dataesr/scientific-paragraphs-categorization huggingface dataset:
Reverse Transcription-Polymerase Chain Reaction RNA extraction and reverse transcription were performed from Pam2CSK4-stimulated and control odontoblast-like cells and from healthy and inflamed dental pulp samples as described  (Keller et al. , 2010; Farges et al. , 2011). Real-time polymerase chain reaction (PCR) was performed in a CFX96 Real-Time PCR Detection System with the Fast Start Master SYBR Green I kit (Bio-Rad Laboratories, Hercules, CA, USA) according to the manufacturer's specifications. The cyclophilin A housekeeping gene (PPIA) was used for sample normalization. Gene-specific primer sequences for NOS1, NOS2, NOS3, and PPIA are listed in Table  1. Annealing temperature was 65 • C for all primer pairs. All runs were performed in duplicate. For each target gene, relative expression was determined after normalization using the Bio-Rad CFX Manager software.
Data indicated that the predominant tissue processes, pathways, and molecular interactive networks detected were proinflammatory in nature, while there was minimal evidence of repair-associated molecular events  [11]  (Figure  3 ). Indeed, increased expression of many well-characterised proinflammatory mediators was detected while further datamining enabled us to identify expression changes in several molecules previously not associated with dental tissue disease. We subsequently speculated that underlying molecular repair-related responses may be occurring and, therefore, further bioinformatically interrogated our datasets and identified the candidate repair-related molecule, adrenomedullin (ADM). This pleiotropic cytokine was upregulated during dental disease and is reported to have antibacterial and immunomodulatory properties, as well as being a known molecular mediator of angiogenic and mineralized tissue reparative processes.
Conclusion We are now developing a better and more complete understanding of the molecular and cellular events which occur   showing the key functions associated with the 16 and 3 molecular networks identified as being significantly activated (≥ 6 focus genes) in carious and healthy pulpal tissue, respectively. Shading of boxes indicates the networks which associated with the function and hence supported its inclusion as being active. Analysis was performed using the Ingenuity Pathways Analysis (IPA) software (http://www. ingenuity. com/products/ipa) on the high-throughput datasets reported in McLachlan et al. [11]. Sixteen and three functional categories were identified as being activated in carious diseased and healthy pulpal tissues, respectively. Carious diseased pulp tissue clearly demonstrated increased molecular network and functional activity compared with healthy pulpal tissue.
Asterisks ( * ) in (a) indicate functions which are associated with immune system cells (as identified by IPA); notably some evidence of hard tissue repair function was also evident (#). Ontological functions identified in (b) likely associate with pulp tissue homeostatic processes. Image (c) shows an example network (network 1 from the carious pulp tissue dataset) which also shows the subcellular localisation of the molecules that were identified as differentially expressed. The activation of this network via intracellular signalling cascades results in the elaboration of key inflammatory-associated chemokines, such as CXCL8 (IL-8) and CCL2, and the matrix metalloproteinases (MMPs) 1 and 9. in the dentin-pulp complex during inflammation and repair following carious disease. While disinfection of the dental tissue is clearly imperative for the health of the tooth, the subsequent interaction between dental tissue defence and repair is complex and the fine-tuning of the regulation of these processes is important for ensuring which response predominates when vital pulp tissue can be clinically retained or regenerated.
Asterisks ( * ) in (a) indicate functions which are associated with immune system cells (as identified by IPA); notably some evidence of hard tissue repair function was also evident (#). Ontological functions identified in (b) likely associate with pulp tissue homeostatic processes. Image (c) shows an example network (network 1 from the carious pulp tissue dataset) which also shows the subcellular localisation of the molecules that were identified as differentially expressed. The activation of this network via intracellular signalling cascades results in the elaboration of key inflammatory-associated chemokines, such as CXCL8 (IL-8) and CCL2, and the matrix metalloproteinases (MMPs) 1 and 9.
Introduction: To evaluate the accuracy of CAD/CAM generated splints in orthognathic surgery by comparing planned versus actual post-operative 3D images. Methods: Specific planning software (SimPlant ® OMS Standalone 14. 0) was used to perform a 3D virtual Le Fort I osteotomy in 10 fresh human cadaver heads. Stereolithographic splints were then generated and used during the surgical procedure to reposition the maxilla according to the planned position. Pre-operative planned and postoperative 3D CT scan images were fused and imported to dedicated software (MATLAB ®) 7. 11. ) for calculating the translational and rotational (pitch, roll and yaw) differences between the two 3D images. Geometrical accuracy was estimated using the Root Mean Square Deviations (RMSD) and lower and upper limits of accuracy were computed using the Bland & Altman method, with 95 % confidence intervals around the limits.
Such comparisons only provide a global approximation of the whole process and do not allow differentiating the errors due to patient registration, model surgery, surgical technique, and method of comparison itself  [1] [2] [3] [4] [5]. New methods of 3D virtual planning integrating fully digitized clinical and radiological data are now fully efficient and surgical wafers can also be generated from these data, without the need for additional human interference  [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16]. These methods presumably offer the highest accuracy of treatment planning, but the overall accuracy of the planning and of its surgical reproducibility has not yet been quantified. The aim of the present cadaveric study was to evaluate the accuracy of CAD/CAM generated splints in orthognathic surgery.
Pre-operative computational image analysis CT scan images in DICOM (Digital Imaging and Communications in Medicine) format were processed using SimPlant OMS Standalone 14. 0 software (SIMPLANT Business Unit, Technologielaan 15, 3001 Leuven, Belgium www. materialisedental. com). The dental casts obtained from alginate dental impressions were scanned using a high-resolution 3D optical scanner (Dental 3D Scanner D-200™, http://www. 3shape. com). The dental scan images were then imported to the software and superimposed on the CT scan images by means of a semi-automated 3D surface registration (Iterative Closest Point registration). In two partially edentulous cases, the missing teeth were replaced by a prosthesis fixed with bone screws to obtain a stable occlusal platform.
Post-operative computational image analysis Post-operative CT-scans with the intermediate splint in place were taken using the pre-operative protocol. Planned pre-and post-operative 3D CT scan images were fused by means of an automated surface matching method by using the skull, which was not repositioned by the surgery, as reference for registration (Fig. 5 ). The differences between the two images were calculated by using MATLAB® 7. 11 (R2010b) software (MathWorks 92190 Meudon France http://fr. mathworks. com/products/ matlab/ ) as follows: 1) The three following 3D anatomical regions were defined for the final evaluation: a) skull, b) maxilla, and c) mandible. 2) The position of three fixed points (screws) within the 3D-coordinate system of the CT scan was determined on the planned pre-(Pt plan1 Pt plan2 Pt plan3 ) *1 and post-operative (Pt ppop1 Pt ppop2 Pt ppop3 ) *2 3D CT scan images.
Objectives: Sialolithiasis, or salivary stones, is not a rare disease of the major salivary glands. However, the aetiology and incidence remain largely unknown. Since sialoliths are comprised mainly of calcium phosphate salts, we hypothesise that drinking water calcium levels and other elements in drinking water could play a role in sialolithiasis. Owing to substantial intermunicipality differences in drinking water composition, Denmark constitutes a unique environment for testing such relations. Design: An epidemiological study based on patient data extracted from the National Patient Registry and drinking water data from the Geological Survey of Denmark and Greenland retrieved as weighted data on all major drinking water constituents for each of the 3364 waterworks in Denmark. All patient cases with International Statistical Classification of Diseases 10th Revision (ICD-10) codes for sialolithiasis registered between the years 2000 and 2010 were included in the study (n=3014) and related to the drinking water composition on a municipality level (n=98).
Strengths and limitations of this study ▪ All patient cases in Denmark with International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10) codes for sialolithiasis registered between the years 2000 and 2010 were included (n=3014) and related to the drinking water composition on a municipality level (n=98). ▪ The drinking water in Denmark displays substantial intermunicipality compositional differences in a country covering only a limited area of land and with a relatively genetically homogeneous population. ▪ The validity of the diagnoses was tested in a subsample (n=200) and showed no differences between low-incidence and high-incidence regions, indicating that systematic misclassification was not present in the data analysed. ▪ On a global scale, all information about the possible medical effects of changes to drinking water, including desalination and other modifying measures, will be valuable for high-level decision-making.
MATERIALS AND METHODS Data collection and validity Data were extracted from the Danish National Patient Registry as all patient cases with International Statistical Classification of Diseases 10th Revision (ICD-10) codes for sialolithiasis registered between the years 2000 and 2010. Care was taken to avoid the same sialolith being counted more than once, such as for a patient diagnosed on more than one occasion (thus, duplicates were excluded). For each case, we recorded the age of the patient at the time of diagnosis, gender, hospital of treatment and municipality of residence during the past 3 years. To evaluate whether the validity of the sialolithiasis diagnosis was comparable among regions, we conducted a test sample on 100 patient records from a low-incidence region and 100 patient records from a high-incidence region.
Drinking water composition and chemistry Within the observation period of study, data on the average drinking water composition (20 variables) were retrieved from the Geological Survey of Denmark and Greenland (table  1 ). All chemical data were obtained as average concentrations (mg/L) from the year 2000 to 2010 for each of the waterworks in the 98 Danish municipalities. In total, data from 3364 waterworks were obtained, and a weighted average was calculated based on the total drinking water volume from each waterworks in the municipality in question and the total †General undersaturation. It should be noticed that the result for Mg-whitlockite is based on a temperature of 25°C. In addition to the total concentrations of all species, pH is known as well. For this reason, the hydrogen carbonate concentration was treated as variable, which seems justified as the value may easily change by exchange with the atmosphere.
Similar analyses were performed to test the effect of drinking water on human saliva composition. When assessing relations between drinking water composition and sialolithiasis incidence, patients who had not resided in the same municipality 3 years prior to diagnosis (n=390) were excluded in order to avoid bias from patients being exposed to drinking water in more than one municipality. The main statistical analyses were performed with SAS V. 9. 3 and additional analyses with R. 28 29  The level of significance was set at p<0. 05.
Incidence, epidemiology and data validity A total of 3014 cases were recorded with a mean of 298 annual cases. For the obtained population size of 5 475 791 citizens (average size of the Danish population between years 2000 and 2010), the mean yearly incidence was 5. 5 cases per 100 000 citizens nationwide (95% CI 5. 3 to 5. 5). Incidence was also calculated for men and women separately being 5. 4 (CI 5. 3 to 5. 5) and 5. 5/100 000/year (CI 5. 4    1B ). Although some variation was present, the mean age among municipalities did not differ. Among all age groups, the lowest incidence of sialolithiasis was among children and adolescents. In the test sample, there was no difference in the validity of the sialolithiasis diagnosis between areas with low and high incidence ( p=0. 880). The incidence differed considerably among municipalities in Denmark ( p<0.
Drinking water and human saliva The saturation indices for Danish drinking water are given in table 1. As shown, the drinking water was indeed supersaturated with respect to some of the main elements of sialoliths, namely hydroxyapatite and Mg-whitlockite. We further speculated that for a correlation to signify causality, it would require that the saliva levels of the ions in question were affected by the drinking water levels of the same ions. So in order to determine which of the ions in drinking water could indicate such a causative relation, we reanalysed saliva data from patients with known drinking water composition from a previous study, performed on 255 healthy subjects distributed among 12 municipalities in Denmark. 30 We found saliva calcium levels to be positively and significantly correlated to drinking water calcium levels (r=0.
Acknowledgements The authors would like to thank professors  Colin Dawes  (Canada),  Henrik Spliid and Erik Arvin (Denmark) ,  Bob ten Cate  (the Netherlands),  Peter Werness (USA) ,  Berit Heitmann  and  Arne Astrup  (Denmark) as well as  Arla Foods  (largest dairy products company, Denmark) for many useful and helpful advices on linguistics, mathematics, drinking water chemistry, precipitation chemistry and dynamics as well as nutritional issues. Contributors All authors contributed to the interpretation of the results and writing of this manuscript. SS wrote and prepared the first draft of the manuscript with input from PH and  NW  within the field of otolaryngology. A-LV performed the main statistical analyses. HELM and AB performed all chemical analyses and AB did the final corrections throughout the manuscript, tables and figure.
cDNA sequences We have identified eight genes orthologous to mammalian odontogenesis developmental genes in a cDNA library from Scyliorhinus canicula  [40]  through a BLAST analysis with mouse sequences of the Bmp, Fgf, Msx and Pitx gene families. We identified sequences belonging to all four gene families, and they were each assigned to one orthology group through phylogenetic reconstruction of gene trees after sequence alignment to sequences identified in other jawed vertebrate genomes (see Additional file 1 for phylogenies). These sequences are identified as ScBmp4 (partial in NCBI [Genbank: EF174300. 1]), ScFgf8 (partial in NCBI [Genbank: DQ647321. 1]), ScMsx1, ScMsx2, ScMsx3, ScPitx1 [Genbank: KJ190312. 1], ScPitx2 [Genbank: KJ190313. 1] and ScPitx3 (partial in NCBI [Genbank: KJ190314.
1]). The ScShh sequence previously published  [37]  was subcloned and used as an additional marker in this study. We amplified selected sequences of these cDNAs and published the new partial sequence in NCBI: ScBmp4 [Genbank: KT261786]; ScFgf8 [Genbank: KT26 1787]; ScMsx1 [Genbank: KT261788]; ScMsx2 [Genbank: KT261789]; ScMsx3 [Genbank: KT261790]; ScPitx3 [Genbank: KT261791]. ScPitx1 and ScPitx2 sequences were amplified from the primers Sc-Pitx1-F (ACAG GCTTTCATATGTTCGG), ScPitx1-R (TGCTGCCGC CTCCGTGTCCG), ScPitx2-F (GGGATCCTTATCTG-CAGTTA) and ScPitx2-R (CTCCCGTGTCAGGGCTC GAG) and their sequence is included in KJ190312. 1 and KJ190313. 1 respectively.
A more precise comparison with mouse tooth buds, including the different members of the gene family, is still complicated as no expression data is published for mouse Msx3 in tooth development, and because of redundancy in Msx1 and Msx2 function in mouse tooth bud mesenchyme  [45]. Overall, our results suggest that the early mesenchymal Msx1-Bmp4 relationships Fig. 7  Apoptosis detection in developing tooth and scale buds in the catshark Scyliorhinus canicula. Apoptotic cells (TUNEL, red), actin (phalloidin, green) and DNA (DAPI, blue) were localized by triple labelling and confocal microscopy imaging. Dorsal views of successive z-planes of a whole-mount lower jaw, merged for all three canals (a, buccal surface with taste buds; b, dental epithelium layer of tooth bud 1, late LM; c, dental epithelium layer of tooth bud 2, late LM; d: schematic of the dorsal view).
The sample set was composed of 45 Rsk2 -/Y and 45 WT littermates (Rsk2 +/Y ). Mouse protocols were complied with the 2010/63/UE directive and the 2013/02/01 French decree, and were thus approved by the CERBM-GIE: ICS/IGBMC Ethical Research Board. Observation and imaging of dental rows. All the heads were prepared in order to remove all non-mineralized tissues to allow good observation and measurement of the dental rows. They were examined and photographed using a Leica stereomicroscope. The measurements were obtained by following the outline of each tooth from the photos of occlusal view of the row. Thus, the length, width, and area of the tooth were produced by Leica software. Some Sprouty mutant dental rows were imaged using X-ray-synchrotron Radiation Facility (ESRF, Grenoble, France), beamline ID 19 and BM5, with a monochromatical beam at energy of 25 keV.
Acknowledgements We thank  E. Maître  for her help in the morphological description of the teeth. We are grateful to the  ESRF  for providing inhouse beamtime for the experimentS on ID19 and  BM5. We thank  A. Hanauer ,  V. Fraulob  and  B. Schuhbaur  for providing, expanding and genotyping respectively the Rsk2 -/Y mouse colony, and  Nicolas Strauli  and  Sarah Alto  for help with the Sprouty mouse breeding. We thank  Y. Kimura  for providing M. auctor and P. debruijni pictures. We are grateful to  A. Langer  and  P. Dolle. We also thank  V. Lazzari  for his critical reading of the manuscript. This work was funded by grants from the  University of Strasbourg , the  Hôpitaux Universitaires de Strasbourg (API ,  2009-2014 , Development of the oral cavity: from gene to clinical phenotype in Human to ABZ), the  IFRO , and  EU-ERDF   A27  (Orodental manifestations of rare diseases to ABZ), the  ENS de Lyon  (to LV), and the  NIH  ( R01 DE021420  to ODK).
Tissue adhesion studies Tissue adhesion was measured using a force sensor device equipped with a hydrogel holder (MTS Systems, dynamometre, Lhomargy, DY34, France, using the Testworks software). A titanium disc was attached to a cylindrical probe (10 mm diameter) with commercial cyanoacrylate glue. The hydrogel (100 μL) was placed on this disc. After 5 min, the gel was pressed either by another titanium disc (10 mm diameter) alone, or with a piece of attached gingiva of pig (1 cm 2 ) glued on a support, for 30 min at 37°C with 0. 1 mN of normal force. We collected adhesion data by pulling the probe with a loading rate of 0. 3 mm. min -1. All measurements were performed in triplicate.
Living cells reduce Alamar Blue reagent in a red color (570 nm). Cells incubated with pure medium (absence supernatant coming from gels) was used as a positive control (live) and cells exposed to a 70% ethanol solution were used as a negative control (dead). Live/Dead observations. The Live Dead Kit (Life Technology, France) is based on a combination of two molecules: the calcein AM and the ethidium homodimer-1 (EthD-1). The polyanionic dye calcein AM labels living cells with an intense uniform green fluorescence. EthD-1, which enters into cells having damaged membranes, provides a bright red fluorescence. Stained cells were observed under epifluorescence microscope illumination (Nikon Eclipse TE200 with 63x PL APO (1. 4 NA) objective equipped with Nikon Digital Camera (DS-Q11MC) and with NIS-Elements software, Nikon, Japan).
Acknowledgements 13 This work was supported by the  "Région Rhône-Alpes"  ( CIBLE N° 11 010877 01 ) and a grant " Bonus Qualité Industrielle: QUATIOS "  OSEO ANVAR RHONE-ALPES 2010. Part of this work was conducted in the frame of the  ANR  project  MALICE  N°  BS09-032 , and within the framework of the  labex CeLyA of Université de Lyon  operated by the  French National Research Agency  ( ANR-10-LABX-0060/ANR-11-IDEX-0007 ). The authors thank  Perceval Guillou  for software assistance during installation of the system and testing,  David Marchat  ( Assistant Professor, Center for Biomedical and Healthcare Engineering, Ecole Nationale Supérieure des Mines de Saint-Etienne ) for providing us a hydroxyapatite sample and  Jean-Paul Roux  ( UMR1033 ) for technical and scientific discussions.
Protocol. Impressions were made as for conventional partial removable denture, followed by intermaxillary relation registration. A trial denture was fabricated, tried in subject's mouth to validate the accuracy of the interarch relationship, and then processed to obtain a radiographic template according to the NobelGuide protocol (e. g. , with at least 6 radiographic markers) (Figure  1 ). A first cone beam computed tomography (CBCT) was made with the radiographic template in place. The remaining teeth were removed from the master model. Ridge (shape and volume) were regularized according to both the clinical findings and the CBCT findings (Figure  2 ). Two parameters were of particular consideration, the data collected during the periodontal examination and the prosthetic needs. The clinical findings included the probing depth, initial radiographic survey, and the preliminary planning following the first CBCT.
An independent radiologist unaffiliated with the clinic interpreted the radiographs. The reference point for the reading was the implant platform. Marginal bone remodeling was calculated as the difference between readings at the examination and the baseline value at time of surgery. The radiographs were grouped as follows: implant insertion, 6 months, 1-year follow-up, 1-year and half follow-up, and 2-year follow-up. Implant survival and bone resorption data were analyzed with descriptive statistics.
acknowledgements  Professor Aurelie KAS MD. PhD. ,  Department of Biophysic UPMC Paris VI, LIB ,  INSERM UMR 678 ,  91 Bd de l'hôpital 75651 Paris Cedex 13 France and Department of Nuclear Medicine, AP-HP Hospital Pitié-Salpêtrière, 47-83 Bd de l'hôpital 75651 Paris Cedex 13 France. Pathology Department, AP-HP Hospital Pitié-Salpêtrière, 47-83 Bd de l'hôpital 75651 Paris Cedex 13 France. Head and neck Oncology concertation meeting,  AP-HP Hospital Pitié-Salpêtrière ,  47-83 Bd de l'hôpital 75651 Paris Cedex 13 France.
Of the four different LEDs, Valo is the only LED device that produces different wavelengths at this emission. Two identical LEDs produce blue light at a wavelength of 465 nm, another at 400 nm, and finally, the last one at 445 nm. Optilux 401 was used as a comparator to an older method of curing, the halogen lamp. According to the manufacturer, it delivers approximately 600 mW/cm 2 of power density within a spectral range of 400 nm-525 nm Valo and Optilux 401 were connected to a surge protector to protect the lamps from voltage spikes and any power peak during photopolymerization. Elipar Freelight 2, Radii-cal, Optilux 401, and Valo in standard mode were tested for 20 s. Valo on high power mode was tested for 4 s and on extra power mode for 3 s, following the lamp's default program. Data for mean irradiance (mW/cm 2 ) and energy (J) were gathered 10 times for each lamp and/or lamp power mode at each distance.