dataesr/scientific-paragraphs-categorization huggingface dataset:
The twelve JCC T spectra were imported into the MALDI BioTyper software (version 2. 0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 3,769 bacteria, including 228 spectra from 96 Clostridium species. The method of identification included the m/z from 3,000 to 15,000 Da. For every spectrum, a maximum of 100 peaks were compared with spectra in database. The resulting score enabled the identification of tested species, or not: a score ≥ 2 with a validly published species enabled identification at the species level, a score ≥ 1. 7 but < 2 enabled identification at the genus level, and a score < 1. 7 did not enable any identification. No significant MALDI-TOF score was obtained for strain JCC T against the Bruker database, suggesting that our isolate was not a member of a known species.
Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to members of the genus Clostridium, and is part of a study of the human digestive flora aiming at isolating all bacterial species in human feces  [1]. It was the 101 st genome of a Clostridium species and the first genome of C. saudii sp. nov. The GenBank accession number is HG726039 and consists of 104 contigs. Table  2  shows the project information and its association with MIGS version 2. 0 compliance  [54]. Growth conditions and DNA isolation C. saudii sp. nov. , strain JCC T (=CSUR P697 = DSM 27835) was grown anaerobically on 5% sheep bloodenriched Columbia agar (BioMerieux) at 37°C. Bacteria grown on three Petri dishes were harvested and resuspended in 4×100 μL of TE buffer.
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [55]  with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank  [56]  and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScanSE  [57]  and RNAmmer  [58]  tools, respectively. Lipoprotein signal peptides and numbers of transmembrane helices were predicted using SignalP  [59]  and TMHMM  [60] , respectively. Mobile genetic elements were predicted using PHAST  [61]  and RAST  [62]. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an Evalue of 1e-05.
Asaccharolytic. C. saudii is susceptible to imipenem, trimethoprim-sulfamethoxazole, metronidazole, doxycycline, rifampicin, vancomycin and amoxicillinclavulanate and resistant to amoxicillin, ciprofloxacine, erythromycin and gentamicin. The G + C content of the genome is 28%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers HG726039 and CBYM00 000000, respectively. The type strain is JCC T (=CSUR P697 = DSM 27835).
Follow-Up and Assessment of Outcome The Marseille Mediterranean University as well as the Direction and Ethics Committee of Timone University Hospital (CPPRB1) approved our study. Follow-up information was obtained in two ways: direct clinical evaluation or telephone interview by the first author (C. T. ), who was not involved in the selection of cases for treatment. We evaluated the probability of initial pain cessation, the onset of sensory disturbance and the rate of recurrence. We analyzed data regarding latency periods until becoming pain free, having a recurrence or developing a sensory disturbance, paying attention to date every event, the use of medication and the need for further surgical procedures so as to accurately assess all the available information. Pain was scored using 3 different scales: the Barrow Neurological Institute (BNI) pain scale (class I: 'no trigeminal pain, no medication'; class II: 'occasional pain, not requiring medication'; class IIIa: 'no pain, continued medication'; class IIIb: 'controlled with medication'; class IV: 'some pain, not adequately controlled with medication'; class V: 'severe pain, no pain relief'), the Burchiel scale (class I: 'pain free, no medication'; class II: 'pain free, on medication'; class IIIa: 'pain improved, no medication'; class IIIb: 'pain improved, on medication'; class IV: 'pain not improved') and the Regis scale (class I: 'no trigeminal pain, no medication'; class II: 'no pain, with medication'; class III: 'pain frequency reduction >90%'; class IV: 'pain frequency reduction 50-90%'; class V: 'no pain reduction'; class VI: 'pain worsening')  [45] [46] [47].
Statistical Analysis Data were recorded using Microsoft Excel 2000. All statistical analyses were performed using R version 2. 12. 0 (R Foundation for Statistical Computing, Vienna, Austria). The R survival package was used for survival analysis. First, a descriptive analysis of the recorded data was carried out among the MBA population. For the evaluation of outcomes such as initial pain cessation, hypoesthesia and recurrence, the time to the event was estimated by using the Kaplan-Meier method. A bivariate analysis was then performed to identify predictive factors among the collected variables. For qualitative variables, Kaplan-Meier curves were used to graphically represent survival among the different groups, and they were compared using the univariate log rank test. For all variables, the effects were estimated and tested by fitting univariate Cox proportional hazards regression models.
Data collection Socioeconomic data (i. e. , age, sex, living conditions, level of education), medical data, and dietary information (e. g. , ability to shop and prepare food, meal consumption, and avoidance of certain solid foods) of the individuals were collected using a general questionnaire that controlled for possible confounding factors [e. g. , socioeconomic factors, neurosensory disorders diagnosed by a medical doctor, and chronic diseases such as cardiac failure, respiratory failure, diabetes, rheumatoid arthritis (listed in the patient's medical file)]. Weight (measured by a calibrated mechanical scale) and height were assessed to calculate the body mass index (BMI). Anthropometric measurements were complemented by the circumferences of the arm and calf. The nutritional status of elderly individuals was assessed using the Mini-Nutritional Assessment (MNA) questionnaire in its complete validated form.
Statistical analysis Data were collected and analyzed using SPSS version 13. 0 for Windows (SPSS Inc. , Chicago, IL, USA). Bivariate analyses were used to measure the association of nutritional status (i. e. , the dependent variable) with socioeconomic variables, feeding characteristics, and oral status. The Chi-square test was used to test the association for categorical variables, whereas the t test was used for two independent quantitative variables. A p of 0. 05 indicated statistical significance. A multiple logistic regression model was constructed to evaluate the relationship between nutritional status and oral health while taking into account the confounding variables of socioeconomic factors, neurosensory disorders, and chronic diseases (p 0. 05). The adjusted odds ratio (OR) was calculated to measure the strength of the association between different variables and the dependent variable (adjustments were performed for age, sex, educational level, and pre-existing chronic diseases).
Statistical Analysis Data analysis was performed using the Statistical Package for the Social Sciences version 17. 0 (SPSS Inc. , Chicago, Ill. , USA). The statistical associations between the demographic characteristics of the dentists and their restorative decisions for approximal and occlusal lesions were assessed using Pearson's χ 2 test. Multiple correspondence analysis (MCA) was conducted to explore the strengths and structures of the associations. p < 0. 05 was considered statistically significant.
Selection of meta-analyses, trials and outcomes To identify eligible studies, we searched MEDLINE and EMBASE. Search equations for each database included the free-text word "split mouth" combined with a filter designed to identify systematic reviews (see Additional file 1)  [10]. Second, we performed a full-text search of the Cochrane Database of Systematic Reviews (CDSR) through www. thecochranelibrary. com and archie. cochrane. org. We also searched the Database of Abstracts of Reviews (DARE). Third, we searched SCIRUS, a science-specific search engine covering full-text articles. The last search was conducted in February 2013, with no restriction on date or language. Two authors independently and in duplicate screened the titles and abstracts of records retrieved by the search, and then screened the selected full-text reports.
Data extraction Two authors extracted the data in duplicate and independently, with discrepancies resolved by discussion. For each systematic review, we recorded the first author, publication year and studied population. For each metaanalysis, we recorded the experimental intervention, the comparator, the outcome and the number of split-mouth and parallel-arm RCTs. We assessed the methods used by the authors for incorporating split-mouth RCTs into meta-analyses: we assessed the presence of subgroup analyses (ie, splitmouth RCTs and parallel-arm RCTs analyzed separately) and/or whether one quantitative synthesis combined split-mouth and parallel-arm RCTs; in this case, we assessed whether the techniques described by Elbourne 2002 or Lesaffre 2009 were used  [9, 12] ; moreover, we assessed whether the authors calculated the standard error of the intervention effect estimate in split-mouth RCTs using appropriate methods (ie, statistical approaches taking into account the paired nature of data; eg, the techniques described by Follmann)  [13].
Our findings are based on recently published systematic reviews covering a fair range of conditions and interventions in oral healthcare. Consequently, our results are more generalizable than could be obtained with focus on a particular topic. Our study has several limitations. We selected a relatively small number of systematic reviews for our meta-epidemiological study. It is difficult to identify reviews with both parallel-arm and split-mouth trials with usual strategies and we acknowledge that unidentified reviews may exist. However, we systematically searched for both Cochrane and non-Cochrane reviews, including a search of full-text articles indexed in the Cochrane library and in the Scirus database. Unfortunately, the latter service is no longer running. We acknowledge that searching additional regional databases (e.
g. , LILACS, PASCAL) and full-text databases (e. g. , HighWire Press, Google Scholar) may be very useful to identify potentially eligible systematic reviews. Eligible reviews may be missing because of reporting bias (including location bias and language bias). However, reporting bias is usually driven by the magnitude/direction and statistical significance of treatment effects. We see no reason for reviews to be missing because of the difference in treatment effect estimates between split-mouth and parallel-arm RCTs. As a consequence, the impact of missing reviews is unpredictable and probably limited on our meta-epidemiological study. On top of the relatively small number of selected reviews, the number of split-mouth and parallel-arm RCTs in each meta-analysis was small. Meta-analyses typically include a limited number of trials: the median number of trials in a large sample of Cochrane meta-analyses was 3  [45].
Acknowledgements We would like to thank all participating patients and families who were involved in this study, the  Reference Center of Rare Oral disease of Paris and Strasbourg  and the national rare disease project. Written informed consent was obtained from all patients (or guardians) participating in the study. The authors would like to acknowledge the technical help of  Audrey Asselin ,  Pr Aurore Coulomb ,  Pr Matthieu Schmittbuhl  and  Megana Prasad  for critical reading of the manuscript.
Grant from other authors This work (MQ, MDM, AB) was supported by a grant from the  French University Paris Descartes  5 (MQ) and by  INSERM  (MQ, AB). This work (AB) was supported by  IDEX (Once Upon A Tooth). This study was supported by  Capes-Coffecub, Brazil-France  (ACA, PMY, MQ, MDM, AB). This work (ABZ) was supported by grants from the  University of Strasbourg , the  French Ministry of Health (National Program for Clinical Research , PHRC 2005 N°4266 Amelogenesis imperfecta; ClinicalTrials. govNCT01746121), the  Hôpitaux Universitaires de Strasbourg (API ,  2009-2012 , "Development of the oral cavity: from gene to clinical phenotype in Human"),  Institut Français pour la Recherche Odontologique (IFRO) , and the  EU-funded project (ERDF)   A27  " Oro-dental manifestations of rare diseases ", an  RMT-TMO Offensive Sciences initiative, INTERREG IV Upper Rhine program.
Preoperative Planning of the Tumor Resections. The planning of the resection strategy, as described in  [13] , is based on the MRI and CT images. If these modalities have not been acquired during the diagnosis, a specific exam should be prescribed. Any scanning sequence of the acquired MRI can be used to perform the planning. The CT being crucial for PSI accuracy, its spatial resolution must be 1 mm or below in the  direction. Tumor delineation is made by the surgeon with the aid of a radiologist on the 2D MRI slices using a segmentation software (ITK-Snap, version 2. 0. 0, Philadelphia)  [38]. The set of MRI images was reconstructed in 3D and brought into the coordinate system of the CT images using a homemade multimodality registration algorithm. Then, the 3D model of the tumor volume was registered with the 3D bony structure extracted from the CT images.
The 3D model of the bony structure with the registered tumor volume was loaded into a visualization and computing software (Paraview, version 3. 14. 1, New York). This software enabled the surgeon to position target planes close to the boundary of the tumor (from 1 up to 6 planes; Figure  1 ). For each patient, the resection strategy consisted in several target planes defining the desired bone-cutting with a safe margin defined by the surgeon (namely, 10 to 15 mm). The safe margins have been decreased to 3 mm according to the possibility of preserving anatomic structures and the effectiveness of adjuvant therapy. For instance, for patient number 9, an unusual 3 mm safe margin was defined in order to preserve the sacroiliac joint. Moreover, sometimes, no safe margin can be easily defined. For example, for patient number 6, the tumor was located in the proximal femur with intra-articular extension, and the resection planning consisted in a 3-plane bonecutting around the acetabulum, free of tumor, to achieve an extra-articular resection of the hip.
Patient-Specific Instruments. Patient-specific instruments (PSI) were designed using computer-aided design (CAD) software (Blender version 2. 65) according to the desired resection strategy. PSI were designed to have bonespecific contact surfaces to fit into unique position on the bony structure of the patient. These contact surfaces were defined by both surgeon and engineer accounting for surgical approach and bone exposure (described below). PSI were equipped with flat surfaces to indicate the target planes and cylindrical guides for 2 mm diameter Kirschner   wires to be pinned on the bony structure (Figure  2 (b)). In addition, PSI provided calibration marks that provided a control over the cutting depth to prevent a soft tissue tear by the saw. The marks represented the distance along the associated direction line measured between the outer edge of the PSI and the deepest bone structure to be cut.
L was defined as the maximum distance (mm) between the cut plane and the target plane. The evaluation parameters SM and L have been already validated for use in bone tumor surgery in a previous experimental study  [37]. CT-scans of the patients have been acquired postoperatively. For each CT-scan, the bone surfaces were extracted using ITK-Snap segmentation software. Then, each postoperative 3D model of the patient was loaded in Paraview visualization software and registered manually with the corresponding preoperative 3D model and planning (Figure  4 ). Accurate registration between pre-and postoperative 3D models was validated through visual inspection of the data. One operator measured the parameters SM and L using Paraview visualization software. The operator measured SM by defining the closest point of each cut plane from the boundary of the tumor.
Inclusion criteria and data collection We included, in this cohort study with prospective data collection, consecutive patients admitted to the stomatological and maxillo-facial emergency unit (EU) of the Lille teaching hospital for facial or cervico-facial cellulitis of dental origin, between April 30 and October 31, 2006. We excluded patients for whom anti-inflammatory treatment prior to EU admission could not be documented. The diagnosis of facial or cervico-facial cellulitis of dental origin was made on clinical and radiological evidence (complete maxillo-facial examination with a panoramic dental radiography) for all patients included. A cervicofacial CT scan with injection of a contrast medium was used if necessary, when there were clinical signs of cervical extension. The main endpoint criterion was the severity of dental cellulitis.
The clinical data was collected prospectively by physicians of the surgical team at consultation in the emergency unit. The pharmacology team checked medical treatments given before hospital admission, during a systematic control consultation in the patient's health record. The following parameters were documented for each included patient: terrain: age, sex, tobacco abuse, alcohol abuse, dental status (considered as good if the patient presented with less than 2 caries), immunodepression or seropositivity for HIV; functional signs before hospitalization: dental pain, swelling, fever, trismus, skin rash, fistulization, dyspnea, dysphagia; characteristic clinical signs of infection: clinical signs, dental portal of entry, localization, extension; the drug treatment received before hospitalization: antalgics, antibiotics, mouthwash, anti-inflammatory drugs (glucocorticosteroids, aspirin at anti-inflammatory dosage, NSAID); the type of management: exclusively medical treatment, surgical treatment, hyperbaric oxygen therapy; the duration of hospitalization.
Acknowledgments  Dr. C. Denglehem ,  Dr. T. Wojcik ,  Dr. C. Tison ,  Dr. J-P. Dujoncquoy ,  Dr. A. Genay ,  Dr. S. Abida ,  Dr. A. Zakhar ,  Dr. O. Abel Wahab ,  Dr. D. Boudana ,  Dr. A. Rougeot , for including patients when on call.
4 ), as well as the dynamics in spatial distribution of mitoses/ apoptoses,  24, 26, 51, 52, 55, 56, [59] [60] [61] [62] [63]  or the exact location of expression domains of signalling molecules in the developing tissues. 22, 58, 59, 64 6] [67]  (For the outcome of 3D methods at later stages of odontogenesis, see the ref. 54 ) Here, data provided by computer aided 3D analyses of the development of the dentition will be reviewed with the aim of updating classical knowledge on early odontogenesis in laboratory mice and humans. Existence of rudimentary tooth primordia will be considered, including their developmental, evolutionary, and pathological aspects. Emphasis will be placed on morphological aspects of early development of the dentition, since the cellular and molecular aspects of odontogenesis are reviewed in other parts of this special issue.
49 ). However, this odontogenic potential of the oral epithelium might be achieved, from the ectomesenchymal cells via migrating neural crest. 98 Tooth development is initiated at specific positions, and the types of developing teeth are determined. 0] [101]  Since a rudimentary anlage of the dentition is also present in the prospective mouse diastema, tooth development has to also be initiated there, before it becomes arrested (Figs. 2e  and 6 ). It is possible that some published data on the initiation of tooth development may not concern the molar but rudimentary tooth primordia in the diastema (yellow and green segments on Fig. 6d ). During further tooth development, morphogenesis and histogenesis progress in parallel. All morphogenetic mechanisms are involveddifferential mitotic activities, apoptosis, cell adhesion and cell migration (segregation), regulated in time and space.
The intraindividual reproducibility of CAL and PPD measurements was very good, with a Cohen kappa equal to 0. 87 and 0. 90, respectively. After written consent from all the subjects (groups 1 and 2) to use their blood samples and undergo clinical oral examinations, their FA were measured in serum by gas chromatography and expressed in grams per litre. This noninterventional study did not require approval by an ethics committee, since the blood samples (5 mL) were drawn from a database of patients consulting check-ups before oral surgery under general anaesthesia, or for regular check-ups in the department of preventive medicine. Blood samples were drawn after an overnight fast from the antecubital vein in nonheparinised test tubes and centrifuged at 15006 g for 30 min at 48 ∘ C. Triglycerides, cholesterol esters, and phospholipids were isolated by thin-layer chromatography.
Methods The work was approved by the Institutional review board of the Rizzoli Institute. We searched the database at our institution for all cases of chordoma diagnosed prior to 2008; after 2008 BNCT was a well-known entity to us and was considered as a separate diagnosis when appropriate. One hundred seventy-four chordomas were found. Of these, 169 had a soft-tissue mass. Five were limited to bone, one of which was a recurrent chordoma sent from an outside institution; detailed information regarding the original lesion was not available. The remaining four cases were re-evaluated in detail, including review of the charts, imaging, and pathology. As all cases were originally diagnosed as chordoma, each underwent vertebrectomy and the entire vertebra had been available for study. Many patients at this institution come by referral, retaining their original films and all but one of these patients were diagnosed before digital imaging was adopted; as a result, not all imaging performed was presently available.
Fragmentation occurred in the linear ion trap analyzer with collision energy of 35. All measurements in the Orbitrap analyzer were performed with on-the-fly internal recalibration (lock mass) at m/z 445. 12002 (polydimethylcyclosiloxane). Raw data files were then processed using Proteome Discoverer 1. 3 software (Thermo Scientific). Peak lists were searched using the MASCOT search engine (Matrix Science) against the P. aeruginosa PA01 database (http://www. pseudomonas. com) [21]. Database searches were performed with the following parameters: 2 missed cleavage sites allowed; variable modifications: carbamidomethylation of cystein, and oxidation of methionine. The parent ion and daughter ion tolerances were 10 ppm and 0. 5 Da, respectively. Subcellular localizations were predicted by PSORTb V3.
The solution was subjected to sonication for 1 h to obtain stable and homogeneous solution. Samples were infused at 10 mL/min flow rate in negative ionization mode. Spectra were acquired at 1000 amu. sec 21 over the 50-1700 m/z range. Phospholipid spectra were analysed via a home-made python script under the scientific data analysis software SciDaVis (http:// scidavis. sourceforge. net/). Three IM enriched samples lipid extracts and two OM enriched samples lipid extracts were used for each culture condition. For each extracts, three spectra were analysed and all these results were combined. The mean value were calculated and the results are presented with error bars corresponding to a 95% confidence interval. Comparisons with the 3 biofilm growth conditions were analysed using one-way analysis of variance (ANOVA).