dataesr/scientific-paragraphs-categorization huggingface dataset:
Sample selection and preparation Consumption data by the general French population were taken from the second French Individual and National Food Consumption Survey (INCA2), conducted between 2006 and 2007  (Dubuisson et al. , 2009; Lioret et al. , 2010) , which described the dietary habits (in terms of quality, quantity, and food preparation) of children and adults representative of the French population. A food sampling has been made on the basis of the INCA2 study  (Sirot et al. , 2009)  taking into account the most consumed products and also some foodstuffs less consumed but suspected to be contaminated at high levels. Samples of foodstuffs were purchased from June 2007 to January 2009 in eight great regions of the French metropolitan territory (when consumed in the region) and each food sample was collected, when possible, in winter-autumn and in spring-summer in order to take into account potential seasonal variations in the contamination.
Assessment of the population exposure The exposure of the population to each PAH congener was assessed for each subject of the INCA2 survey (1918 adults aged 18-79 and 1444 children aged 3 to 17), by combining their individual food consumption data with the contamination data obtained in this study, using the following formulae: E i;k ¼ ∑ n j¼1 C i;j ⋅K j ;k =BW i where E i,k is the exposure of the subject i to the congener k, C i,j is the consumption level of the food j by the subject i, K j,k is the contamination level of congener k in the food j, BW i is the individual body weight of the subject i and n is the total number of foods in the diet of the subject i. Each food item consumed by each subject was assigned the mean contamination level of the food samples collected during seasons in the region of the subject, or the mean of the other regions when the food we not collected in the region.
Nevertheless, food categories reported in the EFSA data collection (coming from target measurement campaign) were samples that are more susceptible to contain PAH (smoked fishes and smoked meat) than samples analyzed in the present study. Compared to another total diet study performed in Catalonia  (Martorell et al. , 2012) , food contamination was found to be very similar, especially for the major contributor categories (mollusks and oil-based products).
Conclusions In summary, the results of the present TDS allowed estimating the general contamination of the French diet in PAHs: mollusks and oil-based products were found to be the most contaminated samples; chrysene, benzo[b]fluoranthene and benz[a]anthracene were quantified in foodstuffs as the most important contributors. PAH4 was furthermore confirmed as suitable indicator of PAHs in food. This study also allowed calculating the exposure of the French population to PAHs through the whole diet. MOEs approach indicates that exposure of this class of compounds through the diet does not represent a food safety issue. Comparison of the present data with the last exposure estimation performed in 2003 in France indicates a three times decrease in the exposure level. Similar trends have been reported in other countries and related mainly to environmental causes (general reduction of industrial and traffic emissions  (Wang et al.
The first tutorial introduced the context of large-scale measurement platforms, how to write and schedule a measurement test, how to schedule the reporting of measurement results, and how to retrieve results for data analysis. The second tutorial gave an overview of the functionality, the architecture, and the hands-on guide on "The Virtual Wall", a generic experimental environment for advanced network, distributed software, service evaluation, and scalability research. Finally, the third tutorial revisited basic concepts of virtual distributed test-labs, such as PlanetLab or EMANICSLab, and provided hands-on training on how to use them for research activities. AIMS 2013 continued with a keynote presentation by Bertrand Mathieu, senior researcher at Orange Labs, France, on management and monitoring challenges in content-centric networking.
Peptides were identified by LC-MS/MS. This differential proteomic approach allowed the relative quantitative identification of 42 different proteins (Table  2 ). An iTRAQ ratio greater than one indicated a higher abundance of this protein in LD isolated from core-expressing Caco-2/TC7 cells than control Caco-2/TC7 cells. Conversely, a ratio less than one indicated that this protein was less abundant in the LD fraction from Caco-2/ TC7 GFP-CP cells than Caco-2TC7 cells. The range of the ratios was rather limited (i. e. 0. 389-1. 837) and consistent with the similarity of the protein profiles observed on 1D-silver stained gels of LD fractions isolated from Caco-2/TC7 or Caco2/TC7 GFP-CP cells. The most abundant protein identified was perilipin-2 (data not shown), as reported previously for Caco-2/TC7 cells  [10]  and confirming the validity of this approach.
(a) 17b-hydroxysteroid dehydrogenase type 2 (DHB2), (b) 3-beta-hydroxysteroid dehydrogenase (3BHS1), (c) lysophosphatidylcholine acyltransferase type 2 (PCAT2), (d) UPF0554 C2orf43 (CB043) and (e) long-chain-fatty-acid-CoA ligase 3 (ACSL3). Scale bars, 10 mm. doi:10. 1371/journal. pone. 0053017. g005 Figure  6. Gene and protein expression in Caco-2/TC7 cells (TC7), Caco-2/TC7 GFP-CP cells (TC7 GFP-CP) and human jejunum of some proteins identified by LC-MS/MS in lipid droplet fractions. (A) Caco-2/TC7 and Caco-2/TC7 GFP-CP cells were cultured on filters for 17 days then supplied with lipid micelles for 24 h. mRNA levels were measured by quantitative RT-PCR for core (HCV core protein), HSD17B2 (17bhydroxysteroid dehydrogenase type 2), HSD3B1 (3-beta-hydroxysteroid dehydrogenase), PLIN2 (perilipin-2), MGLL (monoacylglycerol lipase), LPCAT2 (lysophosphatidylcholine acyltransferase 2), C2orf43 (UPF0554 protein C2orf43) and ACSL3 (long-chain-fatty-acid-CoA ligase 3).
Acknowledgments We are grateful to the following persons for providing reagents:  J. McLauchlan  ( CVR, Glasgow, UK ),  M. Le Gall  ( U872, Paris, France ),  D. Pasdeloup  ( CNRS, Gif-sur-Yvette, France ),  N. Pavio  ( U785, Paris, France ) and  C. Thiele  ( Bonn University, Germany ). We thank  F. Guillonneau ,  M. Leduc  ( Plateforme Proteomique UniversiteParis Descartes  ( 3P5 ),  Paris, France)  and  C. Guerrera  ( Plateau Proteomes Necker, Paris, France ) for LC-MS/MS analysis,  A. Paris  ( INRA, Paris, France ) for helpful advices on steroid metabolism and  A-M Faussat  ( CICC, U872, Paris, France ) for cell sorting by  FACS. Confocal microscopy was performed using the facilities of the  Centre d'Imagerie Cellulaire et de cytometrie (CICC) of UMR S 872. M. Douglas  is acknowledged for critical reading of the manuscript.
302 0. 149 0. 0039 * UBXN4 UBXN4_HUMAN UBX domain-containing protein 4 ER stress response 1. 298 0. 237 0. 16 SCCPDH SCPDH_HUMAN Probable saccharopine dehydrogenase unknown 1. 25 0. 21 0. 018 * CYB5R3 NB5R3_HUMAN NADH-cytochrome b5 reductase 3 Sterol metab. 1. 242 0. 164 0. 0073 * TUBA1A TBA1A_HUMAN Tubulin alpha-1A chain Microtubules 1. 185 0. 345 0. 44 C2orf43 CB043_HUMAN UPF0554 protein C2orf43 unknown 1. 172 0. 195 0. 077 HSD17B11 DHB11_HUMAN Estradiol 17-beta-dehydrogenase 11 Sterol metab. 1. 101 0. 139 0. 089 RAB6A RAB6A_HUMAN Ras-related protein Rab-6A Traffic 1. 097 0. 398 0. 56 ACSL3 ACSL3_HUMAN Long-chain-fatty-acid CoA ligase 3 Fatty acid metab. 1. 072 0. 262 0. 47 RAB5C RAB5C_HUMAN Ras-related protein Rab-5C Traffic 1. 065 0. 217 0. 51 ATP1A1 AT1B1_HUMAN Sodium/potassium-transporting ATPase subunit Transporter 1.
Data collection and analysis Data were collected from routine patient records into a specially designed questionnaire; these included ART and VCR start dates, age, sex, KS stage, baseline CD4 count (measured as cells/μl), VCR treatment relapse, VCR treatment failure and standardised ART outcomes, which were censored at the end of December 2011. We defi ned as VCR treatment failure the failure of KS lesion(s) to regress or the progression of KS lesions at the end of a course of VCR, and relapse as the recurrence of KS lesion(s) ⩾3 months after initial resolution or regression on completing a course of VCR. Data were double-entered into EpiData Version 3. 1 (EpiData Association, Odense, Denmark) and were analysed using both EpiData and SPSS (Statistical Product and Service Solutions, Chicago, IL, USA).
Bimodality assay Five somite Tg(hsp:mKrox20 HA );Tg(cA:h2b-mcherry) zebrafish embryos were HS treated for 10 min at 35 (n ¼ 7) or 37 1C (n ¼ 8), and allowed to develop for 4 h, until B15s, at 28 1C in embryo medium. Anti-Cherry immunostaining was performed with rabbit anti-DsRed primary antibodies (1:200, Clontech) and Alexa594 anti-rabbit secondary antibodies (Jackson ImmunoResearch). Nuclei were counterstained with Hoechst 33342 (Sigma). Stacks made of eleven 16-bit images of the r2-r6 region were taken with a Leica TCS sp5 confocal microscope. The z-step was set 1 mm, such that the total depth corresponded approximately to the depth of one nucleus. Using Fiji software, all images were first smoothened and the projections of the 11 sections were computed by summing the intensity of corresponding pixels.
No background substraction, modification of contrast, luminosity or exposure was performed. Fluorescence levels were quantified in single nuclei after manual segmentation: a circular ROI of 12 pixels was placed on each nucleus identified using the Hoechst staining, and fluorescence intensity was measured and averaged over the 12 pixels. Fifty to 80 nuclei were typically quantified in each rhombomere. The plots shown in Figure  6H -L were obtained using the plot density function of the R software with the Sheather and Jones bandwidth selector. The bimodality of these plots was finally assessed statistically using the 'bimodalitytest' package in R  (Holzmann and Vollmer, 2008).
Acknowledgements We thank  Franc¸ois Giudicelli ,  Patricia Gongal  and  Denis Thieffry  for critical reading of the manuscript, and  Nadine Peyrie  ´ras for personal communications and for providing us with the Tg(cA:h2b-mcherry) zebrafish line. This work was funded by grants from  MESR ,  INSERM ,  CNRS  and  ANR  to PC and from  MESR ,  INSERM ,  CNRS  and  ERC  to DH.
Patients (or Materials) and Methods: Patients with psoriasis (n = 12) and healthy volunteers (n = 11) were treated with a single oral dose of racemic venlafaxine (150 mg). Serial blood samples were collected up to 48 hours after drug administration. Venlafaxine and its metabolites enantiomers were analyzed in plasma samples by LC-MS/ MS coupled with a chiral column Chirobiotic V. Pharmacokinetics parameters were evaluated using the WinNonlin software. Results: Compared with healthy subjects who were similar overall in terms of age, sex, and body mass index (BMI), the means area under the plasma concentration-time curve from time zero extrapolated to infinity (AUC0-∞) for venlafaxine and its metabolites enantiomers did not differ (unpaired t test) in patients with psoriasis. The following.
Right tibiae from the fracture study were dissected from rats, fixed and stored as above and scanned with a lower resolution of 14 μm pixel size due to the size of the bones. The whole tibiae were reconstructed using NRecon v. 1. 4. 4. 0 (SkyScan) and bone histomorphometric analyses in two and three dimensions (2D, 3D) were performed by SkyScan software (CT-Analyser v. 1. 5. 1. 3). For the analysis of trabecular bone, the cortical shell was excluded by operator-drawn regions of interest and 3D algorithms were used to determine the relevant parameters which included bone volume percentage (BV/TV), trabecular thickness, trabecular number, trabecular spacing, structure model index (SMI), trabecular pattern factor and degree of anisotropy. Analysis of cortical bone was performed using a 0. 49-mm-long segment (or 100 tomograms) at 37 % of the tibias' length from its proximal end.
Micro-CT analysis of fracture healing Left femora (fractured side) were scanned at 14 μm resolution using micro-CT (SkyScan 1172). A length of approximately 15 mm of the callus with the fracture in the centre was scanned. Histomorphometric analysis of fracture callus in 2D and 3D was performed by SkyScan software (v. 1. 11. 8. 0). A 'shrink-wrap' algorithm was used to define the tissue perimeter as the volume of interest (VOI). Binarisation of the reconstructed datasets was by two methods that applied different thresholds since the fracture callus 4 weeks after fracture is heterogeneous and may contain low or highly mineralised woven bone; to automatically delineate the low mineralised callus, a specific threshold was applied that excluded the highly mineralised callus and cortical bone. After measurement, another thresholding was applied, which in contrast defined highly mineralised callus and cortical bone, excluding the very low mineralised callus.
We show for the first time that metformin, at the dose given, has no effect on fracture healing in a model of mid-diaphyseal transverse osteotomy in rats. We evaluated the effect of metformin 4 weeks after fracture to examine the endochondral ossification process, and our data show no effect of metformin on callus size or on the speed of the healing process. Diabetes Representative immunoblots are shown, repeated with similar results twice; a, ii all blots were quantified using image J and the pAMPK to tAMPK ratio relative to β-actin was determined for each experiment. Bars represent mean ± SD, n=4 biological samples *P<0. 05. b, i Western blot analysis of pAMPKα1/2, tAMPKα1/2 levels in subcutaneous and visceral fat depots and in femur of ovariectomised wild-type mice treated with metformin (100 mg/kg) for 1 month.
Quantification To determine the contents of 4 and 5 in CM, standard solutions of the isolates were diluted in appropriate concentrations. CM was dissolved in MeOH and insoluble cloudiness was filtered off. Every sample was measured three times by HPLC. Data were obtained on Shimadzu (Kyoto, Japan) UFLC-XR instrument, equipped with on-line degasser, auto sampler, column thermostat, and photodiode array detector using the HPLC protocol described above. The amounts of 4 and 5 were calculated as the percentage of dry weight of CM. Limits of quantification were determined as the signal-to-noise ratio of 10.
Statistical analysis Data are expressed as mean ± S. E. IC 50 values were calculated from averaged measurements at 3-5 different concentrations of the compounds by nonlinear regression using GraphPad Prism software (San Diego, CA) one site binding competition. To calculate the IC 50 values regarding NF-κB inhibition at least three different concentrations measured in quadruplicate in three independent transfection experiments were used utilizing nonlinear regression with Data Analysis Toolbox software (MDL Information System Inc. , Nashville, TN, USA). Statistical evaluation of the data was performed by oneway ANOVA followed by a Bonferroni or Tukey-Kramer posthoc test for multiple comparisons respectively. A p value < 0. 05 was considered statistically significant.
monachorum , which belongs to the Parmeliaceae family. In fact, CM concentration-dependently inhibited PGE 2 generation with a remarkably low IC 50 of 2. 0 µg/mL. In the two 5-LO assays (cell-free and cell-based), IC 50 values of 1. 4 µg/mL and 1. 3 µg/mL, respectively, were determined for CM. In TNF-α-stimulated HEK-293 cells CM inhibited the NF-κB transactivation activity with an IC 50 of 2. 6 µg/mL thereby only moderately affecting the viability of this cell line (measured between 0. 3 and 10 µg/mL; viability ≥ 75. 05 ± 0. 08 % at 10 µg/ mL). The metabolite profile of CM was determined via HPLC-DAD-ESI-MS analysis. Different chromatographic separation steps succeeded in the isolation of three depsides (3 -5) and eight monoaromatic derivatives. By interpretation of mass spectrometric and 1D and 2D NMR data the structures were identified as ethyl haematommate (1), methylbetaorcinolcarboxylate (2), atranorin (3), imbricaric acid (4), perlatolic acid (  5 ), 4-O-metylolivetolcarboxylic acid (  6 ), ethyl-4-O-methylolivetolcarboxylate  (7) , ethyl olivetolate (8), olivetolmonomethylether  (9) , olivetol  (10)  and divarinol  (11).
Notably, MagA (PA4492), MagB (PA4491), and MagF (PA4487), encoded within the same operon as MagD, were among the most enriched binding partners identified and were further investigated (Table  1 ). Proteins encoded by the mag operon display several interesting features (Table  2 ). First, five of them (with the exception of MagB) possess signal peptides and are predicted to be directed to the periplasm  (27). Second, MagB harbors one predicted hydrophobic helix (amino acids 26 to 48). Third, the first and the last genes of the operon encode proteins MagA and MagF, which share 105 out of 269 amino acids. All are annotated in the Pseudomonas genome database (http://www. pseudomonas. com) as being of unknown function. We overexpressed several Mag proteins, raised specific antibodies, and then used them to confirm IPtandem MS (MS/MS) data.
Rabbit polyclonal serum raised against His 6 -MagD 37 was obtained from Covalab. Antibodies against other Mag proteins were obtained by immunization of mice by AgroBio. Small-angle scattering experiments. SAXS measurements were recorded at the ID14-3 beamline of the European Synchrotron Radiation Facility (Grenoble, France). Prior to data collection, a scattering curve of bovine serum albumin reference solution (5. 4 mg/ml) was recorded. Experiments were performed at concentrations of 2. 3 and 8. 2 mg/ml for native His 6 -MagD 37 , 0. 3 mg/ml for the methylamine-activated form, and 0. 6 mg/ml for elastase-incubated His 6 -MagD 37. Between measurements, scattering from a buffer sample was recorded, and these data were subsequently subtracted from the respective sample curves. No radiation damage was observed during the 10-s exposure frames, and all data were recorded at 25°C.
Data were treated by following default parameters of the PRIMUS software package  (49). The radius of gyration (Rg) and the forward scattering value I(0) were estimated using the Guinier approximation  (50). Both parameters, as well the maximum particle dimension, D max , were calculated by the GNOM software  (51). Ab initio models of His 6 -MagD 37 were generated using GASBOR  (24). A final-average model was generated from 10 independent models using DAMAVER through their pairwise superposition  (52). Bacteria and spheroplast preparation for MagD 1-64 -mCherry analysis. GFP-expressing bacteria and spheroplasts were prepared as described previously  (25). Briefly, overnight cultures were diluted to an OD 600 of 0. 15 and incubated up to mid-log phase at 37°C with shaking. Cells were harvested, and spheroplasts were created as described previously  (25, 31).
The magnetic beads were washed three times, and the elution was performed for 10 min at 70°C with reagents provided by the manufacturer. Proteomic analyses. Protein digestion and nano-liquid chromatography (LC)-MS/MS analyses were done as previously described  (25, 26). The details are given in Table  S2  in the supplemental material. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral. proteomexchange. org) via the PRIDE partner repository  (55)  with the data set identifier PXD000189.
ACKNOWLEDGMENTS We thank  Michel Ragno  ( BCI, iRTSV ) for help with protein purification and antibody characterization,  Frank Gabel  ( IBS ) for help with SAXS data collection, the  European Synchrotron Radiation Facility (ESRF) , for access to the BIOSAXS beamline ( ID14-3 ), and  Stéphanie Bouillot  for help with microscopy (BCI, iRTSV). We thank  Marie-Odile Fauvarque  ( BGE, iRTSV ) for interest in this work as well as all team members for stimulating discussions. We thank  Romé Voulhoux  for the anti-XcpY and anti-DsbA antibodies. This work was supported by grants from  INSERM  and the  CNRS. A. D. and I. A. received financial support from the  Rhone-Alpes FINOVI Foundation. M. G. C. is a Ph. D. student financed by the  French Cystic Fibrosis Foundation  (VLM). M. R. -G. , M. G. C. , D.
Using the typical data for the considered application gives P e > 10 3 and S t < 10 -5 and indicates that both Brownian diffusion and inertia have a negligible effect on the particles motion. Therefore, on the basis of the above estimates, it is assumed that particles follow the streamlines from the outlet of the capillary tube until they make contact with the membrane. Moreover, it is also assumed that the molecular interaction forces allow particles to adhere as soon as they make contact. 3. 3. Numerical Results. The set of equations (1-6) was solved using the commercially-available finite element code COMSOL Multiphysics™. Numerical simulations were made in order to test the effect of the membrane permeability and of the position of the outlet of the capillary tube, H 0 on the size of the fluid capture tube at the membrane surface and to characterize the spatial distribution of the filtration velocity u z at the membrane surface.
Acknowledgments We owe thanks to  S Germain  for critical review of manuscript, and  I Ferreira  and  F Boudihel  for expert molecular and immunohistochemical assistance. Ms. A Swaine  reviewed the English language. This study was supported by grants from  Agence Nationale pour la Recherche (ANR) , and  Canc érop ôle-Institut National du Cancer (InCa).
Micro-computed tomography (micro-CT) analysis Analyses of bone micro-architecture were performed using a Skyscan 1076 in vivo micro-CT scanner (Skyscan, Kontich, Belgium). Tests were performed after sacrifice on tibias for each treatment group. All tibias were scanned using the same parameters (pixel size 18 mm, 50 kV, 0. 5-mm Al filter, 10 min of scanning). The reconstruction was analyzed using NRecon and CTan software (Skyscan). The specific bone volume was quantified as the relative Bone volume/total volume measured for each VOI. 3D visualizations of tibias and heads were realized using ANT software (Skyscan) at sacrifice.
RANKL protein detection in Ewing's sarcoma cell lysates by western-blot Total protein extracts in Laemmli buffer (62. 5 mM Tris-HCl, pH 6. 8, 2% SDS, 10% glycerol, 5% 2-mercaptoethanol, 0. 001% bromophenol blue) were separated by SDS-polyacrylamide gel electrophoresis, and transferred to Immobilon-P membranes (Millipore). Membranes were immunoblotted with anti-human RANKL (1/200, Santa Cruz), or antiβ-actin (1/100, Sigma) antibodies. In both cases, secondary anti-rabbit antibody was used at 1/10,000 (Santa Cruz). Antibody binding was visualized with the enhanced chemiluminescence system (SuperSignal West Pico Chemiluminescent Substrate, ThermoSientific). For quantification, luminescence was detected with a Charge Couple Device (CCD) camera and analyzed using the GeneTools program (Syngene).
RANKL Is expressed in the ES tumor microenvironment The expression of RANKL was then assessed in situ in tumor samples taken from A-673 human Ewing's sarcoma models (Fig. 1C ). The immune staining was performed on 40-mm tumor sections by immuno-histofluorescence with antibodies targeting the human form of the cytokine (see Section 2). The staining protocol was designed to avoid cross reactions with the murine form of RANKL, by saturating the murine sites using goat antimouse Fab. A homogeneous expression of human RANKL was observed in sections of A-673 tumors as shown in Fig. 1C , similar results being obtained in another Ewing's Sarcoma model, in TC-71tumor sections (data not shown). The human origin of RANKL production was confirmed in these models by ELISA test comparing the staining with antibodies specific of human or murine species.