dataesr/scientific-paragraphs-categorization huggingface dataset:
5 (258 over-accumulated and 358 under-accumulated proteins, respectively) and 249 proteins were classified as non-modified (see materials and methods and S2 Table for details). According to the functional categories defined by the PseudoCAP database  [15] , the over-accumulated proteins in AC mainly belonged to the "adaptation, protection" (31 hits), "membrane proteins" (27 hits) and "chemotaxis" (17 hits) categories (Fig 2A ), whereas under-accumulated proteins mainly belonged to the categories related to gene expression: "Transcription, RNA processing and degradation" (17 hits); "transcriptional regulators" (28 hits) and "translation, post-translational modification, degradation" (49 hits) (Fig  2B ). Similarly the proteins listed in the "carbon compound catabolism" and in the "biosynthesis of cofactors, prosthetic groups and carriers" categories were rather under-accumulated in AC.
In our study, 15 transcriptional regulators and 11 probable transcriptional regulators were quantified and were mainly under-accumulated suggesting a limited transcriptional activity in AC (S3A Table ). The accumulation of MexL (PA3678, R = 3. 71), the transcriptional repressor of the mexJK multidrug efflux operon was not in contradiction with this proposal. All these data suggested that the general transcriptional activity was lower in AC compared to their unattached counterparts. The attenuated RNA synthesis activity was corroborated by examining RNA maturation and RNA degradation. 13 proteins involved in RNA maturation, especially in rRNA and tRNA maturation were found, they were all under-accumulated in AC. Among the proteins belonging to the "RNA degradation" category, PA4951 (Orn, R = 3.
Analysis of the highest differentially accumulated proteins in attached cells To complete our study, we focused on the highest differentially accumulated proteins in AC compared to their UC counterparts. For this, only proteins whose relative quantity was increased by at least a factor 10 (i. e. 57 proteins) or decreased by one log or more (i. e. 80 proteins) were selected (S7 Table ). Observing so many highly differentially accumulated proteins (137) early as 20 minutes of incubation with GW reinforced the hypothesis of the need for a particular physiology dedicated to the attachment. Among these proteins, 33 proteins have an unknown function and 29 have a probable function according to the Pseudomonas Genome Database  [15]. Because of this high proportion of proteins of unknown function, we first focused on the known interactions between the proteins listed in S7 Table by using the software STRING v.
10 [77]  with the default setting. Among the 80 strongly under-accumulated proteins, 55 were predicted to interact (S1A Fig). In this category, ribosomal proteins were grouped together, as expected, as well as several proteins related to virulence. In addition, the analysis predicted an interaction between PA5133 and PA3787, 2 conserved hypothetical proteins both related to metallopeptidase according to the COG database. Among the 57 strongly over-accumulated proteins, 31 were predicted to be interactants (S1B Fig). The analysis predicted 2 groups comprising 2 interacting proteins (PA0270-PA0565; PA3202-PA5229) all of unknown function. The software STRING also revealed interactions on the one hand between 2 proteins belonging to the P-type ATPase (PA1429-PA3920), both probably involved in the transport of cation and, on the other hand between the proteins PA5055 and PA5065 (UbiB).
Additionally, by rummaging P. aeruginosa PAO1 Protein Interactome  [78] , we found a relevant interaction between PA0950 and PA3664 both linked to oxidation-reduction process. All these proteins with large variations of relative abundance between AC and UC could be part of pathways determinant for surface attachment. Moreover, as protein synthesis appeared diminished in AC, the study of strongly over-accumulated proteins could be of particular interest for identifying proteins involved in the attachment phase. Validation of our proteomic data was carried out by testing the attachment capacity of available mutants inactivated for genes corresponding to the highly over-accumulated proteins in AC. Among the 43 mutants analyzed, 8 strains showed a marked difference in attachment ability compared to PAO1 control (S8 Table ).
The comparison of the 2 analyses could then identify the key components of the attachment phase. From our data, it is obvious that the mechanism of initial attachment to a surface is a complex process involving numerous factors. The proteome dataset reported here will serve as a resource for detailed investigations of surface attachment in P. aeruginosa. Among these proteins, novel anti-biofilm molecular targets could be discovered. In vitro biofilm studies have provided valuable explanations for early events in biofilm infections  [96]. In addition, as AC already exhibited characteristics of slow-growing bacteria after only 20 min, our analysis reinforces the need to develop new inhibitory molecules other than antibiotics that are generally effective on dividing cells.
The peptides were eluted from the trap column onto an analytical 75-mm id x 15-cm C18 Pep-Map column (LC Packings) with a 4-40% linear gradient of solvent B in 108 min. Mobile phases were a mix of solvent A (0. 1% formic acid in 5% ACN) and solvent B (0. 1% formic acid in 80% ACN). The separation flow rate was set at 300 nL/min. The mass spectrometer operated in positive ion mode at a 1. 9-kV needle voltage. Data were acquired using Xcalibur 2. 2 software in a data-dependent mode. MS scans (m/z 300-2000) were recorded at a resolution of R = 70000 (@ m/z 200) and an automatic gain control (AGC) target of 1 x 10 6 ions collected within 100 ms. Dynamic exclusion was set to 30 s and the top 15 ions were selected from fragmentation in higher-energy collisional dissociation (HCD) mode. MS/MS scans with a target value of 1 x 10 5 ions were collected with a maximum fill time of 120 ms and a resolution of R = 35000.
Additionally, only +2 and +3 charged ions were selected for fragmentation. Other settings were as follows: neither sheath nor auxiliary gas flow; heated capillary temperature, 200˚C; normalized HCD collision energy of 25% and an isolation width of 3 m/z. Database search and results processing. Data were searched by SEQUEST through Proteome Discoverer 1. 4 (Thermo Fisher Scientific Inc. ) against the protein database from the Pseudomonas Genome Database website  [15]  consisting of 5570 entries. Spectra from peptides higher than 5000 Da or lower than 350 Da were rejected. The search parameters were as follows: mass accuracy of the monoisotopic peptide precursor and peptide fragments was set to 10 ppm and 0. 02 Da, respectively. Only b-and y-ions were considered for mass calculation. Oxidation of methionine (+16 Da), deamidation of asparagine and glutamine (+1 Da), propionamide (+71 Da) and carbamidomethylation of cysteine (+57 Da) were considered as variable modifications.
05), (vii) Protein abundance in each sample was calculated by summing volumes of all unique peptides, (viii) An additional ANOVA test was conducted at protein level and the proteins with p > 0. 05 were not retained for biological analysis. Quantitative data were considered for proteins quantified by a minimum of 2 peptides and only proteins fulfilling all the criteria mentioned above from the set of identified proteins were included in the final quantification lists. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium  [100]  via the PRIDE partner repository with the dataset identifier PXD002942.
Conventional radiological evaluation The panoramic images are taken in the office of Dr. Gall-Bachet-Dameron-Chevalier with the same device. The images are studied using OsiriX software ®. The primary judgment criteria are evaluated for each protocol step: T-0, T-6, T-12, and T-18, using the following method: • Evaluation of the anteroposterior position of the maxillary permanent canine: -plot of the major axis of the lateral incisor; -plot of the tangent to the mesial edge of the lateral incisor; -plot of the tangent to the distal edge of the lateral incisor; -plot of the tangent to the distal edge of the temporary canine; -plot of the major axis of the central incisor. These five segments determine five sectors numbered from 1 to 5, from the most distal sector to the most mesial sector. Sector 1 is the most favorable for canine development, Sector 5 being the least favorable (Figure  1 ).
Number of required subjects The number of required subjects was calculated on the basis of the comparison of a quantitative variable between two groups of subjects. According to the data from a preliminary study, the standard deviations of the heights measured vary from 0. 29 to 1. 50 ( retained value) depending on the teeth. To show a difference in height of 1 mm between the beginning and the end of the treatment with a power of 0. 80; thus, the number of subjects necessary for this study was set at 35.
Taking the measurements The measurements were performed on virtual casts stored on the Bibliocast platform. An integrated caliper tool was used to make the measurements. The coronal height was measured from the lowest point of the tooth neck to the highest point of the cuspid. We tested the reproducibility of the measurements when the inclination of the model varies with respect to the occlusal plane. To do this, we performed three measurements per tooth: one at +45°, one at -45°, and a one from the occlusal plane, that is to say a measurement at 0° (Fig. 1 ). The reproducibility of the coronary height measurements was assessed using the intraclass correlation coefficient (SPSS software version 17. 0). The analysis was done with two random variables because the random error can come from either the operator (measurement error) or the subject (defective casting).
Methods To ensure a systematic review of the available literature, the following steps were followed: question formulation, definition of electronic database search strategy, retrieval of publications, studies selection, data extraction and evaluation. As a first step, the following questions, that could fulfil the purpose of this work, were formulated: which are clinical advantages and disadvantages of computer guided implant placement compared to conventional treatment protocols? Regarding medical and economic aspect, in which clinical situations guided surgery could be justified? Based on the PICO criteria, a search strategy was developed and executed in MEDLINE (PubMed) electronic database. Search terms were selected and then grouped into categories for "Problem" -"Intervention" -"Control" -"Outcome".
All authors independently read and exanimated titles and abstracts of all studies identified with electronic and hand search and recommended their inclusion or exclusion according to defined criteria. When at least one author considered that a publication met inclusion criteria, full text was obtained and evaluated for its eligibility. Disagreements about inclusion or exclusion were resolved by discussion. Afterwards It was also conducted a search within references of full-text publications evaluated. After assessment process, the following data were extracted from eligible studies: authors, year of publication, study design, patients' population, type of surgical intervention, primary and secondary outcomes. All the authors performed full-text articles evaluation and data extraction together during 1st Conference meeting of the Digital Dental Society (DDS) in Milan, Italy, 16th-17th September 2016; all disagreements were resolved by discussion.
Included studies Evaluation process of articles selected for this review is schematically shown in Fig. 1. The search strategy carried out in MEDLINE (PubMed) electronic database revealed 14 articles; additional manual searches selected further 21 publications. Afterwards the evaluation of the 37 abstracts there were found only four works who respected inclusion criteria. Of these publications, after full text analyses, two were excluded as one did not present a follow-up period  [11] , while the other did not show a control group in which conventional surgical procedures were used  [12]. Finally, only two papers complied with all inclusion criteria  [13, 14]. Data extracted from these two papers were reported in Table  2.
Randomization Patients will be randomly assigned to one of the two arms at a ratio of 1:1. The randomization list will be computer-generated by the study statistician using SAS system software (version 9. 2, SAS Institute, Inc. , Cary, NC, USA). The randomization process will be centralized through a secured website managed by the Bordeaux University Hospital Clinical Trial Unit (CTU) («Unité de Soutien Méthodologique à la Recherche Clinique et Epidémiologique (USMR)»). After confirmation of the patient's eligibility criteria, the investigator will access the website of the CTU, which will provide the patient's unique allocation number and randomization group. Access to the final dataset will be limited to the investigators.
This indicated the presence in these strains of putative ICEs belonging to the ICESt3 subfamily. However, not all these strains showed a positive PCR signal for the ICESt3 integrase gene, which catalyzes the integration into the fda site. This suggested the presence of other recombination modules associated with the ICESt3 conjugation module in S. salivarius ICEs. In this work, we selected 13 strains with different MLST patterns (including 6 strains with a negative PCR signal for the ICESt3 integrase gene) and sequenced their genomes in order to gain access to their ICE sequences. ICEs with a conjugation module closely related to the one in ICESt3 were searched in other NCBI database-available genomes of S. salivarius and in other genomes of Firmicutes. ICE sequences were compared and the putative functions encoded by their genes were analyzed in silico.
1 , ICEs found in these 13 S. salivarius strains all display a conjugation module that is closely related to that of ICESt3 from S. thermophilus (Ͼ90% nucleic sequence identity). ICEs with a closely related full-conjugation module were also detected in 2 genomes of S. salivarius available in the NCBI database (those of strains JF and 1270) (Fig. 1 ). The element of S. salivarius NCTC 8618 (GenBank accession number CP009913. 1) also has a closely related full-conjugation module but is not shown in the figure since it harbors a truncated integrase gene and is therefore defective. Elements with a closely related conjugation module (partial in most of the genomes due to gaps in the assembly) were also detected in the genomes of strains GED7778A (GenBank accession number LRQS00000000), 140 (GenBank accession number JVSQ01000000), 20-02 S1 (GenBank accession number LXMB00000000), 20-12 S2 (GenBank accession number LXMC00000000), and UC3162 (GenBank accession number JYOY01000000).
These elements are not shown in Fig. 1  because their sequences are incomplete. ICEs with a closely related conjugation module (92 to 94% nucleic sequence identity with that of ICESt3) were also identified in the genome of Streptococcus pneumoniae 2842STDY5753514 (mitis group) and Streptococcus parasanguinis DD19 (sanguinis group) (Fig. 1 ). Phylogenetic analysis of the relaxase OrfJ (Fig. 2 ) and the coupling protein OrfK (Fig. 3 ) of these ICEs indicates that they group with OrfJ and OrfK from S. salivarius ICEs. Similar results were obtained for the other proteins of the conjugation module (data not shown). Taken as a whole, these phylogenetic analyses and sequence comparisons clearly showed that transfers of ICEs closely related to ICESt3 have occurred between distinct species from different streptococcal groups.
This is due to an insertion of genes (including one encoding a transposase) in this region of the ICE (Fig. 1 ). The arp1, orfQ, and arp2 genes encode, respectively, a cI-related repressor, an ImmA-related putative protease  (32) , and a putative transcriptional regulator  (33)  that are related to those of ICESt3 from S. thermophilus  (26, 34). Arp1 and Arp2 homologs all share an N-terminal helix-turn helix PF01381 domain that is found in several regulatory proteins, including Cro and cI regulators of the phage. Arp1 proteins also display a C-terminal PF00717 peptidase S24-like domain involved in the autocleavage of the cI repressor induced by DNA damage. OrfQ homologs are characterized by a COG2856 Zn-dependent peptidase ImmA domain, also found in the ImmA protease of ICEBs1 of B. subtilis that cleaves the ImmR repressor in response to DNA damage  (32).
This is the case for ICE_SsaF4-2_fda, which has a conjugation module closely related to the one of ICESt3 (94% nucleic sequence identity over the whole conjugation module) but encodes more distant regulators (with 63, 46, and 73% amino acid identity with those encoded by ICESt3 for Arp1, OrfQ, and Arp2, respectively). Furthermore, all the regulation modules include additional genes (1 to 3 depending on the ICE) between the arp2 and orfQ genes. These genes that encode proteins of unknown function contribute to the diversity of the regulation modules. (iv) Accretions. Accretion of ICEs with other genetic elements was observed: ICEs of strains F1-8 and L60 were in accretion with a putative IME, whereas those of strains F6-1 and L50 were adjacent to 1 or 2 CIMEs (data not shown). Evidence of accretion or recombination events was also found in the sequences of several ICEs of S.
The ICE found in S. macedonicus 33MO carries genes that encode cell envelope proteins: one with a PF03780 domain with cell envelope-related function (E ϭ 7. 93eϪ23) and three membrane proteins. Lastly, ICEs of S. salivarius T93 and S. parasanguinis DD19 harbor the same cargo genes, in particular, (i) a two-component system with a signal transduction histidine kinase (nitrate/nitrite-specific COG3850 NarQ domain, E ϭ 5. 3eϪ13) and a NarL DNA-binding response regulator (COG2197 domain, E ϭ 6. 1eϪ48) and (ii) a cluster of genes encoding a putative LolCDE complex which catalyzes the release of lipoproteins from the cytoplasmic membrane (LolC PF13521 AAA_28 domain, E ϭ 1. 2eϪ09; LolD cd03255 ABC_MJ0796_LolCDE_FtsE domain, E ϭ 1. 2eϪ108; and LolE COG4591 domain, E ϭ 4. 4eϪ14) (Fig. 1 ). Excision testing of 2 putative ICEs: ICE_SsaF1-4_fda and ICE_SsaF4-2_fda.
Test of intraspecies conjugative transfer of 2 putative ICEs of S. salivarius. Both ICE_SsaF1-4_fda and ICE_SsaF4-2_fda were first tagged by a chloramphenicol resistance cassette (Table  1 ). Donor strains were then used in filter mating experiments with two S. salivarius recipient strains: JIM8777 and F1-8, displaying different genotypes (Table  1  and 3 ). Both strains carry an empty fda integration site, and strain F1-8 carries an ICE belonging to the ICESt3 subfamily (Fig. 1 ) in accretion with an IME integrated in the 3= end of rpmG. Some putative transconjugants were recovered when S. salivarius JIM8777 or F1-8 was used as the recipient (Table  3 ). After subculturing, transconjugants were confirmed by detection of the integrase gene (data are shown only for ICE_SsaF1-4_fda [Fig. 5a  and b] ).
For JIM8777 derivative clones, this screen was combined with detection of the pMG36e plasmid and random amplification of polymorphic DNA (RAPD) (Fig. 5a ). F1-8 transconjugants were confirmed by sequencing of an MLST locus (ddlA gene). The site-specific insertion in the fda gene and the excision of the newly acquired ICEs were also confirmed by the PCR detection of attL, attR, attI, and attB sites for both F1-8 (data are shown only for ICE_SsaF1-4_fda [Fig. 5c ]) and JIM8777 (data not shown). This suggests that the elements are still active in these transconjugants (at least for excision). Mating experiments were repeated with at least 3 different cultures of donor and recipient cells (biological repetitions) but very few transconjugants (2 clones for the whole experiment) were obtained, thus preventing any calculation of transfer frequency.
For each mating assay, transconjugants were recovered and confirmed by PCR detection of both the ICE integrase gene and plasmid pMG36e present in the recipients (data not shown). A small number of transconjugant colonies (as for intraspecies transfer of ICE_SsaF1-4_fda, i. e. , 2 clones for the whole experiment) was observed when using S. salivarius as the donor and strains with the same genetic background as the recipients (F1-8/F1-8 mating pairs) or S. thermophilus LMG18311 cells as recipient cells. In contrast, more transconjugant colonies (at least 20 clones for the whole experiment) were obtained using S. thermophilus LMG18311(ICE_SsaF1-4_fda) and E. faecalis JH2-2(ICE_SsaF1-4_fda) as donors and LMG18311(pMG36e) and JH2-2(pMG36e) cells as recipient cells. These results confirm that ICE_SsaF1-4_fda is able to transfer autonomously but also suggest that (i) host factors could impact ICE replication and/or assembly of the conjugation machinery in S.
The 13 selected S. salivarius strains were subjected to whole-genome sequencing. Sequencing was done with an Illumina HiSeq2000 sequencer by Beckman Coulter genomics (2 ϫ 100 bp after paired-end library construction, with at least 60ϫ coverage expected). Observed sequencing depth was higher than 200ϫ for all the 13 genomes. De novo assembly was performed using CLC Genomics Workbench (CLC Bio) with default parameters. A scaffold of the genomes was built by using the Genome Finishing module of CLC Genomics Workbench with the S. salivarius JIM8777 genome as reference. Some assembly gaps were filled by PCR and sequencing. This enabled us to obtain genomes fragmented in less than 75 contigs (less than 30 contigs for two-thirds of the genomes; the median size of the contigs was higher than 40 kb for half of them).
Contigs were first annotated using the RAST annotation server (http://rast. nmpdr. org/) (50, 51). Then, contigs containing genes closely related to conjugation genes of ICESt3 were identified by BLASTN analysis (using the orfO to orfA genes as a query by megaBlast analysis with default parameters and filter disabled), and annotation was completed manually. In NCBI sequence data banks, ICEs closely related to ICESt3 were searched by using microbial nucleotide blast (using the orfO to orfA genes as a query by megaBlast analysis with default parameters and filter disabled) on complete (n ϭ 816; last accessed 29 July 2016) and draft (n ϭ 9,573; last accessed 29 July 2016) genomes of Firmicutes. Hits with more than 90% identity with the whole query sequence were further analyzed. Pairwise comparisons of elements were performed with Artemis Comparison Tool provided by the Sanger Centre using comparison files generated by Double Act (available at http://www.
hpa-bioinfotools. org. uk/ pise/double_actv2. html) (52). Manual editing of comparison figures was performed using Inkscape. Phylogenetic tree construction. Proteins of 27 ICEs were included in the analysis. These ICEs correspond to (i) the 19 ICEs of the ICESt3 subfamily with closely related conjugation modules and (ii) 8 additional ones previously reported to belong to the same ICE subfamily but showing more distantly related conjugation modules  (11, 26). The sequences of signature proteins were aligned using Clustal omega with default parameters  (53). The trees were built with MEGA (54) using (i) maximum likelihood (ML) based on the Jones-Taylor-Thornton (JTT) model including amino acid empirical frequencies (partial deletion of gaps and missing data at 80% cutoff, gamma distribution in 5 categories, and allowance for invariant sites), and (ii) BioNJ methods with the Poisson model  (55).