. Tschopp ,  K. A. Fitzgerald , and  M. J. Eck  for providing cells or reagents. This work was supported by grants from  Fondation ARC (Association pour La Recherche contre le Cancer) ,  Ligue Nationale contre le Cancer  ( Equipe Labellisée ) and the  ANRS (Agence Nationale pour la Recherche sur le SIDA). NZ and MP are supported by fellowships from  Université Paris-Sud. LSDC is supported by a fellowship from  CNPq  ( Conselho Nacional de Desenvolvimento Cientifico e Tecnologico).
Five tissue samples were collected at the same location for each calf, including the right and left cranial, the accessory and the cardiac lobes of the lungs and the tracheobronchial lymphatic node. PCR was conducted with 5 µL of elution buffer (50 µL) with the TaqVet ™ Triplex P. multocida and M. haemolytica kit (Life technologies, USA) according the manufacturer's instructions in a Light Cycler 480 (Roche). A standard plasmid curve for quantification was obtained by successive 10-fold dilutions of a plasmid containing 10 6 DNA copies of the same M. haemolytica amplified nucleotide sequence (Life technologies, USA). In addition, two housekeeping genes previously mentioned in the literature (gapdh and rpl19) were amplified in each sample to normalize the qPCR products using GeNorm software (Biogazelle, qBase+).
PCR results were analyzed using Roche Light Cycler 480 software (release 1. 5. 1) using the standard 2nd derivative and fit points methods for all samples (Roche Diagnostics). Results were similar when the PCR threshold was defined by the software (2nd derivative method) or fixed manually (fit points method) around 100 DNA copies. Results are expressed as the mean of PCR titers for each group and each day, after a logistic transformation, or as the accumulated bacterial shed (ABS), which corresponds to the mean area under individual curves of M. haemolytica detected by qPCR in BALs from T0 to T3 (GraphPad Prism software analysis, La Jolla, California, USA).
Statistical Analysis Statistical analyses were performed using GraphPad Prism software (RRID: rid_000081, La Jolla, USA). For DNA quantification statistical analyses were performed on logarithmic-transformed data. A two-way ANOVA with repeated measures was used for DNA quantification in BAL and for clinical scores. The two-way ANOVA gave a p-value <0. 0001 for interaction between time/group (23. 7 and 17. 1% of total variation respectively). Therefore, we considered that the study had sufficient power for further analyses. As effects of the "day" and "treatment" factors were significant among interactions, Bonferroni adjustments for multiplicity were used between contrasts to compare the treatments on each day. A two-way ANOVA without repeated measures was used for DNA quantification in respiratory tissues.
In the non-treated animals, rectal temperature remained above the temperature of the treated groups at each time point, indicating a significant difference between E2 calves and non-treated calves at T2 (data not shown). Clinical signs started at 6 ± 3 h and peaked between 24 and 40 h after inoculation for most calves. After peak, clinical signs of CON calves slightly decreased throughout the course of infection. In the other groups, clinical signs were very similar to those observed in the CON group until  ; heart rate from 0 to 2 (<80, 80-100, >100); nasal discharge from 0 to 3 (absent, mild, moderate, or profuse); intensity and added lung sounds from 0 to 2 (normal, increased effort, or labored); and appetite from 0 to 2 (normal, decreased, or anorexic). Accumulated clinical scores (ACS) were calculated as the area under daily clinical scores using the trapezoid method.
7 million probes) according to the manufacturer's recommendations. Deletion of TCR loci, as a reflection of V(D)J recombination, were defined by the CGH log 2 copy number ratio, with deletion/rearrangement on one allele defined as 0. 5 to 1. 5, whereas log 2 copy number ratios o1. 5 were defined as biallelic deletions/rearrangements. Data are accessible on the NCBI GEO database under GSE67131. Transgenic mice. The CD4/NPM-ALK (CD4NA) mice were generated as previously described (kindly provided by Professor G. Inghirami, University of Turin, Italy)  12. NPM-ALK/OTI (CD4NA/OTI) mice were generated by crossing the CD4NA line to the OT1 transgenic T cell line (kindly provided by Professor G. Griffiths, University of Cambridge, UK)  14. NPM-ALK/RAG2 À / À (NARAG2 À / À ) mice were generated by crossing the CD4NA line to the RAG2 À / À line (kindly provided by Professor C.
Acknowledgements S. D. T. , L. K. , O. M. , L. B. and L. L. are members of the  European Research Initiative for ALK-Related Malignancies  (www. erialcl. net). S. D. T. receives funding from  Bloodwise. T. I. M. was in receipt of a Gordon Piller PhD studentship from  Leukaemia and Lymphoma Research  at the time of the study. C. J. F. is supported with PhD funding from the bbsrc. S. D. T. , S. M. , I. A. and T. I. M. are supported with funding from the  University of Ha'il, Kingdom of Saudi Arabia. Support  to the  Macintyre Laboratory  includes the  French Institut National de Cancer (INCa) PAIR Lymphoma T-COG  ( N°2008-021 ) and  RT-07 Immature T/My leukemia 'Recherche Translationnelle ' programmes and  MD/ PhD  grant funding to A. T. , the  Enfants et Santeand SocieteFranc¸aise de Cancers de l'Enfant (SFCE)  and the  Association Laurette Fugain  ( ALF2012-09 ).
Case definition The French National Reference Center for Q fever receives samples for C burnetii testing  [4]  from the entire country. Between January 2009 and June 2015, 1555 patients were tested positive for Q fever in our center. Clinical and laboratory data were collected prospectively for all patients-thanks to a standardized questionnaire. For patients who did not benefit from a medical monitoring by our center in our center, data were collected over the phone to complete the standardized questionnaire. All patients with an active C burnetii infection who benefited from a 18 F-FDG PET/CT were included in our study (Fig. 1  and eFig. 1, http://links. lww. com/MD/B217). Among these patients, several subgroups were identified and differentiated according to the diagnosis before  18  F-FDG PET/CT: primary C burnetii infection was defined by the association of clinical symptoms (fever and/or hepatitis and/or pneumonia) with serologic criteria for phase II IgG levels ≥200 and phase II IgM levels ≥50, or by a Polymerase Chain Reaction (PCR) and no endocarditis.
None of the interaction between the two main effects was significant. ***P < 0. 001, **P < 0. 01; ns, P > 0. 05. Fernandez, Guy, Laverze, Bonnefont, Knudsen and Fortun-Lamothe case, we can reasonably assume that feed restriction before corn delivery probably enhanced the hyperphagic behaviour in geese and our results clearly show the major role of hyperphagia in liver fattening. The individual data obtained for feed intake point out the high variability in the feeding behaviour of male geese, in response to ad libitum corn feeding. The causes of this variability deserve further investigations. The heritability of feed intake under ad libitum feeding has been reported to be moderated in geese (h 2 = 0. 29;  Molnar et al. , 2006)  but this should be measured again under our experimental conditions where the expression of hyperphagic behaviour is stimulated.
These studies were followed by Rosenzwajg et al. to determine the effects of IL-2 on induction of Tregs and NK cells in patients with T1DM  (129, 130). They observed an increase in CD4 + FOXP3 + and CD8 + FOXP3 + Tregs, the proportion and duration of which was dose dependent. The Tregs expressed enhanced levels of activation markers and basal pSTAT5 and had a 20-fold higher sensitivity to IL-2 than Teff and NK cells. Global transcriptome analyses showed a dosedependent decrease in immune response signatures. However, although they were able to induce a dose-dependent increase in Tregs, they did not observe a change in glucose metabolism  (126). Low-dose IL-2 is being trialed in other clinical settings, including rheumatoid arthritis, ankylosing spondylitis, systemic lupus erythematosus, psoriasis, Behcet's disease, Wegener's granulomatosis, Takayasu's disease, Crohn's disease, ulcerative colitis, autoimmune hepatitis, and sclerosing cholangitis (TRANSREG, ClinicalTrials.
administered autologous Tregs that had been expanded with CD3/CD28 antibodies and IL-2. FOXP3 expression was found on >90% of the infused cells. A dose escalation of 10-30 × 10 6 Tregs/kg in 1 or 2 doses was studied. After 1 year, 8/12 met the criteria of clinical remission (<0. 5 U/kg/d of insulin) and two were insulin independent. They reported a significant improvement in glucagon-stimulated C-peptide responses and reduced insulin usage at 4 months and 1 year compared to untreated subjects. The infusions were well tolerated and antibody responses to a hepatitis B vaccine and rubella were apparently not affected by the treatment  (182). In a recently completed Phase I trial (NCT01210664), we observed that polyclonal FOXP3 + CD4 + CD25 + CD127 lo Tregs could be efficiently isolated and expanded from patients with T1DM (183).
This trial involved isolation and expansion of autologous Tregs over a 2-week culture period. The cells could then be shipped to a collaborating institution for infusion into patients, suggesting that development of this strategy for adoptive transfer of cells is feasible and need not be limited only to sites that are capable of performing the expansion on site. There were no significant safety signals from the study and the cells maintained their phenotype in vivo: there was no evidence of differentiation of the infused Tregs into other, potentially pathogenic phenotypes. Importantly, using an in vitro non-radioactive labeling technique  (184) , a subset of the adoptively transferred Tregs were observed to survive >1 year post infusion. A similar strategy is being used for treatment of patients with cutaneous lupus erythematosus (NCT02428309).
Solid organ transplants offer the opportunity to isolate, expand, and infuse antigen-specific Tregs from the graft recipient. In an ongoing trial (NCT02091232), Tregs are being isolated from mixed lymphocyte cultures in the setting of CTLA4Ig and infusing sorted Tregs from these cultures (The "ONE" Study). In patients with evidence of renal allograft rejection, another trial is expanding polyclonal Tregs for adoptive immune therapy (NCT02088931).
FUTURe DiReCTiONS Studies being conducted at UCSF and elsewhere have been initiated that utilize either polyclonal Tregs in other kidney and liver transplant settings with a goal of the discontinuation of immunosuppressive drugs (e. g. , NCT02088931). These and other efforts will be essential in determining the potential use of ex vivo expanded cells in patients with these immune dysregulation diseases. Maximizing the functional activity, persistence, and migration of infused Tregs will be essential by either altering the Treg genetically or combining the treatment with growth factors, such as IL-2. Trials of Tregs plus lowdose IL-2 are ongoing (NCT1937468) and others are planned in T1DM. In an effort to increase the persistence of the cells in vivo, Parmer et al. showed that ex vivo fucosylation, which forms the sialyl Lewis X moiety on P-selectin glycoprotein ligand-1, improved in vivo persistence and had improved effects on a murine model of GVHD  (186).
We expect that additional biologics and antigen-based therapies will be introduced to protect and expand Tregs. As mentioned above, antigen-specific Tregs are likely to be the best able to block unwanted immunity. In this regard, we have developed alloantigen-specific Tregs using a modified protocol that can selectively expand Tregs specific for MHC molecules expressed by donor tissue in kidney and liver transplant recipients. Donor-alloantigen-reactive Tregs (darTregs), isolated after leukapheresis, are being tested in patients undergoing liver transplantation at doses up to 800 × 10 6 together with thymoglobulin, everolimus, mycophenylate mofetil (MMF), and solumedrol (NCT02188719). Future studies are likely to include Tregs, engineered to express TCRs, that are specific for auto or alloantigens or even antigens that are on or in the region of target organs to cause localization of the cells to the site of pathology and activation.
Data sources PM data for metropolitan France were available from January 2001 to December 2014 from the French National Reference Center for Pneumococci (NRCP), which, since 2001, has received all S. pneumoniae strains isolated from cerebrospinal fluid (meningitis) collected through the Observatoires Régionaux du Pneumocoque, a network of about 400 laboratories located in the 13 French regions (67% of public and private French laboratories and around 60% of the French population over the period considered). Serotyping is performed using latex particles sensitised with antisera marketed by the Statens Serum Institute as described in previous publications  [4]. Serotypes 6A and 6C were retrospectively identified for the 2001-2009 years using the two new respective factor sera marketed by the Statens Serum Institute in 2010.
For each isolate, date of infection, patient's age, serotype and penicillin G susceptibility, defined by Minimum Inhibitory Concentration (penicillin-non-susceptible is defined as > 0. 06 mg/L) were recorded. Because the NRCP database is not exhaustive and to assess the stability of data-system recording, i. e. to ensure that recruitment bias did not evolve over time, we compared NRCP PM data with those provided by Epibac, a nonindependent national surveillance network, for which a constant coverage around 74% of the French metropolitan population since 1999 was proved  [16]. From Epibac, serotype and penicillin G susceptibility of S. pneumoniae strains was not available. The number of "flu-like" syndromes was provided by the French Sentinelles Network (http://sentiweb. org, accessed: 10 October 2015); demographic data were obtained from the French National Institute of Statistics and Economic Studies (http://www.
Antibiotic consumption Community consumption of beta-lactams and macrolides averaged 21. 23 DDD per inhabitant per day during the baseline period  (2001) (2002) (2003). The national campaign initiated to promote better-targeted antibiotic use led to a marked decline in the consumption of these two antibiotic classes, with 16. 27 DDD per inhabitant per day in 2004. Community consumption then plateaued until 2010, before it started increasing to reach 20. 11 DDD per inhabitants per day in 2014 (Fig. 1 ). Between January 2001 and December 2014, 6025 and 5166 PM cases were recorded in the Epibac and NRCP databases, respectively. In accordance with that stated by Lepoutre et al. [16] , comparisons between Epibac and NRCP PM cases enabled us to confidently conduct time-series analyses of NRCP data.
Indeed, the comparison with Epibac data indicated stable reporting fidelity of the NRCP surveillance system (regression slope -0. 82 (CI), P = 0. 32). An ARMAX model fulfilling goodnessof-fit criteria was obtained for each series, enabling reliable interpretation of the estimations (Fig. 2 , for all serotypes and age series, and Additional file 1: Figure  S1  for age-class series).
Acknowledgments We are grateful to  Michael Padget  for his help in writing. We thank all the microbiologists who participated in the  Observatoires Régionaux du Pneumocoque Network. We also thank  Santé Publique France  to provide Epibac PM data. Finally, this article has benefited from constructive comments made by  Dr Kobayashi ,  Dr Regev-Yochay  and  Dr Simonsen , whose help is gratefully acknowledged.
Funding This work was supported by the  Fondation pour la Recherche Biomédicale (FRM)  (grant number  IMD20131229052 );  French Government's Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (grant number  ANR-10-LABX-62-IBEID ), and  Université Versailles -St-Quentin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
In Brazil, numerous cases have also been reported in the Amazonian region with more than 62 persons infected between 2004 and 2005  [35, 36]. In French Guiana, a French overseas department located on the northern part of the Amazonian region, 13 rabies cases were recorded in cattle and domestic carnivores between 1984 and 2011  [37]. They were all related to vampire bat-associated rabies virus. In 2008, a human rabies case was recorded. The origin of the contamination was not formally established but transmission by a vampire bat bite was favoured  [38] , molecular typing of this virus (polymerase (L) gene, Genbank accession number GU816007) showed a close relationship with the viruses circulating in haematophagous bats in neighbouring countries. The aim of this study was to better understand bioecological factors associated with virus circulation within different bat communities and environments.
Sera were preserved at -80°C and then sent for serological analyses to the NRC for Rabies, Institut Pasteur, Paris. Sixty-one vampires, collected on sites where human attacks were registered, were euthanized and organs collected (brain, heart, lung, kidney, spleen, saliva). Individuals were identified based on external morphology  [44] , associated with forearm measurement, and confirmed with molecular barcoding (sequencing of the cytochrome oxydase 1 and/or cytochrome b,  [43] ) for all species (Genbank accession numbers KU295471-KU295500). Within the two breeding caves (Fig  1 ), captures were implemented every 4-5 months over a 4-year period, between Nov. 2009 and May 2013 (S2 Table ). At each capture session, the population size was estimated visually by two independent observers. Captures were performed with nets, in the caves, during the day time to localize the colony at rest and target captures on vampires only, and avoid disturbing the other species.
Amplification products of the expected size were then sent for sequencing to Beckman Coulter Genomics (Takeley, UK). In addition to the samples analysed in this study, data obtained independently by the NRC for Rabies in its diagnostic and surveillance activities on moribund mammals were included in the analyses. Nine domestic animals (two dogs and seven cattle species) and one bat (Artibeus planirostris), collected in French Guiana between 1989 and 2009 were added. The N gene was amplified and sequenced for the ten animals and the G gene was only generated for the bat sample as previously described  [47] [48] [49]. The two genomic regions (N and G complete gene sequences) were analysed separately. Raw sequences were analysed and edited in MEGA 5. 05  [50]. Sequences were translated into amino acid and both nucleotide and amino acid sequences were checked for irregularities.