dataesr/scientific-paragraphs-categorization huggingface dataset:
c-di-GMP Quantification Indirect c-di-GMP quantification was evaluated using P cdrAgfp plasmid, in which the c-di-GMP depending cdrA promoter is fused to gfp  (Rybtke et al. , 2012). P. aeruginosa strains containing the P cdrA -gfp plasmid were grown overnight and subcultured in LB with gentamicin to a starting OD 600 of 0. 1 (10 8 CFU. ml -1 ). After 4 h incubation at 37 • C in shaking conditions, 1 mL of culture was harvested and re-suspended in the same volume of 1x PBS. OD 600 and fluorescence (excitation 485 nm, emission 520 nm) was measured in a black 96-well plate with see-through flat bottom (Falcon) using a FLUOstarOptima plate reader (BMG Labtech). Quantifications were performed in triplicate and data are presented as relative fluorescent units (RFUs) which are arbitrary fluorescent units corrected for cell density.
The parameter settings were optimized by infusion experiments. Data were acquired in multiple reaction monitoring (MRM) mode using the Analyst software version 1. 6. (Applied Biosystems, Toronto, ON, Canada). Identification and quantification of c-di-GMP was performed by using three specific mass transitions from molecule ion m/z 691 to the product ions m/z 152, m/z 135, and m/z 540. The external calibration was carried out at c-di-GMP concentrations ranging from 10 to 200 ng in 500 μl ddH 2 O using the internal standard cXMP (50 ng). Obtained concentrations of c-di-GMP were normalized against total protein contents of respective cultures, which were determined by the bicinchoninic acid assay  (Smith et al. , 1985). All experiments were performed for three independent cultures each analyzed in duplicate.
LB medium was then pumped with a 2. 5 ml h -1 flow. Biofilms were visualized after 24 and 48 h by confocal laser scanning microscopy (CLSM) with a TCS-SP2 microscope (Leica Microsystems, Heidelberg, Germany), using a 63x oil immersion objective. Image stacks were collected and processed using Leica Confocal Software and Adobe Photoshop. The thicknesses (μm) and biovolumes (in μm 3 /μm 2 ) of the biofilms were measured using the COMSTAT software  (Heydorn et al. , 2000). Each experiment was made in triplicate and 10 positions were analyzed per channel.
Acknowledgments We wish to thank  Bob Hancock  and  Manjeet Bains  for the gift of P. aeruginosa  H103  and  H636 ,  Matt Parsek  for the reporter system P cdrA -gfp,  Anke Neidig  and  Michael Nusser  for technical assistance. The LMSM is supported by the  Région Haute-Normandie (France ,  GRRs Sésa  and IRIB), the  Grand Evreux Agglomeration and European FEDER  funds. The LBCM is supported by the  Région Bretagne (France)  and  European FEDER  funds.
This article reviews the dental literature concerning the potential impact of the removable prosthesis (RP) on the health status of patients with certain systemic diseases. Literature was surveyed using Medline/PubMed database resources, as well as a manual search, up to 2015 to identify appropriate articles that addressed the aim of this review. The research used keywords about associations between RP and six pathologies: Human immunodeficiency virus infection, diabetes mellitus, pulmonary diseases, gastric-Helicobacter pylori, cancer, and cardiovascular diseases. Analysis of literature showed that in patients with dentures having one or more of the six general conditions listed, Candida albicans organism is more frequently found in the oral flora compared to healthy denture wearer. Although causality has not been established and pending further research on this topic, the hygienic practices necessary to minimize the risk of numerous pathologies should be strengthened in the case of these patients, all the more in the presence of physical or psychological disability.
[10] Moreover, the continuous swallowing or respiration of microorganisms from DP exposes patients, particularly the immunocompromised host or polymedicated elderly, to the risk of unexpected infections. Clinical studies are needed to confirm the existence of this risk and demonstrate the effectiveness of prosthetic biofilm control in these patients. [11, 12] e aim of this paper is to investigate the putative risks related to medically compromised patients wearing a removable prosthesis (RP). [13, 14]  this way, the purpose of our literature analysis is to review the knowledge about this subject with. An electronic database and manual searches were undertaken to identify the impact of prostheses on the oral flora of patients with one or more common six general pathologies. Association only between denture wearers (DWs) and in order "human immunodeficiency virus (HIV)," "diabetes mellitus," "diabetic," "pulmonary, pneumonia, diseases" "gastric-Helicobacter pylori, " "cancer, " and "cardiovascular diseases," are conducted.
Data with longer follow-up would be useful. A simple methodology was applied in this trial. We used RECIST as the metric of tumor response assessment. RECIST is not the best way to measure the activity in bone tumors. However, alternative methods [such as the Choi assessment or [ 18 F]2-fluoro-2-deoxy-D-glucose positron emission tomography ( 18 F-FDG PET)] are not standardized, not validated and are difficult to implement in a multicenter trial. Furthermore, RECIST was used in the two previously published trials. There was no ideal method for tumor response assessment in bone tumors. We centrally reviewed the imaging carried out in the present study to compare the tumor assessment carried out according to RECIST or according to the Choi criteria. In 14 patients, tumor response according to the Choi criteria was not feasible because of the use of MRI or because of inadequate contrast product enhancement.
This study was designed as an exploratory, hypothesis generating, proof-ofconcept study. The sample size was chosen (n = 25) based on practical considerations, rather than statistical power and type I error rate calculations, with the aim of demonstrating the biological activity of this targeted therapy on a homogenous group of patients with chordomas. Statistical analyses are descriptive. Study investigations were conducted after approval by the regional Ethics Committee ('Comité de Protection des Patients Nord-Ouest III', date of approval:16June 2009) and after declaration to the French Health Products Safety Agency ('Agence Française de Sécurité Sanitaire et des Produits de Santé', date of approval: 1 June 2009). Informed consent was obtained from each patient. This study was registered in the European Clinical Trials Registry (EudraCT No.
safety and toxicity Volume 26 | No. 10 | October 2015 doi:10. 1093/annonc/mdv300 |  Annals of Oncology original articles sample size calculation and statistical analysis script is a part of the AngioNexT study, which included five different strata: superficial angiosarcoma, visceral angiosarcoma [13], epithelioid hemangiopericytoma [14], solitary fibrous tumor or hemangiopericytoma [15] and chordoma (reported here). http://www. cancer. gov/clinicaltrials/search/view? cdrid=633547&version=healthprofessional. results patient characteristics From May 2011 to January 2014, 27 patients (17 men and 10 women) were enrolled in 12 centers of the French Sarcoma Group (GSF/GETO). The median age was 64 (30-86) years. All patients were eligible, with evidence of tumor progression at the time of study entry.
The level of statistical significance was set at 0. 05. In each classroom, one child chosen at random was examined twice one week later by the same examiner using the ICDAS-II advanced method and the BEWE index to measure intra-examiner reliability. The corresponding Kappa values assessed in 34 re-examined children one week later were respectively 0. 8 (ICDAS-II) and 0. 9 (BEWE). Data were analysed using SPSS19. 0.
3  due to a reduced photon flux. Nevertheless, data quality was sufficient for volume reconstruction. The assumption of the quasi- Exemplary three-dimensional visualization of an IAC microgap map (coloured) superimposed on the CT scan of the dental implant, pointing out the orientation of the latter. Here the implant is a NobelActive (Nobel Biocare, Switzerland) under 333 N cyclic load. The IAC map is calculated according to  Zabler et al. (2012) ; the look-up table is comparable with Fig. 6. stationary conditions after 5000 initial cycles was sufficing as no motion artefacts were observable. From the three-dimensional volume images a projection method was used (see  Zabler et al. , 2012)  to project the fringe contrast with the gap width of the conical plane of the IAC. In addition, a Gaussian blur (50 pixel) was applied to the maps in order to compensate for the very low signal-to-noise ratio.
Recalculations by Finite Element Analysis (FEA) The simulations were performed with the commercial software COMSOL Multiphysics (Comsol Co. , Stockholm, Sweden). In the FEA, we use the static equilibrium equations under small deformation assumption with an isotropic relation: f b + • σ = 0 ε = 1 2 [ u + u T ] ε = 1 + ν E σ - ν E tr(σ)I where f b is the body force, σ is the stress tensor, ε is the strain tensor, u is the displacement, ν is the Poisson ratio, E is elastic modulus, and I is the identity matrix. For recalculating the stress in three-point bending test, about 204,000 tetrahedral elements were used in the mesh. The boundary conditions are the following: • Fixed constraints (u = 0) were applied to the two support edges. • Boundary load of total force (50 N) was applied to the middle area (0.
Material Formalin fixed, paraffin-embedded biopsies from 129 patients with primary SCC of the tongue available at Umea ˚University Hospital and Naples, were included. Sixty-five were men and 64 women. The mean age was 63. 4 years, ranging from 19 to 93 years. The project was approved by the local Ethical Committee (dnr 01-057, 03-201). The majority of patient samples had previously been analysed for expression of p16 and HPV16  [8]. Follow up ranged between 1 and 179 months, with a mean of 46. 6 months. All but seven patients had a follow up of 2 years or longer. Status at the end of the study was staged as alive disease free, alive with disease, dead of disease, dead disease free or dead with disease, but not as first cause of death. Data on status were collected from the clinical files or, when not available there, from the Swedish Death Registry.
qRT/PCR Twenty-seven tongue SCCs, of which 23 had paired clinically normal tumour-adjacent tissue samples and 14 tongue biopsies from healthy controls were included in the mRNA analysis. For example, in the case of a SCC on the left border of the tongue, clinically normal tumour-adjacent tissue was taken from the right side of the tongue. For clinical data on the tumours, see Table  2. Paraffin-embedded samples from 10 of these tongue SCC were included in the protein analysis. Samples previously analysed  [10]  had been homogenized in trizol and total RNA was extracted using either chloroform or an RNA/protein purification kit (Norgen). The remaining samples were homogenized in lysis buffer from All Prep DNA/RNA/miRNA Universal Kit (Qiagen) using Precellys (Bertin technologies). After dilution in water, no difference in RNA quality or yield was observed between the different methods according to measurement with nano-drop and bioanalyzer.
Statistical analysis SPSS version 22 was used for statistical analysis, correlating results from scoring of podoplanin to clinical data. The Chi square test was used for calculation of p-values and a p-value <0. 05 was considered statistically significant. Two-and 5-year survival were used in the survival analysis. Mann-Whitney test was used to analyse mRNA levels. For tumour localisation 1 5 tongue, 2 5 border of tongue and 3 5 overgrowth into floor of mouth. Tumours labelled with * also had paraffin samples included in the protein analysis. TNM 5 T(umour), N(odes), M(etastasis).
gottschalkii (EU919431. 1) with 41/425 bases of difference and 89% similarity with M. smithii (DQ251046. 1) with 45/425 bases of difference. The negative controls remained negative in all the PCR-based experiments. This methanogen was further referred as Methanobrevibacter sp. strain N13. Microscopic examination of colonies indicated a Gram-positive organism forming pairs, tetrads and short chains, (Fig  1 ). The 16S rRNA and mcrA gene sequence-based phylogenetic trees confirmed the BLAST data and the uniqueness of Methanobrevibacter sp. strain N13 (Fig  2 ). All sequences reported here have been deposited in GenBank (LK054623-LK054628 for mcrA gene sequences; LK054632-LK054637 for 16S rRNA gene sequences). Methanobrevibacter sp. strain N13 was deposited in our publicly available collection "Collection de Souches de l'Unité des Rickettsies" (CSUR P1375).
strain N13. No colony was observed in control roll tubes. Methanobrevibacter sp. strain N13 was deposited in our publicly available collection (CSUR P1375). This culture-based study increases knowledge of the repertoire of methanogenic archaea living in dental microbiota, particularly in diseased dental pockets. We cultured M. oralis in 47. 7% of periodontitis patients, a figure in the range of previously published data  [1]. M. oralis was also cultured from one healthy individual (6. 7%), in line with the previously reported 6% prevalence of M. oralis in healthy individuals using molecular detection  [1]. Other PCR-based studies found a higher prevalence of M. oralis DNA in healthy individuals, illustrating that PCR-based studies may overestimate the actual prevalence of methanogens by detecting DNA from dead organisms.
Analysis of O 2 consumption by high resolution respirometry Oxygen concentration was measured by high-resolution respirometry with an Oroboros Oxygraph-2k (Oroboros Instruments), in a standard configuration, with 2 ml volume of both chambers, at 37°C, and 500 rpm stirrer speed. P. gingivalis cells grown at 37°C in anaerobic conditions (Anaerogen, Oxoid) were harvested in the exponential growth phase (OD 600 nm 0. 5), washed or not in PBS according to the experimental conditions tested, and transferred into oxygraph chambers. Acquisition was started after 2-3 minutes of equilibration at 37°C in oxic conditions and after closing of the chambers. Measurements were performed on two independent cultures, and the data shown represent typical results. Data were recorded at 1 s intervals using the Datlab 4 Acquisition software (Oroboros, Innsbruck, Austria).
When the experiment was performed in aerobic conditions with the same concentration of paraquat, the survival of the cydAB mutant was not affected compared to WT (data not shown). In anaerobiosis, restoring cydAB expression in trans partially restores the wild-type phenotype in the cydAB mutant (Fig  3 ). However, the reason why overexpressing the cyd operon by plasmid-based complementation did not totally restore the resistance of the mutant to paraquat is not understood. The expression of sodB (PGN_0564) encoding the superoxide dismutase was monitored in P. gingivalis wild type and cydAB mutant. In E. coli redox-cycling drugs were able to activate the SoxR (sodB activator) in anaerobic cells, thus without superoxide production, as long as alternative respiratory acceptors were provided  [31].
Western-blot Protein extracts were run in 10% SDS-PAGE and transferred onto PVDF membranes (Bio-Rad, Transblot). Membranes were blocked overnight in PBS/4% skim milk/0. 1% Tween-20 (Sigma-aldrich). Primary (anti-PPARγ, SC-7273, clone E-8; anti-GAPDH, SC-365062, clone G-9; both from Santa Cruz Biotechnology) and secondary (Goat anti-mousse IgG HRP, Dako, P0447) antibodies were successively added in PBS/Tween/milk, each being left for 1h before detection with the Clarity Western ECL Substrate using the Chemidoc MP System (Bio-Rad). Quantifications were performed using the image Lab software (Bio-Rad).
Acknowledgments We thank  Dr Tagg  for the JIM9125 (DC117A) and JIM9126 strains,  Dr Diana R. Martins  for other JIM strains,  Malgorzata Nepelska  for the Caco-2 PPARγ cell-line;  Fabienne Devime  and  Rozenn Dervyn-Hirel  for technical advices.
This work was supported by  Institut National de la Recherche Agronomique  and financed by grants from the  European Community 's  Seventh Framework Program  (FP7/2007-2013),  MetaHIT , grant agreement  HEALTH-F4-2007-201052 , the  ANR  project  MetaGenoPolis  ( ANR-11-DPBS-0001 ) and the  ANR Blanc FunMetaGen. BC was a recipient of a grant from the  ministère de la Recherche et de l'Education Nationale  ( ED425 ).
Acknowledgements Authors are very grateful to  Drs. Ricardo Cabral ,  Laura Brain  and  Claudia Bonnin  (The  Dental Faculty, Universidad Nacional de Córdoba, Argentina ) for their assistance in implementing this clinical trial, and to  Jan Mulder  ( Global Oral Health Department, Radboud University Medical Centre, Nijmegen, The Netherlands ) for analysing the data. We thank  Dentsply, Germany  and  GC Europe, Belgium  for supplying the glass-ionomers and  3M ESPE, Argentina , for supplying the adhesive system and resin composite. The study was co-financed by institutional funds from the  SECYT ,  Universidad Nacional de Córdoba (Argentina)  and the  Global Oral Health Department, Radboud University Medical Centre, Nijmegen  (The Netherlands).
Most animals restrain their movement activities to familiar areas which leads to home ranges. Although understanding both establishment and shifts of home ranges is highly relevant for basic science and conservation, pinpointing the factors that shape the dynamics of home ranges remains a challenge. Evidently home ranges are influenced by the underlying landscape. Landscape composition, i. e. , the fraction of different land cover types, has recently been shown to affect home range size. Yet, the explicit spatial configuration of the landscape, a factor which is known to be of central importance in spatial ecology, is not taken into account by most studies. We quantify the effect of landscape configuration on summer home range sizes across multiple spatio-temporal scales using GPS data from two behaviorally distinct ungulate species, red (Cervus elaphus) and roe deer (Capreolus capreolus), in the Bavarian Forest National Park, Germany.
Deer data Red deer were caught during winter in the years 2002-2009. Animals were attracted to a corral by food (grass silage, hay, apple, pomace, sugar beets). Within the corral, the deer are guided to a capture facility, were the GPS collars (Vectronic Aerospace, Berlin, Germany) can be attached through hatches in the wall. A second approach was to tranquillize deer by dart gun on sites where they were attracted by food. We collared 14 male and 18 female red deer individuals. Four individuals were collard two or more times over the duration of the study. Roe deer were captured during the winter months (October-March) in the years 2005-2010 using wooden box traps. A total of 40 roe deer (24 male, 16 female) were collared, with five animals collared two or more times over the years of the study.
Land cover types and environmental data To characterize the landscape in our study area we considered five land cover types: ''coniferous forest,'' ''deciduous forest,'' ''mixed forest,'' ''meadow'' and ''regeneration areas,'' i. e. , areas containing mature trees killed by bark beetles and showing now regrowing vegetation, characterized by a shrubby appearance. Anthropogenic areas (e. g. , roads) and water bodies were not taken into account as they cover only a negligible area within the study area. The land cover classification was derived through digitalization from aerial images from the year 2008. In order to take into account the rapid forest dynamics due to bark beetle outbreaks, we update the land cover classification for every year of the study  (2002) (2003) (2004) (2005) (2006) (2007) (2008) (2009) (2010).
Statistical methods To investigate the influence of different land cover types and the landscape configuration on home range sizes, we used linear mixed models (R version 3. 0. 2, R Development Core Team 2013; package ''nlme'',  Pinheiro et al. 2013 ) on the log transformed home range areas (km 2 ) and included spatio-temporal autocorrelation structures following the framework proposed by  (Bo ¨rger et al. 2006a ). We used the year of measurement nested in individuals (ID) as a random effect, as individuals were sampled repeatedly in subsequent years. After inspection for colinearity we removed the variables ''mixed forest'' and ''elevation'' for the red deer data set as both variables showed a Pearson correlation index. 0. 7 with ''regeneration area'' and ''configuration index''. Furthermore preprocessing steps revealed a quadratic fit of elevation and configuration index, hence these two variables were fitted with a quadratic term in the model.
ACKNOWLEDGMENTS We would like to thank  Achim Poethke  who helped to greatly improve previous versions of this manuscript and  Joseph Chipperfield  and  Oliver Mitesser  for statistical advice. This work was financed by the  German Federal Environmental Foundation (Deutsche Bundesstiftung Umwelt) , the  EU-programme INETR-REG IV  ( EFRE Ziel 3 ), and the  Bavarian Forest National Park Administration. M. Bevanda thanks the ''Frauenfo ¨rderung'' of the University of Bayreuth  for financial support. E. A. Fronhofer  thanks the  Eawag  for financial support. We kindly thank  Ingo Brauer ,  Horst Burghart ,  Ru ¨diger Fischer ,  Martin Gahbauer ,  Helmut Penn ,  Michael Penn , and  Lothar Ertl  for technical support.
Results The data used came from a national survey conducted in France in 2010 on all the cattle slaughterhouses and from the national cattle database for cattle movements. After removal of missing data, information regarding 4,557,593 cattle slaughtered in 181 slaughterhouses was used (91. 1% of cattle slaughtered in France in 2010). Among these, post mortem inspection allowed the identification of 6,431 cattle harboring at least one cyst (i. e. regardless of its stage of development) and 603 harboring at least one viable cyst. Three significant clusters for cattle with all types of cysts were detected (Figure  A ). Only one significant cluster was detected in eastern France when cattle with viable cysts only were taken into account (Figure  B ).
The data collected for each dog included the following: age, sex, breed, breed type (chondrodystrophic or non-chondrodystrophic), the duration of clinical signs before surgery, the assessment of preoperative neurological status, diagnostic imaging modalities used, affected intervertebral discs, postoperative assessments of the neurological status at 24 h after the surgery, at discharge, and at medium-term follow-up (at least 6 months postoperatively), postoperative complications, and the owners' satisfaction. Dogs having several herniated discs with at least one ventral chronic compression were also included: in those dogs ventral compressions were treated by TLPLC and lateral compressions were treated by another technique like hemilaminectomy. Dogs were excluded from the study if there was a lack of follow-up data.
The Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines were developed to address the lack of reproducibility in biomedical animal studies and improve the communication of research findings. While intended to guide the preparation of peer-reviewed manuscripts, the principles of transparent reporting are also fundamental for in vivo databases. Here, we describe the benefits and challenges of applying the guidelines for the International Mouse Phenotyping Consortium (IMPC), whose goal is to produce and phenotype 20,000 knockout mouse strains in a reproducible manner across ten research centres. In addition to ensuring the transparency and reproducibility of the IMPC, the solutions to the challenges of applying the ARRIVE guidelines in the context of IMPC will provide a resource to help guide similar initiatives in the future.