dataesr/scientific-paragraphs-categorization huggingface dataset:
B. cenocepacia H111 is sensitive to several antibiotics, is easily amenable to genetic manipulation, and its physiology and virulence in various infection models are well studied  (11) (12) (13) (14) (15) (16). Together, these properties make its genome a valuable addition to the growing number of sequenced BCC genomes. Genomic DNA was prepared according to Wilson  (17). A combination of Roche 454 GS-FLX Titanium 3-kb-span paired-end libraries (~25ϫ coverage), Roche 454 GS-GLX Titanium fragment reads (~25ϫ coverage), and Illumina 36-bp fragments (50ϫ coverage) were assembled into 71 contigs using the CLC Genomics Workbench version 5. 0 software (CLC bio, Aarhus, Denmark). To fill the small gaps in the assembly that were probably caused by ambiguities in GϩC-rich regions of the genome, we sequenced a large-insert library (8 to 12 kb) using the PacBio RS II kit to approximately 30ϫ coverage (Pacific Biosciences, Menlo Park, CA, USA).
cenocepacia H111. Conversely, the facultative pC3 replicon is larger than that of B. cenocepacia J2315 at 1. 04 Mb versus 0. 88 Mb. The pC3 replicon codes for specific traits, such as virulence and stress resistance, and is less conserved among BCC members than chromosomes 1 and 2  (20, 21). The genome was annotated using the RAST pipeline  (22). The results of the automated annotation were augmented and curated using the Artemis software package  (23). The genome contains 6,933 open reading frames, which is comparable to the gene content of other B. cenocepacia genomes. Nucleotide sequence accession numbers. The sequences of the three replicons of B. cenocepacia H111 have been deposited at DDBJ/EMBL/GenBank under the accession no. HG938370, HG938371, and HG938372.
These data suggest that preexisting stocks of IL-1α and IL-33 protein are rapidly released in the lung after silica. The early lung release (1 h) of IL-1α and IL-33 after silica preceded the increased expression of pro-IL-1β and the release of mature IL-1β. Indeed, the levels of lung IL-1β transcripts (Figure  1c ) and BALF IL-1β protein (Additional file 1: Figure  S1b ) were mainly increased between 6 and 24 hours following instillation. Cellular lung inflammation was first monitored by BAL total cell and neutrophil (GR1+ cells) counts. Neutrophil accumulation was also quantified by assessing lung expression of CXCR2. Although the expression of this chemokine receptor has been reported in macrophages, CXCR2 is mainly expressed by recruited neutrophils and can be used as a biomarker of neutrophilic inflammation  [22].
Broncho-alveolar lavage (BAL) and alveolar cell number Mice were sacrificed with an intraperitoneal injection of sodium pentobarbital (20 mg/mice) and bronchoalveolar lavage was performed by cannulating the trachea and lavaging the lung 4? with 1ml of NaCl 0. 9%. The broncho-alveolar lavage fluid (BALF) was centrifuged at 281g, 10 min, 4? C (Centrifuge 5804R, Eppendorf, Hamburg, Germany). Cells recovered in BAL were counted then fixed in 1. 25% paraformaldehyde and analyzed with FACS calibur (BD Biosciences) using FlowJo software. Neutrophils were identified by labelling with anti-GR1-PE (clone RB6-8C5, BD Biosciences, Erembodegem, Belgium) and their number calculated in function of total BAL cells counted with a Burker cell chamber. Fc receptors were blocked with anti-CD16/CD32 (clone 2. 4G2, BD Biosciences) to reduce nonspecific binding.
Acknowledgements This work was funded by the  Fonds de la Recherche Scientifique M? dicale (FRSM) , by  Actions de Recherche  Concert? es, Communaut?fran?aise de  Belgique ,  Direction de la Recherche Scientifique  ( ARC 09/14-021 ), by  Fondation Contre le Cancer , by the  Fonds de la Recherche Scientifique (FNRS ;  Project PDR T. 0119. 1314633768 ), by the  European Commission  under  FP7-HEALTH-F4-2008  (Contract no. 202047 ) and by  Agence Nationale  de s? curit?sanitaire de l'alimentation, de l'environnement et du travail (ANSES, France). F. H. is a Research Associate with the  FNRS, Belgium.
Population The HELENA cross-sectional study is a population-based, multi-centre investigation of the nutritional and lifestyle status of adolescents, carried out in ten European cities (Vienna in Austria, Ghent in Belgium, Lille in France, Dortmund in Germany, Athens and Heraklion in Greece, Pecs in Hungary, Rome in Italy, Zaragoza in Spain and Stockholm in Sweden). Data were collected from October 2006 to December 2007. A detailed description of the HELENA study design and sampling procedure has been published elsewhere  [19, 20]. The study was approved by the ethical committees and performed following the ethical guidelines of the Declaration of Helsinki. All study participants and their parents provided a signed informed consent form. The total HELENA population consisted of 3,528 eligible adolescents (52.
3 % females) aged 12. 5-17. 5 years. For the current analyses, adolescents were included if data were available for two non-consecutive 24-h dietary recalls and the food frequency questionnaire (FFQ), resulting in 1,215 eligible subjects. Since for Heraklion, Pecs and Rome no full set of dietary data were available (i. e. two 24-h dietary recalls and a FFQ), subjects from these cities were excluded from the present study. In the HELENA population, non-participants did not differ in sex or age. For this paper, age and BMI did not differ between excluded and included cases, while less boys and more adolescents from high socio-economic status (SES) were included (p = 0. 002 and p = 0. 010, respectively). Data on glucose and lipid homoeostasis were only available in a subpopulation (N = 387); they did not differ in sex, BMI and SES but had a higher age (p < 0.
Socio-demographic determinants Collected demographic data included information on sex, age, city and SES by means of a standardised self-reported questionnaire. SES was examined by parental education and by the Family Affluence Scale (FAS). Education level of mother and father was reported as "lower education", "higher secondary education" and "university education". A modified version of the FAS developed by Currie et al. [21]  was used as a proxy of SES status; the scale is based on the concept of material conditions in the family. For the purposes of the HELENA study, the FAS was slightly modified by replacing the item on frequency of family holidays by Internet availability at home. The adolescents completed a questionnaire asking about the number of cars (0-3 depending on amount) and computers at home (0-3 depending on amount), having access to Internet at home (0 no, 1 yes), and whether the adolescent had his or her own room (0 no, 1 yes).
24-h dietary recall to assess dietary intake Dietary intake was assessed by two non-consecutive 24-h recalls. The 24-h recalls were collected by use of a computer-based self-administered tool, the HELENA-Dietary Intake Assessment Tool. This assessment tool is based on six meal occasions (breakfast, morning snacks, lunch, afternoon snacks, evening meal, evening snacks) referring to the previous day. Adolescents selected autonomously all the consumed foods and beverages from a standardised food list  [24, 25]. Items not available in the list could be added by the participant at any moment. Consumed foods were translated to nutrients by use of the German Food Code and Nutrient Data Base (Bundeslebensmittelschlüssel, BLS, version II. 3. 1) [26]. Consequently, differences in fortification levels between countries were not taken into account.
Body composition The protocol used to collect anthropometric data has been previously described  [33]. Measurements were done while participants were barefoot and in underwear. Weight was measured to the nearest 0. 1 kg using electronic scales (Type SECA 861). Height was measured to the nearest 0. 1 cm with the head aligned in the Frankfort plane using a telescopic height-measuring instrument (Type SECA 225). BMI was calculated as body weight in kilograms divided by the square of height in metres. In addition, BMI was adjusted for age and sex to give a BMI z-score using the British Growth Reference Data from the Child Growth Foundation  [34] , and overweight was classified following the International Obesity Task Force  [35]. The triceps and subscapular skinfold thickness and waist and hip circumferences were measured on the left side of the body.
Statistics Analyses were performed with PASW Statistical Program version 19. 0 (SPSS Inc, IBM, IL, USA). Two-sided level of significance was set at p < 0. 05. Non-normal data were transformed using the logarithmic or square root transformation to perform analyses, but data were back-transformed in the original units for representation. The regression analyses were all corrected for age, sex, SES, city and breakfast skipping. Estimated marginal means from the regression were used for the graphs. For significance levels between consecutive categories of RTEC consumption, the "repeated" contrasts were run with RTEC non-consumers as reference category. Socio-demographic differences (age, sex, city and SES) between different RTEC consumption groups were examined by means of a logistic regression with RTEC consumption as outcome.
Descriptive data In total, 1,215 adolescents (44 % boys, 12. 5-17. 5 years old) with valid FFQ and two-day 24-h recall data were included in the analyses. Based on the FFQ, 29 % was classified as breakfast skipper and 65 % was classified as RTEC consumer (defined as RTEC intake once a week or more). RTEC consumers were younger than RTEC non-consumers (14. 7 vs. 15 years, p = 0. 01). An equal number of boys and girls was RTEC consumers, but boys were more often daily consumers (36 %) than girls (29 %) (p = 0. 031). RTEC consumption (especially frequent consumption) was more frequent in adolescents from the lowest FAS families (p = 0. 002). No differences were seen depending on parental education. Although the prevalence of RTEC consumption was different between study centres (Athens in Greece 76 %, Dortmund in Germany 64 %, Ghent in Belgium 63 %, Lille in France 69 %, Stockholm in Sweden 63 %, Vienna in Austria 58 %, Zaragoza in Spain 67 %), no significant differences were seen after correction for sex, age and FAS (p = 0.
Also, this higher vitamin D intake is probably due to an overall healthier dietary intake and not due to the fortification of RTEC since there was no vitamin D fortification in the food composition database RTEC items. RTEC could also contribute to a healthy diet via the accompanying food. Literature has shown higher milk/ yoghurt intake in RTEC consumers but mixed results concerning fruit intake  [6, 10]. Our study found a higher milk/ yoghurt consumption frequency and quantity in RTEC consumers over the day; daily RTEC consumers even had 2. 65 times more chance to fulfil the daily milk intake recommendation  [39]. RTEC consumers also had a higher fruit intake frequency, but when they consumed fruit, they consumed the same absolute amount as RTEC non-consumers. Consequently, RTEC consumers have a more routine habit of fruit consumption, independently of the portion size.
Strengths and limitations In contrast to existing studies, data were derived from a multi-centre European sample of adolescents. The extensive standardised information on diet (including detailed information of, e. g. carbohydrate subtypes), anthropometry and blood biomarkers makes it a valuable source for public health. RTEC analyses were corrected for breakfast skipping to examine the effect of RTEC consumption independently of breakfast skipping. Special focus was on diet with not only extensive information on daily nutrient composition, but also by using an all-integrating DQI and by focusing on milk and fruit intake (both prevalence and quantity). Besides, RTEC intake was linked with adolescents' body composition (BMI, waist and fat%) and glucose and lipid status. Nevertheless, several limitations exist.
Acknowledgments Many thanks to  Anke Carstensen  and  Petra Pickert  for their contribution to laboratory work and to  Inge Huybrechts  for designing the diet quality index. The  HELENA Study  was carried out with the financial support of the  European Community Sixth RTD Framework Programme  (Contract  FOODCT-2005-007034 ). The writing group takes sole responsibility for the content of this article. The European Community is not liable for any use that may be made of the information contained therein. An unconditional grant from  Cereal Partners Worldwide S. A. was received for performing the statistical analyses in this manuscript.
Reverse transcription was performed in with SuperScriptIII Kit according manufacturer's instructions (Invitrogen). cDNA was subjected to quantitative real-time PCR using primers for Il1b, Il6 or Ccl2 (Qiagen) and GoTaq qPCR-Master Mix (Promega). GAPDH and 18S expression was used for normalization. Raw data were analyzed using the Relative Expression Software Tool (REST, http://www. rest. de. com/).
Statistical analysis Statistical evaluation of differences between the experimental groups was determined by using Mann-Whitney non-parametric test, or Log Rank test for survival. All tests were performed with GraphPad Prism [GraphPad Software Inc. , San Diego, CA, USA; www. graphpad. com]. A P-value ,0. 05 was considered significant and symbolized with *; ** for p,0. 01 and *** for p,0. 001. A Pvalue. 0. 05 was considered not significant and symbolized with ns.
New orally active anticoagulant (NOAC) agents are specific inhibitors of activated factor Xa (FXa) (rivaroxaban and apixaban) or thrombin (dabigatran). It is expected that NOACs will improve antithrombotic treatment. Cancer patients are a particular group that could benefit from treatment with NOACs. However, NOACs present some significant interactions with drugs frequently used in cancer patients, which might influence their pharmacokinetics, compromising their efficacy and safety. In the present review, we analyzed the available data from the subgroups of patients with active cancer who were included in Phase III clinical trials that assessed the efficacy and safety of NOACs in the prevention and treatment of VTE. The data from the Phase III trials in prophylaxis of VTE by rivaroxaban or apixaban highlight that these two agents, although belonging to the same pharmacological group (direct inhibitors of factor Xa), have substantially different profiles of efficacy and safety, especially in hospitalized acutely ill medical patients with active cancer.
A limited number of patients with VTE and active cancer were included in the Phase III trials (EINSTEIN, AMPLIFY, and RE-COVER) which evaluated the efficacy and safety of NOACs in the acute phase and secondary prevention of VTE. Although, from a conceptual point of view, NOACs could be an attractive alternative for the treatment of VTE in cancer patients, the available data do not support this option. In addition, due to the elimination of the NOACs by the liver and renal pathway as well as because of their pharmacological interactions with drugs which are frequently used in cancer patients, an eventual use of these drugs in cancer patients should be extremely cautious and be restricted only to patients presenting with contraindications for low molecular weight heparins, fondaparinux, or VKAs.
However, less than 5% of patients included in these studies had active cancer; consequently, safe and generalized conclusions cannot be supported by the data published so far. The data from the subgroup analysis on the efficacy and safety of NOACs in the acute phase and secondary prevention of VTE in patients with active cancer are encouraging. The Twice-daily Oral Direct Thrombin Inhibitor Dabigatran Etexilate in the Long Term Prevention of Recurrent Symptomatic VTE Phase III trial has been completed, but the results have not yet been published. Thus, it is not known whether long-term administration of dabigatran in the secondary prophylaxis of VTE is an effective and safe treatment, especially in cancer patients. According to the data analyzed in the present review, specific Phase III trials assessing the efficacy and safety of treatment with rivaroxaban, apixaban, or dabigatran in patients with active cancer and VTE should be carried out.
According to the pharmacokinetic and pharmacodynamic properties of NOACs and their interactions with drugs which are used in cancer patients, future studies should be carefully designed taking in consideration the type of chemotherapy and the adjuvant anticancer treatments. Since the data published so far on the efficacy and safety of specific FXa inhibitors in the prevention and treatment of VTE in cancer patients are very limited, the need for specific dose-finding clinical trials in cancer patients is highlighted. Taking into consideration that the cancer-related VTE risk is strongly dependent on the histological type of the cancer cells, the burden of the cancer, and the type of the anticancer treatment, the modelization of the antithrombotic efficacy of the specific FXa inhibitors in cancer-induced hypercoagulability might offer substantial information for a more accurate design of future clinical trials.
38 The inhibition of clot-bound FXa or thrombin by NOACs may offer the advantage of in situ inhibition of thrombogenesis in cancer patients who present with chronic compensated disseminated intravascular coagulation. The data from the Phase III clinical trials presented in this review do not allow any comparison between the specific inhibitors of FXa or thrombin or between apixaban and rivaroxaban. However, we have to highlight that both rivaroxaban and apixaban bring a different concept to the management of VTE as compared with that of dabigatran. The design of the EINSTEIN and AMPLIFY trials simplifies the treatment of VTE. Oral administration of a single antithrombotic drugrivaroxaban or apixaban -during the acute phase of VTE as well as during the long-term secondary prevention of VTE recurrence is an efficient antithrombotic strategy.
Patient condition dramatically improved following the initiation of the anti-infectious course. Concurrently, microbiological investigations were contributive with initial identification of a methicillin susceptible Staphylococcus epidermidis and the consecutive isolation of an Actinomyces sp. strain using BacT/Alert SN ® anaerobic medium (BioMerieux, Craponne, France) and pricking out the broth on Columbia agar supplemented with 5% plain sheep blood (BioMerieux, Craponne, France). The latter (named CRL1) was identified as A. meyeri using Matrix-Assisted Laser Desorption-Ionization Time of Flight (MALDI-TOF) mass spectrometry. Subsequently, a sequence analysis of the 16S rRNA gene was carried out. A total of 1441 continuous nucleotides were determined using the Sanger method. The sequence of isolate CRL1 (GenBank accession number KC522297) was compared to all bacterial sequences available from the GenBank database using the BLAST program (http://www.
Statistical analyses The clinical data, virus titrations and Mhp DNA quantifications obtained in the different groups were compared by Kruskal-Wallis test using Systat 9 software. Plasma IgG and postprandial nutrient concentrations were subjected to a variance analysis, using the MIXED procedure of SAS (SAS Inst. Inc. , Cary, NC). Plasma total IgG concentrations were analyzed using the repeated statement and taking into account the day of sampling, feed restriction (FR), infection (I) and the corresponding interactions. Because of non-normal distribution and non-homogenate variances for glucose, urea and AA plasma concentrations due to the major effect of time, statistical analyses of these data was performed separately at each sampling time and data were logtransformed to be normalized when necessary.
Viral infection led to a reduction in feed consumption in the MH1N1-AL group. It was strongly marked during the 3 first days, with pigs eating 30 g of feed per kg of body weight on average against 60 g before H1N1 infection (P = 0. 001). This resulted in a reduction of weight and mean weight gain (MWG) as compared to other groups (P = 0. 006) (Figure  2 ). In contrast, H1N1 infection had no impact on feed consumption in the MH1N1-FR group in which pigs were eating on average 30 g of feed per kg of body weight both before and after inoculation. In this group, MWG was identical to MWG measured in C-FR. At necropsy, all co-infected pigs had macroscopic lesions of pneumonia (data not shown). They extended into apical, cardiac and diaphragmatic lobes with no difference in the mean score severity between MH1N1-AL and MH1N1-FR groups (17.
Acknowledgments The authors thank colleagues from  Anses Ploufragan/Plouzanelaboratory  for helpful contributions: AndreKeranflec'h,  Jean-Marie Guionnet  and  Yann Bailly  for animal care and sampling; Stephane Queguiner,  Stephane Gorin  and  Nicolas Barbier  for technical help in the virology laboratory and tissue sampling at necropsy; Severine Ferrefor preparing the Mhp inoculum and performing Mhp quantification;  Stephanie Bougeard  for her advice in statistical analysis. They also thank colleagues from  INRA :  Francis Le Gouevec  and  Alain Chauvin  for the surgical procedure,  Marion Girard ,  Nadine Me  ´ziere,  Yolande Jaguelin ,  Francoise Thomas ,  Michel Lefe  `bvre and  Jean-Noe ¨l Thibault  for help during blood sampling and for laboratory analyses. They are indebted to  Jean-Noe ¨l Sialelli  and  Fabien Vautrin ,  FARM'APRO, France , for helpful discussions.
This work received financial support from  FARM'APRO. FARM'APRO  participated in the study design but had no role in the data collection and analysis, decision to publish, or preparation of the manuscript. Remuneration of the Anses' personnel from the  unit ''Production of decontaminated pigs  and testing'' was partially supported by the  Conseil General des Cotes d'Armor. This funder had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Image acquisition, analysis and software Infected THP-1 cells were incubated with Alexa647 labeled Tf for 5 minutes. Then we exposed the cells to the acidic washing procedure as described above and finally fixed them with 2% PFA. THP-1 cells were mounted on objective slides with Mowiol and z-stacks of infected GFP expressing cells were acquired with a Zeiss LSM510 Meta. 3D reconstruction of z-stacks was done with Bitplane Imaris V6. 4. 2. We also used this software to calculate the volume of the cells by GFP expression and the volume of internalized Tf by Alexa647 fluorescence. In general, images were never modified apart from enhancing contrast and/or brightness. Statistical analyses were performed using the GraphPad Prism V5 software package. Statistical tests used were the unpaired two-tailed T test and the Mann-Whitney test and regression analyses with p-value calculations.
Selection of single nucleotide polymorphisms The initial part of the study focused on a mutational analysis of TLR2, 4 and 9 genes in nine dogs with SNA belonging to various breeds. This analysis revealed two non-synonymous SNPs in the coding region of TLR2: C137A (rs22410121) and C1547T (not reported in the canine genome database). Eight non-synonymous SNPs were identified in the TLR4 exons: T23C (not reported in the canine genome database but described by Kathrani et al. [20] ), C107T (not reported previously), T500C (rs22145736), A600C (rs22189454), A688G (rs22189456), G1039A (not reported in the canine genome database but described by Kathrani et al. [20] ), A1571T (rs22124023) and G1807A (rs22123995). Four non-synonymous SNPs were identified in TLR9 exon: G1138A (not reported previously), A1372C (not reported previously), A2158G (rs22882109) and G2927A (not reported previously).