dataesr/scientific-paragraphs-categorization huggingface dataset:
Distribution and adjusted odds ratios of asbestos exposure among women and men for the risk of lung cancer from a pooled dataset Odds ratios and confidence intervals were calculated for one unit of increase in the log-transformed asbestos exposure score by mixed-effects logistic regression adjusted for age, gender, smoking status, and center. cOdds ratios and confidence intervals were calculated for one unit of increase in the log-transformed asbestos exposure score by mixed-effects logistic regression adjusted for age, smoking status, and center.
Distribution and adjusted odds ratios of asbestos exposure stratified by MIRLET7BHG genotypes for the risk of lung cancer from a pooled dataset. 91 (0. 81-1. 02) 1. 16E-01 0. 91 (0. 78-1. 05) 1. 77E-01 0. 94 (0. 80-1. 11) 4. 75E-01 0. 92 (0. 78-1. 09) 3. 41E-01 1. 10 (0. 85-1. 42) 4. 75E-01 0. 83 (0. 57-1. 20) 3. 14E-01 GA+AA 1.
Acknowledgments The authors gratefully acknowledge  Drs. Margaret Spitz ,  Xifeng Wu  and  Sheng Wei  for providing data from the  University of Texas MD Anderson Texas Lung Study. Financial Support: This work was supported by the  National Institutes of Health  ( CA092824 ,  CA090578 ,  CA074386 , and  ES00002  to  D. C. C. / Harvard  studies). Sponsors had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Fig. 4AeC  show that the number of sulfur vesicles was greatly reduced (only one or two dark vesicles per cell) in the first subculture of Ravot medium containing L- cystine. Intriguingly, these SVs were much larger (from 150 nm to 250 nm) than those previously observed in the medium supplemented with sulfur. EDX analyses confirmed the presence of sulfur in these larger dark vesicles (data not shown). In the second subculture of Ravot medium with L-cystine, T. prieurii continued to produce vesicles. However all vesicles observed by Cryo-EM were clear vesicles (Fig. 4DeF ). Indeed, EDX analysis revealed that these clear vesicles do not contain sulfur in detectable amounts (data not shown). Whole cells of T. kodakaraensis, a model organism for which numerous genetic tools are available, were also examined by Cryo-EM.
Acknowledgments AG and collaboration between PF and CG were funded by the  Agence Nationale de la Recherche , project  Thermov esicules  ( ANR 12-BSV3-003-01 ). PF and SG were supported by the  European Research council , project  EVOMOBIL  ( FP/2007e2013 ) e  ERC  Grant Agreement no. 340440  to PF. This work benefited from the facilities and expertise of the  Imagif Cell Biology Unit of the Gif campus  (www. imagif. cnrs. fr)which is supported by the " Conseil G en eral de l'Essonne ". We thank  Sylvain Bernard  for his assistance in Raman spectroscopy.
The map was created using Systems Biology Graphical Notation language with the help of CellDesigner software and encompasses 36 components (proteins/genes) and 54 interactions. The simplification of this complex network paves the way for the development of novel therapeutic strategies to eradicate HIV-1 infection. Agents that induce the selective death of HIV-1-elicited syncytia might lead to the elimination of viral reservoirs and hence constitute an important complement to current antiretroviral therapies. Cell Death and Disease (2015) 6, e1846; doi:10. 1038/cddis. 2015. 204; published online 6 August 2015.
Acknowledgements. This work was supported by grants from the  Ministry for Health of Italy  to  MP ('Ricerca Corrente ' and Ricerca  AIDS RF-IMI-2009-1303225 ) and the  Italian Ministry of University and Research  ( FIRB 2012-2017 ). EU grant ' VII Framework ' contract n°FP7-Health-2007A 'Apoptosis systems biology applied to cancer and AIDS'. JLP is supported by funds from  Agence Nationale de la Recherche , NATIXIS, SIDACTION, the  French National Agency for Research on AIDS and viral Hepatitis (ANRS) ,  Electricité de France ,  Fondation Gustave Roussy, Laboratory of Excellence LERMIT  with a grant from  ANR  ( ANR-10-LABX-33 ) under the  program 'Investissements d'Avenir'   ANR-11-IDEX-0003-01  and  INCA  ( INCA-DGOS-INSERM 6043 ). GK is supported by the  Ligue contre le Cancer  (équipe labelisée);  Agence National de la Recherche (ANR)-Projets blancs ;  ANR  under the frame of E-Rare-2, the  ERA-Net for Research on Rare Diseases; Association pour la recherche sur le cancer (ARC) ;  Cancéropôle Ile-de-France ;  Institut National du Cancer (INCa) ;  Fondation Bettencourt-Schueller ;  Fondation de France ;  Fondation pour la Recherche Médicale (FRM) ; the  European Commission (ArtForce) ; the.
In cases of KU, anterior chamber taps were performed. The presence of HSV and VZV in aqueous humor (AH) was evaluated by polymerase chain reaction (PCR) or by the Witmer-Goldmann coefficient in paired AH and serum samples (considered positive if greater than 2). All the patients were examined and diagnosed by the same ophthalmologist (ML). Clinical and biological data were anonymously recorded from clinical files. The corneal sensitivity was tested in central cornea, with a Cochet-Bonnet contact esthesiometer (CBE) (Luneau, France), as previously described  [36]. This choice was supported by the fact that more than 60% of HSVinduced hypoesthesia are detectable in the central cornea  [37]. Patients finally selected for the study were those with clinical signs of keratitis or KU, a typical past history of VZV or HSV keratitis or KU, and/or a positive test in AH.
Diffusion tensor imaging Investigations were performed on a 1. 5T system (Sonata scanner, Siemens, Erlangen, Germany). The MRI protocol consisted of an axial 3D T1-weighted scan (TR/TE, 11/4 ms), a FLAIR scan (TR/TE/TI, 9480/112/2390 ms), an axial T Ã -weighted GE scan (TR/TE, 1330/33 ms), and an axial echo-planar imaging (EPI) DTI scan (TR/TE, 5700/110 ms; FOV, 24x24 cm; image matrix, 128x128; number of sections, 30; section thickness, 2 mm; nominal voxel size, 1. 875x1. 875x2 mm; number of signal intensity averages, 3) with diffusion gradients set in 25 non-collinear directions by using 2 b-values (b = 0 and 500 s/mm2) to minimize the signal loss due to the strong diffusion gradients. The DTI scanning took approximately 7 minutes 30 seconds. The DTI data were processed on a voxel-by voxel basis with dedicated software (DPTools [http://www.
fmritools. org]). A correction algorithm was applied to the DTI dataset to account for distortions that were related to eddy currents induced by the large diffusion-sensitizing gradients. It relied on a 3-parameter distortion model including scale, shear, and linear translation in the phase-encoding direction, as previously described  [18]. A single physician (FB) carried out the MRI acquisition. Image analysis was performed by another physician (GN) who was masked for the group (patient or control) and for the side affected by the herpetic ocular disease (if applicable). Fiber tracking was performed with dedicated software (MedINRIA[http://www-sop. inria. fr/ asclepios/software/MedINRIA]). White matter fiber tracts were created in 3D on the basis of similarities between neighboring voxels in shape (quantitative diffusion anisotropy measures) and orientation (principal eigenvector map) of the diffusion ellipsoid and co-registered on the FA map by using a special algorithm previously described  [39, 40].
The principal diffusion direction method  [40] [41] [42]  was used, in which the eigenvector corresponding to the largest eigenvalue is extracted from the diffusion tensor field generated from the DTI datasets in the region where the diffusion is linear. The FA threshold value was 0. 20; and the angulation threshold, 45°to prevent fibers from sudden transition and to keep tracking based on the connectivity of the neighborhood, as described elsewhere  [40, 42]. The 3D fiber reconstructions were colorcoded so that blue represented the superior-inferior; green, the anteroposterior; and red, the left-right direction. Tractography was used to locate the trigeminal pathways. Regions of interest of 1. 875×1. 875×2 (x×y×z) voxels (total = 12 voxels = 84mm 3 ) were manually drawn on the reconstructed fibers, in order to include all the visible part of the extra-axial emerging trigeminal fibers (fig.
1 ). As there are many crossing fibers in the intra-axial trigeminal nerve and near the root entry transitional zone, measurements in these regions may have lead to important partial volume effect. Data were anonymously recorded before processing to retrospective statistical analysis using STATA software (Statacorp LP, USA). Categorical variables were analyzed using the χ 2 test and continuous variables were analyzed using the non-parametric Kruskall-Wallis test for mean comparison and non-parametric Spearman test for correlation. Statistical significance was defined as P < 0. 05 (2-tailed).
11 n all endemic areas, a falciparum gene-fl ow map should be envisaged to help implementation of control measures and identify key sites for malaria monitoring. Importantly, in endemic countries where artemisinin resistance has been recorded, a greater parasite biomass will be exposed to partner drugs and thus molecular surveys must include partner drug monitoring, with use of molecular markers if available. 2, 12 eal-time detection and monitoring of the geospatial distribution of antimalarial drug-resistant parasites is now a possibility, as is prevention of their dissemination Comment in neighbouring endemic areas. However, substantial work remains to be done to harmonise and validate collected data. Currently, a major concern is the interpretation of molecular data because of the high diversity of the K13 gene: except for four mutations (C580Y, R539T, R543I, and Y493H), no clinical or in-vitro data have been associated with the other K13 mutant alleles.
CONCLUSION As a conclusion, analyzing platelet responses to PRR agonist stimulation in whole blood, platelet-rich plasma and in transfusion platelets concentrate would help clarify the relative contributions of platelets on inflammatory process. How can the small platelet, without a nucleus, be so intelligent? of Etablissement Français du Sang Auvergne-Loire, Saint-Etienne, France for their technical support throughout our studies. This work was supported by grants from the French National Blood Service -EFS (Grant APR), France; the Association for Research in Transfusion (ART), Paris, France; the Agence Nationale de la Sécurité et du Médicament et des produits de santé (ANSM -AAP-2012-011, Reference 2012S055); the "Agence Nationale de la Recherche" (ANR), reference ANR-12-JSV1-0012-01; and the Association "Les Amis de Rémi," Savigneux, France.
For many years, a better understanding of the regulation of these signaling pathways has resulted in intense drug development. The antitumoral efficacy of recombinant FasL, TRAIL and TNFα ligands or derivatives, has been evaluated in preclinical and clinical studies as monotherapy. The development of TNFα as a systemic treatment has not been translated to patient due to significant hepatotoxicity and lack of efficacy  [53]. Similar acute toxicity toward normal cells has been reported for recombinant FasL. However, a more promising recombinant molecule (APO010) has been under investigation in a phase I clinical trial (NCT00437736). However, a great step forward in the treatment of irresectable extremity soft tissue sarcomas has been achieved in the recent years with the addition of TNFα to isolated limb perfusion with chemotherapy (melphalan)  [64].
Analysis of the expression of 84 inflammation mediator genes as well as that of five housekeeping genes (HKG) using the RT² SYBR Green Mastermix (Qiagen) was performed according to manufacturer's recommendations. PCR arrays were performed using the Stratagene MX3005p System (Agilent Technologies). Cycle thresholds were downloaded from the machine and analysed using the ∆∆Ct method via Qiagen PCR array online system (http://www. sabiosciences. com/pcrarraydataanalysis. php). Data was normalised to the mean values of the five HKG. Fold-regulation calculations were performed using SABiosciences' data analysis softwares. Fold-regulation values greater or less than two indicate an upregulation or downregulation, respectively.
4 display an activity improved by one order of magnitude or more and dependent on the rod length and the overall valency of the system. In a second set of experiments, dose-response was measured at lower concentrations for 1. 5. 4, 3. 5. 4 and 3. 4 (Fig. 3 , bottom). Data fitting to 1:1 hyperbolic decay afforded IC 50 values of 67 nM, 24 nM and 161 nM, respectively. Thus, these experiments confirmed that also in the cellular model inclusion of a rigid spacer at the dendrimer core has a strong positive effect on the antagonist activity. Dendrimer 3. 5. 4 (IC 50 24 nM) is 40 times more active than 8. 4 and among the most potent DC-SIGN antagonists reported. 13 The data also confirm the impressive activity of the divalent ligand 3. 4, but, as in the SPR study, suggest that higher local concentration of the ligand is beneficial to effectively block the infection.
Animals Healthy experimentally naive rhesus monkeys were purchased from the purpose-bred colony of the Biomedical Primate Research Centre (BPRC) in Rijswijk, the Netherlands. CIA-susceptible rhesus monkeys were preselected on the basis of absence of the dominant class I major histocompatibility complex (MHC) CIA resistance marker Mamu-B*001  [29] [30] [31]. The total study group comprised 19 young adult, healthy rhesus monkeys (Macaca mulatta) of either sex. Both male and female monkeys (5Á25-8Á50 kg) were used. Individual data are given in Table  1. Before entry into the study, the animals were examined by the BPRC veterinarian staff. All animals were declared in good health and showed no signs of (infectious) diseases. Haematological and clinical chemistry values were all within the normal range.
The animals were monitored until psd 70 days to assess a possible delayed onset or rebound of CIA after cessation of the treatment. FR104 drug levels were determined by ELISA (see Materials and methods). FR104 levels of approximately 100 mg/ml were recorded in the first 4 days after administration (Supporting information, Fig. S3a ). In order to determine the minimal level of FR104, sera were collected just before the animals were dosed. Minimal FR104 levels ! 30 mg/ml were detected until day 49 (Supporting information, Fig. S3b ). These levels of FR104 demonstrated effective suppression of a pathogenic autoimmune response in a rhesus monkey experimental autoimmune encephalitis (EAE) model  [39]. Anti-FR104 antibodies were not detected during the period of treatment (data not shown). Hence, all animals were included in the analysis.
4  and Supporting information, Table  S1 ). We also asked whether the treatment with FR104 and abatacept induced changes in lymphocyte subsets. For that analysis we sampled PBMC on days 0, 7, 14, 21 and at the day of necropsy. In addition, we performed the same analysis on cells isolated from axillary and inguinal lymph nodes at the day of necropsy. No differences were found for major lymphoid subset populations such as B cells, T cells or natural killer (NK) cells (data not shown). In all animals, only in the subset of CD3/CD4/CD25 high /FoxP3 cells did we find an effect of the treatment with FR104, namely a significant reduction in the percentage of cells with this phenotype on day 21 and at the day of necropsy for PBMC and aLN (Fig. 5a ). The corresponding analysis of the CD3/ CD4/CD25 high /CTLA-4 subpopulation could not confirm whether these cells were genuinely regulatory T cells, as we did not observe an effect of FR104 treatment (Fig.
(g) The average serum IL-6 level/day was calculated from the total production as determined by area under the curve analysis divided by the number of days the animals were in experiment. (h) The average serum CRP level/day was calculated from the total production as determined by area under the curve analysis divided by the number of days the animals were in experiment. Significance relative to placebo-treated group was tested with the Mann-Whitney U-test. *P < 0Á05. abatacept) than CII-specific IgG production (90% for FR104 and 74% for abatacept). The more robust effect of FR104 on the production of CII-specific IgG may be explained by inhibition of helper T cells that promote antibody isotype switching. Our current data are compatible with observations by Mihara et al. , that CTLA-4 Ig treatment prevents B cell maturation resulting in a suppressed expansion of both IgG-and IgM-producing autoreactive B cells  [51].
1C ). These data suggested activated CD8 C DC were undergoing enhanced autophagy, however, while autophagosome accumulation can be consistent with increased autophagy, it can also indicate a failure of autophagosomal turnover due to an impaired fusion of autophagosomes with lysosomes. To distinguish between these scenarios, we analyzed autophagy-mediated degradation of endogenous LC3 that provides a measure of how much autophagy-mediated degradation a specific cell type is undertaking. To do this, we monitored the accumulation of LC3-II in the presence of lysosomal protease inhibitor bafilomycin A 1 (BafA). Activated CD8 C DC underwent significantly more autophagic flux relative to CD8 ¡ DC as evidenced by their significantly increased LC3-II accumulation in the presence of BafA (Fig. 1D ).
2% bovine serum albumin ( pH 7. 4). The cells were then incubated in the dark at 37 °C for 15 min with the compounds. Changes in intracellular calcium concentration upon addition of CXCL-12 (SDF-1), the specific ligand for CXCR4, were simultaneously measured in all 96 wells in a black-wall microtiter plate and in real time with the FLIPR. The data were expressed as fluorescence units versus time and were analysed using the FLIPR Control Software (Molecular Devices) and IC 50 values were calculated using GraphPad Prism 4. 0 software (San Diego, CA).
Acknowledgements Support was provided by the  CNRS , the  University of Burgundy  and the  Conseil Régional de Bourgogne  through the  3MIM  Project. S. P. and P. D. thank the  Ministère de l'Enseignement Supérieur et de la Recherche  for PhD grants. COST action TD 1007 PET-MRI  is also acknowledged for financing STSM of S. P. This work, in part, was supported by funding of the K. U. Leuven  ( GOA/10/014  and  PF/10/018 ) and the  Foundation of Scientific Research  ( FWO no. G. 0485. 08  and  G. 0528. 12 ). Support was provided by  Yorkshire Cancer Research  ( HEND376 ) and the  University of Hull.
Antibodies were diluted in PBS, 0. 5% BSA, 2% human serum. Images were obtained with a spinning disk microscope equipped with a CoolSnap HQ2 camera (Photometrics) and a 20x and a 63x objective. All images were acquired with MetaMorph 7 imaging software (Molecular Devices) and analysed with ImageJ. For staining of dying cells in vivo, vaccinated TC1-GFP bearing mice received an intra-tumoral injection of propidium iodide (1 mg/ml) and were sacrificed 30 min later.
Transcriptomic analysis Tumor RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions and gene expression was analyzed with the nanostring technology. 36 lanes of Nanostring data were processed using Accelrys Pipeline Pilot. The geometrical mean of the positive control probe counts were computed for each lane and a scaling factor computed for each lane being the average of the geometrical means of all lanes A was divided by the geometrical mean of that particular lane. This scaling factor was then applied to all probe counts for all lanes as a means to normalize for the technical variability of the platform. The house keeping genes ACTB, GAPDH and RPL4 were then used to normalize for any RNA loading differences. This was performed in the same manner as the positive control probes where the scaling factor was computed from the geometrical mean of the housekeeping genes.
The positive control and housekeeping normalized counts were then logarithmically transformed and used for all subsequent analysis. One way ANOVAs were used to test if any of the probes counts were significantly different between sample groups. Pearson correlations were to identify pairs of correlating genes. All statistical testing was done using the R statistical language version 2. 15. 2. p < 0. 05 were deemed to be statistically significant. Multiple testing corrections were performed for all tests using the method of Benjamini and Hochberg. Visualization of the data and test results were done using GraphPad Prism 5.
Cytotoxic assay with tumor-derived myeloid cells F4/80 + myeloid cells were purified from tumor cell suspensions using F4/80-biotin Ab (eBioscience), and streptavidin-beads before sorting with Automacs (Miltenyi Biotec). Purified cells were treated 5 minutes at 37°C with DNase (100 μg/ml) to remove cell debris. F4/80 + cell suspension were > 90% pure. Purified myeloid cells (2 × 10 5 ) were added on the top of a monolayer of TC1-GFP + cells (2 × 10 4 cells) and co-cultured for 48 h at 37°C. TNFα was blocked with anti-TNFα at 10 μg/ml (Abcam). Images were obtained with an inverted microscope (TE2000-E; Nikon) equipped with a 20x objective, and Metamorph imaging software.
Statistics Unless otherwise indicated, results are expressed as means ± SEM of 3 to 6 mice. All experiments were repeated at least twice, yielding similar results. Data were analyzed with GraphPad Prism5 software. p values were calculated by the unpaired Student's t test or Oneway ANOVA and Tukey test for multiple comparison. Values ≤ 0. 05 were considered significant. *p < 0. 05; **p < 0. 01; ***p < 0. 001.
ACKNOWLEDGMENTS We are grateful to  Plexxikon  for providing the PLX3397 inhibitor. We would like to thank  Olivier Lantz  for providing IFNγKO mice,  Thomas Henry  for CCR2KO mice,  Quitterie Largeteau  and  Marianne Mangeney  for the generation of the TC1-GFP cell line, the staff of the imaging and flow cytometery (CYBIO) facilities of the  Cochin Institute  for their helpful advice,  Pascale Villefroy  for the preparation of IFNα, and  Arnaud Pommier  for advice on multicolor flow cytometry. We would like to thank also  Vincent Feuillet ,  Elisa Peranzoni  and  Emmanuel Donnadieu  for critical review of the manuscript. The Johannes team is member of  LabEx CelTisPhyBio  ( 11-LBX-0038 ) and of  Idex Paris Sciences et Lettres  ( ANR-10-IDEX-0001-02 PSL ) and the Tartour team is member of the  Labex Immunooncology and of the Siric Carpem.
Multilocus sequence typing Multilocus sequence typing (MLST) of ESBL-positive E. coli isolates was performed using seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA), as described previously  [49]. Primer sequences were obtained from the E. coli MLST database website (http://mlst. ucc. ie/mlst/dbs/Ecoli) (Table  7 ). The cycling conditions were as follows: initial denaturation at 95 °C for 5 min, followed by 30 cycles of initial denaturation at 95 °C for 30 s, primer annealing at the melting temperatures for 30 s, and extension at 72 °C 1 min and followed by a final extension at 72 °C for 10 min. The PCR products were treated with exonuclease I and shrimp alkaline phosphatase (Affymetrix, Santa Clara, CA, USA) and sequenced at the Genomics Core Facility (Penn State University) with the same primers used to generate PCR products.
The association between the ET-1 concentration and identified genotypes was realized by adapted software for descriptive statistics, Statistical Package for the Sociological Sciences (SPSS v 21. 0). Results: Our study showed that the concentration of ET-1 was significantly higher in patients compared to controls and that the mutated allele prevails in patients F (G) = 0. 78 and there is a minority in controls F (G) = 0. 3. Secondly the homozygous genotype GG is associated with higher concentrations of ET-1 in patients and controls, heterozygous genotype AG is associated with intermediaries' values and AA genotype is related to lower values. Conclusion: Although the polymorphism studied is an intronic polymorphism, it is involved in the change in serum concentration of ET-1 and is a candidate gene in susceptibility to SCA.