dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods This retrospective study was approved by the ethics committee CPP Lyon Est IV. The Centre Léon Bérard (CLB) sarcoma database was searched for patients with a diagnosis of SFT. Two hundred and thirty three patients' files were identified between January 1994 and December 2011. The vast majority of these patients were registered in the CLB database for histology review or multidisciplinary meeting discussion but only 66 patients were actually managed at the CLB, of which 30 had advanced disease and are the subject of this report. Data were extracted from individual patients' files and analysed. All cases were reviewed by an expert pathologist in the field of sarcomas (DR). Patients and tumor characteristics were described using the median and range for continuous variables and percentages with 95% Confidence Interval (95% CI) for categorical variables.
Acknowledgments The authors thank  Pr Arnaud Basdevant  for his advice in the manuscript revision and  Dr Florence Marchelli  and  Patricia Ancel  who were involved in data collection and sampling at the  Center for Research on Human Nutrition, Pitie-Salpetriere Hospital, Paris. We are also grateful to  Dr Mary Osborne-Pellegrin  ( INSERM U698 ,  Bichat Hospital, Paris ) for help in editing the manuscript.
Bone Histomorphometry Four-micrometer sections originating from all the regions of the retrieved bone samples (n ϭ 6 patients) were processed for histomorphometrical analysis and observed by two different researchers in a blind manner. Digital images were acquired and captured at ϫ100 magnification with an Olympus light microscope. For each area of interest, the bone volume (BV) was calculated both as a percentage of the total tissue volume (TV) and in m 3 , whereas bone surface/bone volume (BS/BV) was calcu- lated in mm Ϫ1. Marrow star space volume (MSV) was calculated as follows: MSV ϭ (volume of marrow space/volume of trabeculae and marrow) ϫ 100. All analyses and measurements were performed with ImageJ software, version 3.
Statistical Analyses For histomorphometry, the data are expressed as the means Ϯ SD, and statistical analyses were performed with Student's test. A p value less than. 05 was considered to be statistically significant. For SR-HT data, statistical analyses were performed with Sig-maStat 3. 5 software (Systat Software Inc. , Richmond, CA, http:// www. systat. com). Statistical significance of all quantifications was assessed by two-tailed t test. p values were considered significant when Ͻ. 05.
Synchrotron Radiation-Based Holotomography For SR-HT, the volume of interest considered was 895 ϫ 1,016 ϫ 1,376 m 3 , divided into a stack of eight (172-m-thick) voxel data sets in the vertical (z) direction (an example is given in Fig. 3A ). The voxel data sets (32-bit float volumes per sample) were converted into the respective signed 8-bit data sets (gray scale from Ϫ128 to ϩ127), and the distribution of gray values was analyzed with the software package VG Studio MAX 1. 2 (Volume Graphics GmbH, Heidelberg, Germany, http://www. volumegraphics. com). In both the human mandible control and the human in vivo SC-treated mandible biopsies analyzed, the histogram could be formally divided into three sectors: the first (left-most), with an x value of ϽϪ50, represented a fully mineralized phase (i.
However, the stem/progenitor cells residing in the periosteum and endosteum possess a limited regenerative potential  [24]. In contrast, mesenchymal stem cells contained in dental pulp have a high differentiation potential  [6, 25]. Therefore, we sought to study the bone regeneration process in injured human mandibles repaired with autologous DPSC/collagen sponge biocomplex implants [10]. We have reported here the situation in seven patients 3 years after the interventions. After obtaining the initial data revealing that the regenerated bone had an unusual hardness and a nonphysiological architecture for the site, we performed histomorphometric analysis. This demonstrated, in a statistically significant way, that stem cells had regenerated a compact rather than a spongy bone type. At this point we were compelled to find more sophisticated, other than extremely reliable methods to assess our biopsies further.
ACKNOWLEDGMENTS This work, arising from a collaboration between COST NAMABIO partners (F. R. , A. G. , and G. P. ), was supported by  Second University of Naples  Grant  2009-10  (to G. P. ) and by  European Union Grant P. O. N. (European Structural Funds for National Operating Programs)   01_02834 2011/14  (to G. P. and V. T. ) for support with allocation of industrial ID19 Beamtime use at the  ESRF (F). We sincerely thank  Dr. Paul Tafforeau  and  Dr. Elodie Boller  for their help at the  ESRF  during the x-ray holotomography experiments.
Of 1056 participants enrolled at baseline, 842 were dentate, and 626 were alive and attended a follow-up visit (81% of surviving dentate participants). Two hundred six subjects were excluded from the present analysis for antibiotic prophylaxis requirements (n=81), missing baseline cardiovascular data (n=63), logistical reasons (n=47), or no longer being dentate (n=15), a necessary condition for periodontal and microbiological assessments. Thus, we include 420 for analyses of longitudinal change in clinical periodontal status and progression of IMT, representing 79% of dentate subjects not requiring premedication, in accordance with American Heart Association criteria. 15 Among these 420, 364 (87%) also had longitudinal bacteriological data.
Carotid Ultrasound Bilateral carotid arteries were scanned longitudinally in the common carotid artery (CCA), internal carotid artery and bifurcation, as described. 11 The optimal angle of insonation was used to measure the CCA-IMT in the near and far walls extending from 10 mm distal to the flow divider and stopping at 20 mm below the flow divider. In addition, to minimize measurement error, a rigorous follow-up protocol involved (1) identification of internal landmarks, (2) utilization of a carotid mask to maximize superimposable visualizations at both visits, and (3) utilization of the same ultrasound machine at both visits. Carotid IMT measurements were performed off-line using IMAGE-Pro V. 5. 1 (Microsoft) image analysis software, outside of plaque by 1 reader. 11 In accordance with the third Manheim consensus,  19  we selected digital frames corresponding to the minimum observed arterial diameter during the cardiac cycle, which represents diastolic phase.
Statistical Analysis Analyses were performed using SAS 9. 2. Periodontal status was defined on the basis of clinical and bacterial periodontal measures as follows. Clinical periodontal status was defined by either (1) fullmouth mean probing depth (MPD) values or (2) the percentage of measured sites with PD≥3 mm (%PD≥3). These variables were selected a priori on the basis of previous research demonstrating their strong correlation with underlying bacterial profiles  22  and clinical signs of inflammation. 23 e also considered mean attachment loss and the percentage of sites with AL≥5 mm (%AL≥5) to assess the sensitivity of associations to commonly used epidemiological definitions of periodontitis. 24 or each microbial species, bacterial counts were natural log-transformed, averaged within the mouth, and standardized by dividing these values by the natural log-transformed population standard deviation.
Acknowledgments We thank  INVEST staff George Loo ,  Mariana Cukier ,  Yira Flores ,  Publio Silfa ,  Kenia Martinez ,  Shantanu Lal ,  Bernadette Boden-Albala , and  Janet DeRosa  for their devoted patient care;  Miriam Herrera-Abreu ,  Romi Celenti  and  Jun Yang  for the laboratory analysis of the dental plaque samples; and most importantly the participants. Participants were seen at the  Columbia University General Clinical Research Center, NIH  grants  1UL1RR024156  and  UL1 TR000040.
Scoring The examiners were installed in a dark room. Explanations of the cluster analysis determined by De Rouck et al. were provided by a periodontist (AS). The classifications were discussed with a focus on the specificities of each cluster using unambiguous clinical pictures from the paper by De Rouck et al. The clinicians were presented with 159 slides assigned in random order (three clinical slides of each subject: the front view of the occlusion for maxillary and mandible, the maxillary anterior teeth, and the mandibular anterior teeth) on a large screen, with each slide projected for eight seconds. All clinicians were invited to attend a class for an update on gingival biotypes. The clinicians were asked to assign one of the three possible biotypes to each case. A total of 19716 responses were collected; this significant range of data was entered for statistical analysis.
Study Population The study included 43 cases with primary ITAC of the nasal cavity and paranasal sinus, treated in the CENTRE Hospitalier Universitaire de Montpellier between 1986 and 2012. Thirty-eight patients underwent radical surgery, 4 underwent biopsy, and data was unavailable for one patient. Tumor samples were obtained from paraffin-embedded specimens for both immunohistochemical and mutation analyses. Histologic classification was performed according to the World Health Organization guidelines. Histological slides were reviewed by two pathologists blinded to the clinical data. Patient information was obtained from medical records. Records were reviewed for age, sex, race, history of exposure to dust or smoking, site and stage of tumor, type of treatment, and follow-up status.
0 mmol/L MgCl 2 and 0. 25 μmol/L of each forward and reverse primer. The primer sequences are as follows: KRAS-F: 5'-GGCCTGCTGAAAATGACTGAA-3'; KRAS-R: 5'-ATTAGCTGTATCGTCAAGGCACTC-3'; BRAF-F: 5'-ATGAAGACCTCACAGTAAAAAJAGG-3'; BRAF-R: 5'-AGCAGCATCTTAGGGCCAAA-3'. The cycling conditions were identical for all amplifications and were as follows: 95 °C for 5 min, followed by 50 cycles of 95 °C for 15 s, 63 °C for 25 s with an initial 11 touchdown cycles (0. 5 °C/cycle), and 72 °C for 25 s. The melting conditions included one 95 °C cycle for 1 min, one 40 °C cycle for 1 min and one 65 °C cycle for 2 s, followed by a gradual increase from 65 to 95 °C at 0. 1 °C/s. All samples were tested in duplicate. The HRM data were analyzed using Rotor-Gene 6000 software (v. 1. 7; France). For each sample, the normalized melting curves were evaluated, and the samples were compared with the wild-type sample controls in a deduced difference plot.
A list of all the beds was drawn up. A random sample of approximately 25% of the beds was chosen for examination (185 beds). By the day of examination, if there was no hospitalized patient corresponding to a sampled bed, the bed immediately after on the list was chosen instead. The data were collected between March and June 2006. Subjects with aggressive behavior and lack of cooperation were excluded. A total of 161 patients were examined. All the procedures were part of standard cares as patients have regular oral and salivary examinations.
Data analysis The questionnaires were built and filled with EPI-INFO (TM) Version 3. 3. 2. The mean OHI-S was computed and the scores were classified into three levels: Excellent (0); Good (0. 1-1. 2); Fair (1. 3-3. 0); Poor (3. 1-6. 0) [26]. Analysis of variance (ANOVA) was used to test the differences in the mean scores of oral hygiene and DMFT and its components using SPSS for Windows Statistical Software Package Version 17. 0. Chi-square test was used to test the differences between frequencies. Stepwise logistic regression analysis was used to identify DMFT predictors. Predictors' candidates were age, gender, diagnosis of psychiatric disorder, length of hospitalization, saliva flow and degree of disability. The level of significance was set at 0. 05.
1% had been filled, 26. 4% had been lost because of caries (31. 5% lost because of caries or other reasons). Bivariate analysis using Chi-square tests (Table  4 ) showed that DMFT over 16 was associated with age over 45 (p < 0. 0001), length of hospitalization over 5 years (p = 0. 0233), disability (p = 0. 0021) and plaque index over 1 (p = 0. 0111). The subjects were divided into two categories according to the DMFT (DMFT-16): 16 or less (n = 80) Logistic regression models were used to identify factors associated with the DMFT-16. All the variables listed in Table  3  and Table  4  were introduced in the first model in order to control possible confounding effects. In SPSS, the binary logistic regression according to the "forward LR" method kept 2 variables. The logistic regressions analysis showed that age and Degree of disability were significant contributors to the fact of having a high DMFT.
The remaining cells were then pelleted and resuspended in an equal volume of 0. 1 M glycine buffer, pH 2. 8, and rotated continuously at room temperature. Duplicate aliquots were removed at 15, 30 and 60 min and diluted 1:10 in 10 mM Tris-HCL, pH 8. 0, and placed on ice. Once the assay was complete, all aliquots were serially diluted in 10 mM Tris-HCL, pH 8. 0, and plated on BHI agar followed by a 48 h incubation at 37uC in a 5% CO 2 atmosphere. Percent survival for each time point was determined by dividing the CFUs of each time point by the initial CFUs multiplied by 100. Data represents the average of two separate experiments performed in duplicate.
After injection, larvae were kept at 37uC under atmospheric conditions and survival was recorded at selected intervals. Kaplan-Meier killing curves were plotted and estimation of differences in survival were compared using the logrank test. A P value # 0. 05 was considered significant. All data was analyzed with GraphPad Prism 5. 0 software. In addition to cnm+ and cnmcontrol strains (OMZ175 and UA159, respectively), a cnm-inactivated mutant strain, OMZ175-cnm, was also included to serve as a control to monitor Cnm dependent larvae death  [10].
mutans, strains that contained the cnaB/cbpB/cnm collagen binding protein genes (Smu77/V1996, Smu81, Smu86 and Smu109/OMZ175) or the genes for the T7SS (Smu26, Smu44, Smu80 and Smu102) were assayed for virulence in the G. mellonella model (Figure  6 ). For comparison purposes, we also included the type strain UA159 (lacking both cnaB-cbpA-cnm and T7SS) and a cnm mutant of OMZ175 (OMZDcnm). As previously seen  [10] , OMZ175 was significantly more virulent than UA159 and inactivation of cnm strongly attenuated the virulence of OMZ175 (data not shown). Along these lines, strains Smu77, Smu81 and Smu86 expressing cnaB-cbpA-cnm were significantly more virulent than UA159 (Figure  6A ). Strains Smu77/V1996 and Smu86 (serotypes c and e, respectively) were as virulent as Smu109 (OMZ175), a well-characterized serotype f strain  [9, [86] [87] [88] [89] , whereas Smu81 killed G.
The slices were stained with a Modified Goldner's Masson Trichrome solution and observed under an optical microscope (DMRB microscope, Leica, Wetzlar, Germany). Since contact between the devices and dental germs or roots is considered to be a cause of failure, in this orthodontic use, the relationship between the screws and the dental structures was measured using Morphometrie10H software, under a 4-fold magnification lens. The ratio between the contact length between the screws and the dental root related to the total length of the screws was calculated. Similarly, measurement of the ''bone-to-implant contact'' length was assessed, since this is considered to be a quantitative measure for the osseointegration of the device. The ''bone-to-implant contact'' rate was calculated as follows: screws surface length in contact with bone tissue / (total screws surface length -screws surface length in contact with dental germ or root) (Fig.
1 H-MAS NMR spectroscopy investigation In order to probe hydrogen environments in such organoapatite hybrids, 1 H MAS NMR data were recorded. The results have been added in Table  2. Fig. 4  reports the 1 H NMR spectra obtained, pointing out two intense broad peaks centered on -0. 05 and 6. 81 ppm, respectively. The NMR peak near -0. 05 ppm can be assigned to apatitic OH -ions from the Hap phase  [28] ; and the peak observed around 6. 81 ppm may presumably be assigned to surface-adsorbed water on apatite crystals, as was previously found for hydroxyapatite ceramics with colloidal-like dimensions  [29]. It is clear from Table  2  that the chemical shifts and line widths (FWHM) of the proton NMR spectra vary as we compare the profiles for different amounts of Na2ATP. The line widths (FWHM) for apatitic OH-ions increase from 0.
Clinical investigations PWV was measured at a constant room temperature of 19-218C and calculated using Complior (Colson, Garges les Genosse, France) as previously described  [18]. Briefly, two pressure waves were recorded transcutaneously at the base of the neck for the right common carotid artery and over the right femoral artery. PWV was determined as the foot-to-foot velocity. Pulse transit time was determined as the average of 10 consecutive beats. The distance travelled by the pulse wave was measured over the body surface as the distance between the two recording sites. Ultrasound examinations were performed by two trained ultrasonographers using the Aloka SSD-650 (Aloka, Zug, Switzerland), with a transducer frequency of 7. 5 MHz. Acquisition, processing and storage of B-mode images were computer-assisted using the M'ATHS software (Metris, Paris, France).
ACKNOWLEDGEMENTS This work was supported by the  French-Swedish Foundation ; the  Swedish Research Council  (grant number  2011-2988 ); the  Swedish-Heart and Lung Foundation  (grants number 20120474 and 20120827); la  Mairie de Paris  ( research programme 'Research in Paris 2009/2010 '); the  Fondation pour la Recherche Medicale  (grant number  FRM DCV-20070409250 ), the  Caisse Nationale d'Assurance Maladie ; the  Agence Nationale de la Recherche  (grant number  ANR 09-GENO-010-01 ); and the  Plan Pluri-Formation (French Ministry of Research).
Gene expression was quantified by real-time PCR by using the LightCycler Fast Start DNA Master (Roche) with 0. 2 μL of cDNA corresponding to 2 ng of total RNA in a 20-μL final volume, 2. 25 mM MgCl 2 , and 0. 5 μM of each primer. PCR was performed for 45 cycles at 95°C for 15 seconds, at the specific annealing temperature for 25 seconds, and at 72°C for 30 seconds. Amplification specificity was checked by using a melting curve. Specific gene primers for each factor of interest were designed for real-time PCR analysis by using Primer3 and Ensembl software (Table  3 ). Results were analyzed with LightCycler software version 3. 5 (Roche) by using the second derivative maximum method to set the threshold cycle (C T ). Quantitative analysis was carried out by using standard curves and normalization with the GeNorrm software and methodology  [35] , with four reference genes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin, β-2-microglobulin, and hypoxanthine phosphoribosyltransferase 1 (HPRT).
Endogenous peroxidases were blocked by using 3% H 2 O 2 for 5 minutes. Non-specific background was blocked by using TBS1X containing 10% FBS for 45 minutes. Sections were incubated overnight at 4°C with monoclonal mouse anti-human type I collagen (clone I-8H5, 1 μg/mL; Acris Antibodies, San Diego, CA, USA). The Envision ™ FLEX + (Dako, Glostrup, Denmark) with Dako autostainer instrument was then used for staining analysis. Bone formation area was quantified by using stained histological sections. Images were analyzed with Photoshop and ImageJ software. The ratio of all bone formation area on total biomaterial area was measured on three to five sections at different levels of the biomaterial (near the surface and in the center of biomaterial).
Statistical analysis For cell growth analysis, all measurements were performed on three different sources of MSCs and three different batches of PGCAP. In vivo experiments were performed in triplicate. All data are expressed as mean ± SEM. Statistical comparisons were made by using analysis of variance (ANOVA) in which a P value of less than 0. 05 was considered significant. Differences between groups or individual conditions were evaluated by using Student Newman-Keuls test.
69-fold), PL (3. 9-fold), TC (2. 19-fold), and FCS (3. 8-fold). In contrast, IGF-1 concentration was slightly higher in PPP and PL than in PGCAP. Few concentrations of IL-1α and IL-1β were detected in PGCAP, although IL-1β was slightly higher in PGCAP than in PPP (Table  4 ). We further showed that fibrinogen was highly concentrated in PGCAP as compared with PPP and was similar to TC (data not shown). Together, these results suggest that the cryoprecipitation process allows concentrating plasma and platelet-related molecules such as fibrinogen, growth factors, and SDF-1α. The influence of PGCAP on MSC phenotype was investigated at each culture passage (from P0 to P3) by flow cytometry. We showed that MSC phenotypic profile was unchanged regardless of the culture condition since more than 98% of expanded MSCs were positive for CD90, CD105, and CD73 and were negative for CD45 (data not shown).
Physical characteristics and biocompatibility of biomaterials Two different biomaterials (Table  1 ) and three different compositions (Table  2 ) of biomaterials were analyzed by scanning electron microscopy. Pictures shown in Figure  3a  illustrate data obtained from Ceraver. To evaluate the biocompatibility of the various biomaterials selected, MSCs were seeded on each biomaterial and cultured for further analysis by scanning electron microscopy and for proliferation evaluation. As shown in Figure  3a , the pores of each type of biomaterial were colonized by MSCs. This suggests that the chemical composition or structure of biomaterials did not interfere with the cell colonization. A kinetic study of MSC proliferation was performed by using the different biomaterials (Figure  3b ). At days 7 and 14 of culture, BM F allowed significantly higher MSC proliferation than the other biomaterials tested (Figure  3b ).
Ectopic implantation of MSC-loaded biomaterials embedded in PGCAP promotes bone formation in nude mice Bone formation ability of MSC-loaded biomaterials embedded in PGCAP was investigated after ectopic implantation in a nude mouse model. BM A and BM F were tested in combination with ni-MSCs versus i-MSCs, in the presence or absence of PGCAP. Four weeks after implantation, biomaterials were analyzed ex vivo by confocal microscopy (Figure  6 ). When unloaded biomaterials were implanted, we observed mouse cell invasion inside both BM A and BM F , suggesting that biomaterial implantation induced host cell recruitment. We then tested biomaterials in the presence of GFP + ni-MSCs or i-MSCs after 21-day culture in the presence or absence of PGCAP. We first demonstrated that MSCs remain GFP + after 21-day culture (data not shown).
When these MSCloaded biomaterials were implanted in mice, GFP + /CD90 + cells were observed inside the pores of all types of biomaterials and inside PGCAP (Figure  6 ). These results suggest that, after 4-week implantation, MSCs survived in the host independently of the various tested conditions. We then performed histological analysis on decalcified biomaterials before and after 4-week implantation. We showed that fibroblast-like cells were homogenously detected in PGCAP and BM A (Figure  7 ) or BM F (data not shown) pores just before implantation (see magnified views of the boxed areas). After the implantation period (Figure  7 ), vessels were observed in all biomaterials, suggesting that vascularization induction was not dependent on the presence of PGCAP and osteogenic induction. We observed that, after 4-week implantation, the biomaterial exhibits large bone-like tissue zones with some of the characteristics of woven bone (in pores and PGCAP) when it was embedded in PGCAP and loaded with ni-MSCs or i-MSCs (Figure  7 ).