dataesr/scientific-paragraphs-categorization huggingface dataset:
Crystal structure of VAS(Cro013448) To understand the mechanism of VASb etter,t he crystal structure was solved (Table  1a  nd Figure  3 ; PDB ID:5 O98). It closely resembles the structure of salutaridine reductase from Papaver somniferum (SalR;P DB ID:3 O26;i. e. ,t he molecular replacement template  [15]  )a nd the recently determined structures of two SDRs from Mentha piperita:  [16]  menthone-neomenthol reductase(MNMR;e. g. ,PDB ID:5L53) and isopiperitenone reductase (IPR;e. g. ,P DB ID:5 LCX;F igure S10). Crystallizationo fV AS was carriedo ut with and without the oxidized cofactor NADP +. A fter solution of the structuresi tw as clear that the apo enzyme active site also had ah igho ccupancy of NADP + ,t hus indicating that VASi sp urified from E. coli as ah oloenzyme. Adjacenttot he nicotinamide moietyo ft he cofactor is the canonical SDR catalytic triad consisting of Ser167, Tyr223 and Lys227.
Mutationsint he VASactive-site triad To explore the mechanism of action of VAS, the amino acids Lys227,S er167 and Tyr223, whichf orm the catalytic triad of    [a]  761 897 (28 422) unique reflections  [a]  85 013 (6006) multiplicity  [a]  9. 0 (4. 7) mean I/s(I)  [a]  17. 0 (1. 5) completeness  [a]  [%] 99. 5 (96. R merge = AE hkl AE i j I i (hkl)ÀhI(hkl)ij/AE hkl AE i I i (hkl). [c] R meas = AE hkl [N/(NÀ1)] 1/2 AE i j I i (hkl)ÀhI(hkl)ij/AE hkl AE i I i (hkl) , where I i (hkl)i st he ith observation of reflection hkl, hI(hkl)i is the weighted average intensity for all observations i of reflection hkl,a nd N is the number of observations of reflection hkl. [d] CC1 =2 is the correlation coefficient between intensitiestaken from randomh alves of the dataset. [ e] The data set was spliti nto "working" and "free" sets consisting of 95 and 5% of the data, respectively.
somniferum SalR (pink;PDB ID: 3O26), M. piperita MNMR( green;PDB ID:5 L53) and human CBR1 (blue; PDB ID:1WMA). However,int he last case the flap domainism erely as hort loop connecting the equivalent of b4a nd a4i nV AS. The full structural superposition is shownasas tereoview in FigureS10. C), D) The region highlighted in A) with the protein depicteda sam olecular surface, with and without the docked substrate, respectively. N otethat the cofactor loop almost entirely covers the nicotinamide "half" of the NADP + ,except for the outeredgeof the nicotinamide ring bearing C-4, and that this is occluded by the docked substrate, whichc losely matches the dimensions of the active-sitepocket. E) The samer egion as D), but from above with the protein in cartoon. The NADP + is coloured green (carbona toms)b ut with the nicotinamide C-4 atom in yellow.
Experimental Section Cloning of Cro013448 and Rse2785:S equence data for C. roseus and R. serpentina were obtained from the Medicinal Plant Genomics database (http://medicinalplantgenomics. msu. edu/). Cro013448 was cloned from C. roseus cDNA by using primers with overhangs (5'-AAGTT CTGTT TCAGG GCCCG GCCGC CATGG GTACC and 3'-ATGGT CTAGA AAGCT TTATTC AAAC GATGA CTCCT CGC) for directional cloning into the E. coli expression vector pOPINF. [25] R. serpentina Cro013488 homologue (Rse2785) was also cloned into pOPINF after amplification from R. serpentina cDNA by using primers with overhangs (5'-AAGTT CTGTT TCAGG GCCCG TTGAG TAATAC ATCC GTCATa nd 3'-ATGGT CTAGA AAGCT TTACT CAAAC GATGA CTCCT CAC). Amplified gene fragments were ligated into pOPINF vector by using the In-Fusion kit (Clontech-Takara, Mountain View,C A, USA).
Crystals were cryoprotected with well solution containing ethylene glycol (25 %) for % 1min and flash-cooled in liquid nitrogen. Crystals were transferred robotically to the goniostat on beamline I02 at the Diamond Light Source (Oxfordshire, UK) and maintained at À173 8Cw ith aC ryojet cryocooler (Oxford Instruments). X-ray diffraction data were recorded with aP ilatus 6M detector (Dectris, Baden-Dättwil, Switzerland) and were then integrated by using XDS  [26]  and scaled and merged by using AIMLESS  [27]  with the XIA2 expert system. [28] The best data set was processed to ar esolution of 1. 55 in space group P2 1 2 1 2 1 ,with approximate cell parameters of a = 59, b = 61, c = 162 (see Ta ble 1f or as ummary of data collection statistics). The structure was solved by molecular replacement by using PHASER  [29]  and the crystal structure of SalR (PDB ID:3 O26  [15]  ), with which it shares 53 %a mino acid sequence identity,a st emplate.
The asymmetric unit contained two monomers, corresponding to an estimated solvent content of 44 %. After refinement of this preliminary model by using REFMAC5,  [30]  phases were improved through density modification (incorporating twofold averaging) in PARROT,  [31]  to yield am uch improved electron density map at 1. 55 resolution. This enabled an ew model of VASt ob eb uilt from scratch by using BUCCANEER,  [32]  and this was completed by several iterations of manual rebuilding in COOT  [33]  and restrained refinement in REFMAC5 with use of isotropic thermal parameters and TLS group definitions obtained from the TLSMD server (http:// skuld. bmsc. washington. edu/ ~tlsmd). [34] Model geometries were validated with MolProbity  [19]  before submission to the Protein Data Bank (see Table  1f  or as ummary of model statistics).
(0. 614) Wilson B value[ 2 ]28. 8 Refinement resolutionr ange[a]  []55. 30-1. 55 (1. 59-1. 55) reflections: working/free[e]   80 707/4304 R work /R free [a,f] 0. 169/0. 190 (0. 382/0. 379) Ramachandran:favoured/allowed/disallowed [g] [%] 98. 3/1. 7/0. 0 RMSD of bondd istance []0. 010 RMSD of bonda ngle [8]1. 50 no. of proteinr esidues (ranges): chains A/B 282 (7-103;1 15-299)/283 (7-107;1 18-299) no. of water molecules/NADP + molecules 397/2 mean B factors:protein/water/NADP + / overall [ 2 ] 38. 2/44. 6/27. 4/38. 6 PDB ID 5O98 [a] Figures in parentheses indicatev aluesf or the outerr esolution shell. [b].
Figure3. X-ray structure of C. roseus vitrosamine synthase( VAS). A), B) Orthogonal cartoon representationso fV AS, in which the core structure is coloured in magnolia and the flap domain andcofactor loop are showninred and cyan,r espectively. The black spheres indicate where thereisab reak in the backbone trace of the flap domaincorresponding to aregion that could not be resolved in the electrondensity. Also shown as van der Waals spheres are the bound NADP + cofactor( light brown with C-4 in yellow) and the dockeds ubstrate (ice blue). Additionally,i nB), the flap domains of close structural homologuesa re shown afters uperposition of their full structures onto that of VAS. Specifically,these are P. somniferum SalR (pink;PDB ID: 3O26), M. piperita MNMR( green;PDB ID:5 L53) and human CBR1 (blue; PDB ID:1WMA).
Acknowledgements We gratefully acknowledge support from the  ERC  ( 311363 ) and a  BBSRC Institute StrategicP rogramme grant  ( MET ; B B/J004561/1 ) to S. E. O. A. S. was supported by aB BSRCD TP studentship. We acknowledge the  DiamondL ight Source  for access to beamline I02 under proposal  MX9475 , with support from the  European Community 's  Seventh Framework Program  ( FP7/2007-2013 ) under Grant Agreement 283570 (BioStruct-X). We acknowledge  Vincent Courdavault  for helpful discussions regarding the activity.
A coronoradicular reconstruction (CRR) has conventionally used a metallic inlay core (MIC) or a single-fiber-reinforced composite (sFRC) but extensive dentin removal can lead to root fracture. We propose herein a multi-fiber-reinforced composite (mFRC) based on a bundle of thin flexible fibers that can be adapted to the root anatomy without removing additional dentin. The aim of this study was to compare the mechanical behavior of the root reconstructed with mFRC, MIC, or sFRC using a finite element analysis (FEA). Models with or without a ferrule effect were created using Autodesk © software and divided into four parts: root, post, bonding composite or cement, and zirconia crown. For both models, extreme stress values (ESV), stress distribution, and risk of fracture were calculated for an oblique force (45 ∘ ) of 100 N applied to the top of the buccal cusp.
Statistical analysis (mean, standard deviation and student test) was performed using Microsoft Excell 2007 (Microsoft, Redmond, Washington). For all cases showing qualitative and quantitative hypermetabolism, clinical and paraclinical oral assessments were performed to establish associations between functional abnormalities and implant pathologies. This study was approved by the ethics committee of our institution, all data has been anonymized, and the rights of patients were respected at every step of the study. This human observational study conforms to the STROBE statement.
0 69. 5 3. 7 -2. 4 0. 006 0. 002 Z5XKA5 Z5XPG4 Uncharacterized protein Fructokinase 16. 3 34. 7 3. 5 -2. 4 0. 004 0. 010 Z5XL46 Z5XSZ9 Uncharacterized protein Phosphoenolpyruvate carboxylase 22. 3 98. 9 3. 5 -2. 5 0. 009 0. 004 Z5XTG9 Z5XNW2 4-hydroxybenzoyl-CoA thioesterase L-arabinose isomerase 15. 1 55. 2 3. 5 -2. 5 0. 009 0. 002 Z5XSZ1 Z5XW70 Redoxin Glyceraldehyde-3-phosphate dehydrogenase 21. 1 53. 1 3. 3 -2. 5 0. 002 0. 000 Z5XR97 Z5XN13 Flagellar basal body-associated protein FliL-like protein Fic family protein 15. 4 56. 7 3. 3 -2. 6 0. 010 0. 006 Z5XMQ9 Z5XV74 LOG family protein Cytoplasmic asparaginase I 50. 0 37. 0 3. 3 -2. 6 0. 001 0. 009 Z5XQ14 Z5XSC3 Uncharacterized protein UPF0250 protein AOG27_03855 30. 5 10. 4 3. 3 -2. 7 0. 007 0. 003 Z5XQI8 Z5XN10 5-methyltetrahydropteroyltriglutamate--homocysteine Alcohol dehydrogenase 38.
IBU-PCL Membrane Reduces Proliferation of Pg-LPS-Stimulated Cells To assess if the IBU-PCL membrane influences EC and FB proliferation in an inflammatory context, cells were challenged by Pg-LPS during 6-48 h. Exposure to Pg-LPS induced an increased proliferation of both EC and FB seeded on the PCL membrane at 24 and 48 h (Figure  2A, B ). Interestingly, these increments were not observed for cells seeded on the IBU-PCL membrane. To evaluate the impact of IBU on EC migration, a scratch assay has been performed. Data showed that early treatment of Pg-LPS-stimulated EC with IBU significantly reduced their migration rate (42% decrease at 12 h; p < 0. 05) (Figure  2C ). Proliferation of EC (A) and FB (B) after 6, 24 and 48h and EC migration after 6-24 h (C). These different conditions have been measured by using the AlamarBlue test (A,B).
EC and FB proliferation has been evaluated on PCL and IBU-PCL membranes and with or without Pg-LPS stimulation. Data are expressed as the mean ± SD. * Difference between cells with or without IBU, p < 0. 05, † difference between stimulated cells with or without IBU, p < 0. 05. Epithelial migration has been evaluated through the in vitro scratch assay (C) after injection of IBU (50 µg/mL) at baseline (T0), 2 h (T2) and 4 h (T4) at 6, 12 and 24 h in EC stimulated with Pg-LPS. Data are expressed as the % of wound closure ± SD; * p < 0. 05.
Histomorphometric Analysis For histomorphometric evaluation, prepared sections were deparaffinized, rehydrated and stained with hematoxylin. After dehydration, slides were mounted with Distrene-plasticizer-xylene (DPX) resin (Sigma), and computerized images were captured on a microscope (RM 2145 DMRB microscope, Leica, Rueil-Malmaison, France). Palatal root areas of the first molars were analyzed to examine the extension of epithelial downgrowth, connective tissue attachment and alveolar bone loss. For histomorphometric analysis: epithelial attachment (EA) was measured from the cemento-enamel junction (CEJ) to the apical limit of the epithelium, and the alveolar bone level (BL) was measured from CEJ to alveolar bone crest (ABC) using imaging software (ImageJ, 1. 46r, National Institute of Mental health (NIMH), Bethesda, Maryland, USA).
Clinical data Individual oral examinations were performed the same day in a medical examination room. One post-graduate student in Orthodontics conducted all the examinations according to WHO requirements  [26]. Artificial light, equipment (gloves, mask and gauze pads) and prepackaged sterilized instruments (single use mirror and periodontal probe) were used for the oral examinations. The number of teeth with carious lesions at D3 level according the Eckstrand classification  [27] , teeth with fillings and missing teeth were recorded. The DMFT Index was calculated for dental caries experience assessment according to the World Health Organization criteria  [26]. An orthodontic assessment of malocclusion using the Dental Aesthetic Index (DAI) was also measured  [26, 28]  (Table  1 ). The DAI is a clinical index adopted by the World Health Organization to assess malocclusion in epidemiological studies.
Statistical analyses The statistical analyses were performed using the software SPSS for Windows, version 17. 0, USA. The alpha error was set at 0. 05. Reproducibility concerns the degree to which repeated measurements in stable persons provide similar answers. The test-retest reliability of the CPQ 11-14 was assessed by repeating the administration of the CPQ 11-14 two to three weeks after the first administration to 71 subjects who felt there had been no change in their oral health status since their first test. Reproducibility was measured by calculating the intra-class correlation coefficients (ICC) for the global score and each domain score with a two-way random effects model; ICC = 0. 70 is recommended as a minimum standard for reproducibility  [29]. Reliability or internal consistency is a measure of the extent to which items in a scale are correlated, thus measuring the same concept.
Description sample Among the 764 school children eligible for the study, 43 (5. 6%) did not return the signed consent form and 19 (2. 5%) were absent from school during the data collection. The sample included 702 Lebanese children aged 11-14 years recruited from public and private schools. Three of them were excluded for behavioral problems during the completion of the questionnaire and six others did not cooperate enough for dental examination. Finally, 693 were included (response rate: 98. 7%). The mean age was 13. 14 ± 0. 82 years and 54. 4% were boys. The mean CPQ 11-14 score was 15. 60 ± 14. 55, range from 0 to 110. The distributions of CPQ11-14 for domain scores and global score are given in Figs. 1  and 2  respectively. According to the CPQ, 67. 2% of the children had experienced oral symptoms in the previous three months, 63.
Material and methods The developed model is implemented within the software ABAQUS  [26]  through a UMAT subroutine encoded in FORTRAN. The bone, the teeth and the ligament are considered homogeneous and isotropic with a linear elastic mechanical behaviour. Their material properties are extracted from the literature  [27, 28]. The vascularization of the ligament is considered homogeneously distributed throughout the volume leading to an oxygen concentration variation equal to the relative volume variation of the ligament as: = = c f V t V f Tr t ( ) { [ ( )]} Where c O2 is the oxygen concentration into the PDL, V vasc is the var- iation of the volume of the PDL, V init its initial volume and Tr ( ), the trace of the strain tensor. The function f is assumed to be with a linear variation and defined such that no deformation is set for an oxygen concentration of 10% (as the normal average concentration in the blood).
and Utting et al. [24, 25] , assumption is made in the current work that there is equilibrium between osteoblasts and osteoclasts activity at the average oxygen concentration of 10% in the blood (normal physiological level). The bone remodelling process leading to the tooth displacement occurs interface the bone and the PDL. Hence, only the cells located at this interface are considered active. An algorithm is developed (similar to the one developed in Ref. [29]  for detecting the bone trabecular surface) to localize the cells close to the bone/PDL interface that enables to track its moving in space. To carry out the bone density evolution analysis, input data are required. Histology experiments were carried out on pig's PDL teeth to quantify the initial cells density distribution. An average density of 1.
, 2004) , mortality and healthcare costs and decrease health-related quality of life  (Anderson et al. , 2009; Lamarsalle et al. , 2013; Savage and Anderson, 2013). A retrospective database analysis in France concluded that staphylococcal infections led to approximately 1. 0 and 1. 4 additional hospitalizations per patient, 22. 1 and 22. 4 additional hospital days, and an excess cost of €15,475 and €13,389 after cardiothoracic and orthopedic surgeries respectively  (Schmidt et al. , 2015). The rate of in-hospital mortality was 2. 6 times and six times higher among infected patients than non-infected patients in cardiothoracic and orthopedic procedures  (Schmidt et al. , 2015). Methicillin-resistant S. aureus carriage could increase the risk for the development of SSIs. In a systematic review, patients colonized with MRSA were four times more likely to develop invasive infection than patients colonized with MSSA  (Safdar and Bradley, 2008).
FUNDING This study was supported by  IHU Méditerranée Infection, Marseille, France  and by the  French Government  under the " Investissements d'Avenir" (Investments for the Future) program  managed by the  "Agence Nationale de la Recherche " (ANR, fr:  National Agency for Research)  (reference: Méditerranée Infection  10-IAHU-03 ). This work was supported by  Région Provence Alpes Côte d'Azur and European funding FEDER PRIMI. AS was supported by a  CIFRE PhD Grant  from the  "Association Nationale de la Recherche et de la Technologie ".
Transmission electron microscopy (TEM). Samples were fixed by immersion in 2. 5% glutaraldehyde and 2. 5% paraformaldehyde in cacodylate buffer (0. 1 M, pH 7. 4), and post-fixed in osmium tetroxide 1% in 0. 1 M cacodylate buffer for 1 h at 4 °C, dehydrated and then treated with propylene oxide for 30 min under stirring. Samples were incorporated into Epon 812. Semi-thin sections were cut at 2 μm with ultra-microtome (Leica Ultracut UCT), stained with toluidine blue and analyzed histologically by light microscopy (Microscope Digital Camera DP72; CellSens Entry, Olympus, Tokyo, Japan). The ultra-thin sections were cut at 70 nm and contrasted with uranyl acetate and lead citrate and examined at 70 kV with an electron microscope Morgagni 268 D. Images were captured digitally by Mega View III software (Soft Imaging System).
Yet, indications in implant dentistry may go beyond diagnostics. In fact, the inherent 3D datasets may further allow surgical planning and transfer to surgery via 3D printing or navigation. Nonetheless, effective radiation doses of distinct dental CBCT machines and protocols may largely vary with equivalent doses ranging between 2 to 200 panoramic radiographs, even for similar indications. Likewise, such variation is also noticed for diagnostic image quality, which reveals a massive variability amongst CBCT technologies and exposure protocols. For anatomical model making, the so-called segmentation accuracy may reach up to 200 μm, but considering wide variations in machine performance, larger inaccuracies may apply. This also holds true for linear measures, with accuracies of 200 μm being feasible, while sometimes fivefold inaccuracy levels may be reached.
While the required 3D acquisition for dental applications was initially realized by medical computed tomography (CT), dental CBCT rapidly took over  [1, 5]. The main reasons for the triumph of CBCT are its capabilities of volumetric jaw bone imaging at reasonable costs and doses, with a relative advantage of having a compact, affordable, and nearby or in-house equipment. For the clinicians involved in implant rehabilitation, the power of a dental 3D dataset is not only situated in the diagnostic field, but also in the potential of gathering integrated patient information for presurgical and treatment applications related to oral implant placement. Nowadays, rapid advances of digital technology and computer-aided design/computer-aided manufacturing (CAD/CAM) systems are indeed creating challenging opportunities for diagnosis, surgical implant planning and delivery of implant-supported prostheses.
While there is still a huge demand for maximised integration of 3D datasets acquired from various imaging sources, there is also a call for simplified solutions. Yet, when striving for optimized patient-specific implant rehabilitation, the ultimate goal remains to fully integrate the available 3D imaging data thus creating the virtual patient, aiding presurgical simulation and peroperative transfer to the surgical field with further prosthetic rehabilitation  [1, 5]. The aim of the present state-of-the-art paper is to present a narrative review providing support for the hypothesis on using CBCT for oral implant planning and to attempt formulating recommendations for justified and optimized CBCT imaging. Requirements for optimized use of CBCT and the related limitations are presented including a maximized use of available 3D CBCT data.
Methods In order to find the relevant literature included in this article, an electronic search of MEDLINE (PubMed) database was performed. This literature search included studies published in English language or with an English language abstract published prior to November 30th, 2016. To classify the available literature, specific search queries were used (Table  1 ). In particular, these queries were combined in order to divide the available literature by specific topics. Figures  1  and 2  show the results of the searches and classification processes. The performed electronic search was complemented by hand-searching, and the final selection of publications was performed after consultation of the working group, consisting of all coauthors of this paper. Disagreements regarding study inclusion were discussed by the investigators.
Which parameters influence image quality in CBCT? Image quality performance of CBCT devices may vary widely, similar to, but not only related to exposure protocols and radiation dose ranges  [1, 7, 8]. CBCT images are usually considered offering a high spatial resolution with voxel sizes of reconstructed CBCT datasets ranging between 0. 08 and 0. 4 mm  [1]. Small voxel sizes could be diagnostically useful for cases in which small structures such as root canals and periodontal tissues need to be depicted. Variation is also observed when it comes to segmentation accuracy. The latter is a crucial factor when going for an integrated virtual planning including jaw bone models, fabrication of radiographic and surgical guides as well as further prosthetic models. Depending on the CBCT and the parameter settings, a 200 μm accuracy level should be feasible  [1, 5].
7 ), esthetic challenges in the anterior maxilla, insufficient bone volume, shape and quality, the use of more advanced surgical techniques (grafting, distraction, zygomatic implants) and the integrated presurgical planning and virtual patient approach (Table  2 )  [2, 4, 5, 8, 17, 19, 22, 23]. One of the most frequent applications of presurgical use of CBCT is the computer-aided planning and transfer for oral implant placement. This approach inevitably requires 3D datasets for further planning in a dedicated software and potential transfer to the surgical field  [2, 4, 5, 8, 17, 19, 22, 23]. The advantage of such a digital planning is expected to be an integrated approach of biomechanical, functional, and esthetic aspects to strive for a more predictable outcome, meanwhile avoiding complications  [2] [3] [4].