dataesr/scientific-paragraphs-categorization huggingface dataset:
The 13 best fit to the data in all cases was found using the Gaussian distribution model. The SLD profile 14 through the interface was modelled by dividing a 300 Å region into 10 Å sections with an 15 interlayer roughness fixed to 5 Å to smooth out each interface. The volume fraction of alginate 16 was then calculated in each section and converted to an SLD by assuming the rest of the layer 17 was filled with the subphase water. In all adsorbed alginate datasets it was observed that the 18 volume fraction of alginate had reached background well before the model cut off at 300 Å 19 except for the 2. 5 ppm MVG where the model had to be extended to 350 Å to reach background. 20 Using the modelled volume fraction distribution, an adsorbed amount was obtained from the area 21 under the Gaussian polymer segment density distribution curve.
NEUTRON REFLECTION 15 Each calcite crystal was first measured in three saturated calcium carbonate water contrasts, 16 D 2 O, H 2 O, and water contrast matched to calcite (CMC = 4. 69 x 10 -6 Å -2 ). A representative 17 dataset is shown in the supporting information (Figure  S2 ). Previous experiments have shown 18 that the surface roughness of calcite does not increase over time in the presence of water 19 saturated with calcium carbonate powder. 27 The surface cleanliness was confirmed by the 20 absence of any reflected signal above the background level in the CMC contrast (not shown). 21 Measuring the reflectivity in contrast matched water is especially useful due to the high 22 sensitivity to adsorbed layers at the surface. Unlike silicon crystals, which always have a surface 23 oxide layer and always show a signal in contrast matched water, if the surface of calcite is 1 completely clean there will be no signal recorded.
11, 26, 34 3 ALGINATE ADSORPTION 14 Figure  3  presents experimental neutron reflectivity data of the calcite/water interface in the 15 presence of (a) 2. 5 ppm MVM and (b) 2. 5 ppm MVG alginate in three contrasts, D 2 O (purple 16 squares), H 2 O (green circles), and water contrast matched to calcite (CMC, yellow triangles). 17 Corresponding SLD profiles are provided in the supporting information (Figure  S3 ). Alginate 18 solutions were introduced to the sample cells at concentrations of 0. 5 and 1 ppm in D 2 O. Three 19 water contrasts were recorded for the highest concentration, 2. 5 ppm. The concentration of 2. 5  20   ppm was chosen to be just above the turning point of the plateau for both MVM and MVG 21 alginates in solution depletion isotherms (Figure  2 ). This represents concentration where the 1 surface is expected to be covered but before the onset of multilayer formation or precipitation.
7 Figure  3b  shows the experimental data measured for 2. 5 ppm MVG in all three water contrasts. 8 The data was fitted to a Gaussian layer model, as above, and again found to give good agreement 9 in all datasets. The SLD of the H 2 O contrast was again found to be higher than literature (3. 28± 10 0. 07 x 10 -6 Å -2 ) as for MVM alginate. The polymer distribution was found to extend further into 11 solution compared to MVM, suggesting that the MVG molecule is less attracted to the calcite 12 surface. This may also be related to a greater degree of cross-linking by calcium ions compared 13 to MVM alginate. 17 The modelled roughness, 34. 5 ± 0. 7 Å, is large and the reflected signal 1 (above the critical edge) was much lower than for other measurements and reached background 2 at lower Q. The larger roughness indicates more calcium is released into the solution to achieve 3 equilibrium when compared to MVM alginate.
Upon fitting the datasets, 9 the maximum of the Gaussian polymer distribution is found to lie away from the calcite surface 10 (Figure  5a ) and the adsorbed amount is lower than for MVG in pure water (0. 7 ± 0. 3 compared 11 to 2. 8 ± 0. 3 mg m -2 ). The surface roughness was also found to be lower 27. 3 ± 0. 5 Å compared 12 to 34. 5 ± 0. 7 Å. The reduction in surface roughness by pre-saturation of the MVG with 12 mM 13 MgCl 2 was not as pronounced as expected, suggesting that the affinity of MVG alginate for 14 calcium ions is high even if the charge is compensated by other divalent ions. The composition 15 of the alginate (i. e. the proportion and order of M to G residues) plays a greater role in the extent 16 of calcite surface roughening than the availability of divalent ions in the solution.
Attempts were made to 11 cleave the surface rather than polish, however, it was not possible to obtain an area large enough 12 for reflectivity studies (roughly 20 cm 2 ) without introducing large steps, causing the cells to leak. 13   The roughness of the polished crystals was assessed by X-ray reflectivity on a Rigaku SmartLab 14 X-ray diffractometer (ISIS, Rutherford Appleton Laboratory, Didcot, UK). This measurement 15 gave an approximate indication of the quality of the surface (data shown in supporting 16 information, Figure  S1 ). Crystals, which had an X-ray roughness less than 15 Å, were then used 17 in neutron reflectivity experiments. 18.
6° and 2. 0°, to cover the Q 17 range of interest (0. 006-0. 2 Å -1 ). To ensure no contribution from the edges of the sample, a 18 constant beam footprint of 30 x 45 mm 2 was maintained on the sample surface. The dQ/Q 19 resolution varied between 1. 5-10% over the Q range measured, during data fitting a value of 4% 20 resolution was used. The data reduction was performed using the COSMOS software. 30 The calcite crystals were cleaned by UV-Ozone treatment (BioForce Nano Procleaner). After 1 irradiation, a small drop of filtered calcium carbonate saturated water was placed on the surface 2 to assess wettability. If the droplet spread the crystal was considered clean, placed immediately 3 against a Teflon trough and sealed in a neutron reflectivity cell (details of cell reflection sample 4 cell are given in Stocker et.
At Nantes UHC, this involved four out of 12 patients (33. 3%). At Perpignan Hospital Centre, this involved all patients treated during the COVID-19 lockdown period. The decision to transfer these patients to private hospitals was taken in order to reduce the workload at the hospitals managing COVID-19 cases. These patients were included in the data relating to the patients treated during lockdown so as not to artificially emphasize the difference between the lockdown period and the two comparison periods. Dental traumas and wounds that are generally treated under local anaesthesia in ambulatory care and therefore mobilize little material and limited human resources were deliberately excluded from this study. Knowing that trauma activity fluctuates considerably from one week to another, it was decided to choose a period equivalent to that specified (from March 16 to April 15) and also a period of 2 months (from March 1 to April 30) as comparison periods.
First identi cation was attempted with MALDI-TOF Mass Spectrometry (Bruker, Daltonics, Bremen, Germany) as previously reported  15. The generated spectra from this strain were analyzed using Biotyper 3. 0 software, by comparing them to those properly and regularly incremented in the local URMS database (https://www. mediterranee-infection. com/urms-data-base). MALDI-TOF MS could not correctly identify the strain Marseille-P3740, a molecular investigation was therefore carried out by amplifying the 16S rRNA gene using the primer pair fD1 and rP2 (Eurogentec, Angers, France). Then, it was sequenced using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and 3500xLGenetic Analyzer capillary sequencer (Thermo sher, Saint-Aubin, France), following the protocol previously reported  16. Using CodonCode Aligner software (http://www.
Genome characteristics Genomic DNA extraction was realized using the EZ1 DNA tissue kit (Qiagen, Hilden, Germany) adapted to EZ1 biorobot. It was sequenced by the MiSeq instrument (Illumina Inc, San Diego, CA, USA) using the Nextera Mate Pair and Nextera XT Paired End (Illumina) sample preparation kit, following the same protocol previously used  19. Three known softwares were used to correctly assemble this genome, including Spades 20 , Velvet  21  and Soap Denovo 22. To manage trimmed or untrimmed sequences, MiSeq and Trimmomatic softwares were used, respectively  23. In addition, we used the GGDC (Genome-to-Genome Distance Calculator) web server available online (http://ggdc. dsmz. de) to calculate the genomic similarities  24. This allowed us to obtain DNA-DNA hybridization (DDH) values of these compared genomes.
Results Strain identi cation and phylogenetic analysis MALDI-TOF mass spectrometry could not correctly identify the strain Marseille-P3740. Thus, the obtained reference spectrum was added to the local database. Similarity analysis based on 16S rRNA of strain Marseille-P3740 against GenBank showed the highest nucleotide sequence similarities of 96. 31 % sequence identity with Collinsella intestinalis strain JCM 10643 (Genbank accession number: NR_113165. 1), which was the phylogenetically closest species. This value obtained is below the threshold of 98. 65% recommended to delimit the species barrier in bacteria  24, 26. Therefore, the strain Marseille-P3740 was considered as a potentially new species belonging to the genus Collinsella within the Coriobacteriaceae family in the phylum Actinobacteria (Figure  1 ).
Regarding the behavior in solution of these powders, we show that copper is easily accessible for materials treated at 600 • C and 900 • C, and that this is much less the case for powders treated at 1200 • C. Copper ions are located at the HAp crystal surface for the XCu-600 samples (i. e. , directly accessible), substituted for calcium in the β-TCP structure for the XCu-900 samples (i. e. , easily accessible due to the solubility of β-TCP), and inserted into the HAp structure for the XCu-1200 samples (i. e. , poorly accessible due to the non-solubility of HAp)  [7]. Specific surface areas were obtained using MicroActive Software for a TriStar II PLUS Version 2. 03 Instrument (Micromeritics, Merignac, France). Phase compositions were determined by X-ray powder diffraction (XRPD, X'Pert-PRO PANalytical, Malvern, UK) followed by Rietveld treatments to extract the respective amounts of HAp and β-TCP (this procedure was detailed in the related previous work  [7] , and the results will not be explained again here).
Shaping by 3D Printing for Biomaterials Since the first patent on stereolithography was filed in 1986, the additive manufacturing sector has been expanding rapidly. Indeed, different techniques have been successively developed to respond to the problems of complex shaping of certain materials. The use of CAD (Computer Aided Design) software makes it possible to free oneself from the geometric constraints induced by the use of a mold. Processes such as fused deposition modeling (FDM), robocasting, powder bed printing, or stereolithography are processes are mainly used in industry  [82]. With the emergence of these new technologies, it would seem trivial to form a glass with a complex geometry using these processes. However, due to its particular physicochemical properties, little progress has been made in the 3D printing of glass materials.
To our knowledge, this type of approach has not been described in clinical routine. In a first step, the DICOM (Digital Imaging and Communications in Medicine) data acquired during the CT (Computed Tomography) cone beam is exported to the Blue Sky Plan 4 dental planning and design software (Blue Sky Bio, Libertyville, IL, USA). This software allows the selection of the region of interest, the maxilla in its dento-alveolar region in this case. Based on thresholding, only the dental and bone structures are kept. They are used to generate a three-dimensional object file in STL (Standard Triangle Language)  [129]  (Figure  6 ). In the second step, all stl data were imported into the Autodesk MeshMixer computeraided design software  [130, 131]. The areas adjacent to the defect are isolated and smoothed.
Then, using the extrusion function, the two surfaces are transformed into penetrating volumes. The Bollen fusion of the two elements allows to obtain a unique volume, which is smoothed. Finally, the fit on the initial stl is checked and the undercuts that prevent the insertion of the part are removed (Figure  7 ). In the second step, all stl data were imported into the Autodesk MeshMixer computer-aided design software  [130, 131]. The areas adjacent to the defect are isolated and smoothed. Then, using the extrusion function, the two surfaces are transformed into penetrating volumes. The Bollen fusion of the two elements allows to obtain a unique volume, which is smoothed. Finally, the fit on the initial stl is checked and the undercuts that prevent the insertion of the part are removed (Figure  7 ).
Conclusions The research and development of new materials for medical applications is a rapidly growing field. Biomaterials are an interface between chemistry, physics, and medicine, with the challenge of replacing living organisms. Natural or synthetic materials have been used for a long time. However, the last few years have seen the rapid development of CAD/CAM systems based on 3D imaging of the patient. They open up a new area for the shaping and use of biomaterials offering a multitude of therapeutic approaches to clinicians. The literature review proposed here shows how, from bioglass shaped by The stl file is then sent to a slicing software such as Cura and is transformed into gcode format, the format used by 3D printers. In the slicing software, it is possible to control the printing parameters to optimize the quality of the 3D part (printing speed, nozzle temperature, placement of supports, filling of the part, etc.
Streptococcus mutans (S. mutans) is a group of viridans mostly located in oral flora among the wide and biodiverse biofilm. It plays a significant role not only in caries formation but also triggering intracerebral haemorrhage. The durable and stable bond interface, besides bacteria elimination, is one of the crucial factors influencing the resin composite restoration performance. This study aimed to evaluate universal adhesives (UAs) with regard to in vitro bond strength to dentin, and the inhibition of the S. mutans growth and compare them with UAs modified with antimicrobial agents through a systematic review and meta-analysis. Two reviewers performed a literature search up to April 2021 in 5 electronic databases: PubMed MedLine, Scielo, ISI Web of Science, Scopus, and EMBASE. Only in vitro studies reporting the effect of modifying UAs with antimicrobial agents on the bond strength to dentin and/or on the inhibition of the S.
mutans were included. Analyses were carried out using Review Manager Software version 5. 3. 5 (The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, Denmark). The methodological quality of each in vitro study was evaluated following the parameters of a previous systematic review. A total of 1716 potentially relevant publications were recognized. After reviewing the title and abstract, 16 studies remained in the systematic review. From these, a total of 3 studies were included in the meta-analysis. Since data from the studies included in the antimicrobial outcome included zero values, they could not be meta-analysed. Including 0 values in the analysis will lead to several biases in the analysis, so these data were discarded. The antibacterial effect against S. mutans of UAs modified with antimicrobial agents was higher than the non-modified adhesive systems.
Literature Search The literature search was independently performed by two reviewers (C. E. C. -S. and R. B. ) up to 18 April 2021. The following five electronic databases were screened: PubMed MedLine, Scielo, ISI Web of Science, Scopus, and EMBASE, to identify articles that could be included. The search strategy and keywords used in PubMed are listed in Table  1. The full search strategy for Scielo, ISI Web of Science, Scopus, and EMBASE databases was presented as Supplementary Material (Tables  S1-S4 ). Respectively, the reviewers also handsearched the reference lists of included manuscripts for identification of supplementary papers. Following the initial screening, all articles were imported into Mendeley Desktop 1. 17. 11 software (Glyph & Cog, LLC, London, UK) to remove duplicates.
Study Selection Two independent reviewers (L. H. and R. B. ) evaluated the titles and abstracts of all the manuscripts. Studies for full-text review were selected according to the eligibility criteria: (1) in vitro studies reporting the effect of modifying UAs with antimicrobial agents on the bond strength to dentin, and/or on the inhibition of the S. mutans; (2) assessing the bond strength of UAs to dentin substrate with a resin-based material as an antagonist; (3) including a control group in which UAs systems were used following the instructions of manufacturers; (4) including mean and standard deviation data in MPa on micro-shear, shear, micro-tensile, and tensile bond tests; (5) evaluating the bacterial activity of S. mutans; (6) publishing in the English language. Papers that involved substrates further than those established in the inclusion criteria were not considered for this review.
Clinical trials, case series, case reports, pilot studies, and reviews were also excluded. Full copies of all of the potentially pertinent manuscripts were analysed. Those that seemed to meet the inclusion criteria or had insufficient data in the title and abstract to make a clear decision were designated for full evaluation. The full-text papers were assessed in duplicate by two independent investigators. Any disagreement or variations in view concerning the eligibility of the included manuscripts was resolved and decided through consensus and discussion by a third reviewer (C. E. C. -S. ). Only studies that fulfilled all of the eligibility criteria listed were included for review.
Data Extraction Data of interest from the manuscripts involved were tabulated using a standardized form in the Microsoft Office Excel 2019 spreadsheets (Microsoft Corporation, Redmond, WA, USA). These data contained demographic data (year of publication), universal adhesive, antimicrobial agents, outcomes, and main results. If any information was partially missing, the corresponding authors of the involved papers were contacted twice via e-mail to retrieve the missing data. If authors did not answer within 3 weeks after the first communication, the missing information was not included. For the articles that displayed the information in graph formatting and for which the original data could not be retrieved from the investigators, mean and standard deviation were obtained by calculation using WebPlotDigitizer 4.
Statistical Analysis Meta-analyses were performed using a software program (Review Manager v5. 4. 1; The Cochrane Collaboration, Copenhagen, Denmark). The analyses were performed using the random-effects model, and pooled effect estimates were obtained by comparing the standardized mean difference between bond strength values of unmodified universal adhesives versus the antibacterial containing universal adhesive. In studies where several experimental groups were compared with the same control group, data from the experimental groups (mean, standard deviation, and sample size) were combined  [42]. A p-value < 0. 05 was considered statistically significant. Statistical heterogeneity of the treatment effect among studies was assessed using the Cochran Q test and the inconsistency I 2 test.
Results A total of 1716 publications were identified from all databases. A flowchart that outlines the study selection process agreeing to the PRISMA Statement is displayed in Figure  1. The literature review retrieved 1609 publications for the initial examination after the duplicates were removed. Next, 1593 studies were excluded after reviewing the titles and abstracts, leaving a total of 16 studies  [33, 37, [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]  to be examined by full-text reading. Of these, 13 studies were not included in the qualitative analysis  [33, 37, 43, 44, [46] [47] [48] [49] 51, 52, [54] [55] [56] , totalizing 3 articles  [45, 50, 53] ; the reasons for exclusion are mentioned in the supplementary material (Table  S5 ).
Results A total of 1716 publications were identified from all databases. A flowchart lines the study selection process agreeing to the PRISMA Statement is displayed 1. The literature review retrieved 1609 publications for the initial examination duplicates were removed. Next, 1593 studies were excluded after reviewing the abstracts, leaving a total of 16 studies  [33, 37, [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56]  to be examined by full-text re these, 13 studies were not included in the qualitative analysis  [33,37,43,44,46-49 56] , totalizing 3 articles  [45, 50, 53] ; the reasons for exclusion are mentioned in th mentary material (Table  S5 ). The characteristics of the manuscripts included in this systematic review ar rized in Table  2. Several antimicrobial agents including fluorinated graphene methacrylate (EgMA), 0.
However, these studies have many limitations. In vitro experiments are by definition performed outside the organism and are far from clinical applications. They do not recapitulate the complexity of the organism and the various interactions between cells and organ structure. Despite the development of alternative methods (in silico computer models and simulations, isolated tissue/organ for tissue or organ bath system, databases)  (19, 20) , animal models are still mandatory and must be used for scientific purposes. In 2015, 192 million animals were used for scientific purposes  (21). Historically, discovery of vaccines, pathologies, diagnostic tests, and therapeutic methods require the use of preclinical animal models, however the use of animal is still debated from an ethical point of view.
Some authors have used total cellular RNA from stimulated pulp tissues of mice's molars to perform real-time polymerase chain reaction (RT-PCR) by targeting pro-inflammatory cytokines like IL-1β, IL-6, and TNFα  (36). Others have used enzyme-linked immunosorbent assay (ELISA) to directly quantify these pro-inflammatory cytokines from samples of pulp tissue homogenates  (47). Finally, cell surface marker expression may be assessed using flow cytometry. A combination of the different methods can provide a wider range of data rather than the use of only one technique provided that the amount of pulp tissue is sufficient (48) (Figure  1 ).
Acknowledgments We are indebted to the late  Antonio Richieri-Costa  ( 1946-2019 ), a geneticist at the  Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo , who kindly provided the human dental records. He sadly passed away before the completion of this investigation. We thank  Mathilde Bouchet  for her help in the production of 3D reconstructions of dental rows using the Nanotom within the  ANIRA-IMMOS platform  of  SFR Biosciences  and  Paul Tafforeau  for his help in use of the Synchrotron X-ray microtomography at the  ESRF in Grenoble. We are grateful to the following investigators for complementary DNA:  Andrew McMahon ,  Shh ;  Matthew Scott ,  Ptch1 ;  Chen-ming Fan ,  Gas1 ;  Robert Krauss , Cdon, Boc; and  Atsushi Ohazama ,  Sostdc1 ,  Axin2. We thank  Paul Sharpe  and  Cynthia Andoniadou  for helpful comments relating to the manuscript.
Funding The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by a grant to  M. Seppala  and  M. T. Cobourne  from the  European Orthodontic Society. G. M. Xavier was supported by the  Academy of Medical Sciences (Wellcome Trust ,  British Heart Foundation ,  Arthritis Research UK ) and was the recipient of  National Institute of Health Research (NIHR) UK Clinical Lectureship ;  D. Stonehouse-Smith  is a  NIHR Academic Clinical Fellow in Orthodontics.