dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2016). In some cases, this implies that antibiotic therapies may expose patients to detrimental sideeffects by accelerating pathogen adaptation and raising the risk of antimicrobial tolerance and spread in the commensal bacterial flora if bacteria are exposed to low antibiotic concentrations. The first study demonstrating the real "inducer" property of antimicrobials on biofilm formation at subinhibitory concentrations dates back to 1988  (Schadow et al. , 1988). The adherence of coagulase-negative staphylococci was increased to 65% after rifampicin treatment. Since then, numerous works focusing on the effect of low antibiotic doses on biofilm formation were published. Although several studies have shown that aminoglycoside antibiotics act as antagonists of biofilm formation in vitro (see previous section of this paper), opposite data were collected and highlighted the ability of the same molecules to significantly induce the sessile growth of a variety of bacterial species.
Data validity was confirmed by in vivo assays (catheterrelated infections in the mouse). Results showed that serum concentrations of cloxacillin, corresponding to the MBICs determined by ATBFG (either 2 or 4 µg/ml), allowed reduction to 3 log the bacterial biomasses colonizing the catheters for three clinical strains, whereas the simple MICs of the antibiotic were inefficient on biofilm formation. In a CF context, the use of ATBFG on clinical P. aeruginosa strains also showed the capacity of two aminoglycosides (amikacin and tobramycin) to prevent bacterial adhesion at concentrations close to the MICs  (Olivares et al. , 2017). Only in vitro assays were performed in this study but an intermethod reproducibility was conducted through Crystal Violet staining and a tissue culture system, which validated the inhibitory effect of the antimicrobials on the early adhesion of P.
Real-time detection was performed on a real-time PCR system (Roche LightCycler 480) directed by the LightCycler 480 Software (version 1. 5. 1. 62). Thermal cycling conditions were: Reverse transcription 20 minutes at 55°C, pre-Incubation 3 minutes at 95°C, 50 cycles of DNA amplification (95°C for 15s, 58°C for 30s) and 30s of cooling at 40°C.
This clinical evaluation was approved by French National Protection of Person Committee (NCT04337424). Considering that covid-19 was more severe for aged population, as expected, the average age of active patients is higher than healthcare worker population. The same related with the inflammation markers (e. g. CRP) was observed. Serology was only performed on healthcare workers. EasyCOV a simple and quick SARS-CoV-2 saliva detection for mass screening Here we developed a new simple saliva SARS-CoV-2 detection test based on RT-LAMP technology that we called EasyCOV (Figure  3 ). After saliva collection with a pipette under the tongue, 200 µl of saliva are transferred in a 0. 5 ml tube in which a salivary inactivation solution is present. The tube is then incubated at 65°C for 30 minutes in a simple thermoblock.
But was still able in some case to detect virus in cured patients on late control visit. The specificity was 95. 7% meaning a very low rate of false positive result. However, among healthcare worker population EasyCOV test detected one presymptomatic subject. Future works must investigate the real status of the remaining few false positive. EasyCOV saliva SARS-CoV-2 detection is then suitable for on the spot use in the context of population screening. Reference of Clinical assay: NCT04337424.
Acknowledgements We thanks  Nicolas Doll  from  New England Biolabs France  for technical support,  Caroline Goujon CNRS  for helpful scientific discussion,  Victor Petit ,  Sofia El Annabi, Alexandre Lassaigne from Skillcell, Patrick Collet ,  Yann Pichot ,  Marine Bittel  from  TRONICO ,  Marc Delmas , from  PMB ,  Pascaline Dubs ,  Guillaume Rochet  from  CNRS ,  Thomas Hottier  and  Jérome Bayette  from  Labosud, Christophe Carniel from VOGO  for technical discussions, developments and kind support. Sys2diag members for their day basis support during such complicated period. This work was financially supported by the  CNRS, SkillCell ,  Region Occitanie  and  DGA (AID).
Statistical methods The load to failure average and standard deviation values of all groups in the as-received state and after 30 hours of artificial aging were measured. The bending moment was calculated at the time of implant fracture, which included the lever arm extension [cm] multiplied by the fracture load  [N]. The two-sample t-test was used to compute significant differences within each group before and after aging at a p value of 0. 05 using statistical analysis software (Minitab® 16. 2. 1, Pennsylvania, USA). Significant differences within each group before and after aging were set at the level of alpha = 0. 05.
Acknowledgements This study was supported by  Institute National des Sciences Appliquées de Lyon research funds. A part of the funds was also provided by the  European Commission , under the project  H2020   SISCERA  (contract number  737954 ). We would like to thank Z-systems, Straumann,  TAV Dental , and ZiBone ceramic implant companies for providing zirconia dental implants, the  CLYM (Centre Lyonnais de Microscopie : www. clym. fr)for providing access to their microscopy facilities and  Nicolas Vaché  for assisting us with nickel electroplating. The authors have no conflict of interest.
Data collection and analysis Following the correction of the eight theoretical tests, students' knowledge acquisition was evaluated through an eleven multiple-choice questions test (questionnaire n o 1) summarizing the course content. Students filled this test directly on Moodle (virtual classroom group) or with a paper version (traditional classroom group), as well as a second questionnaire that aimed to determine factors potentially correlated with their knowledge acquisition and to evaluate their satisfaction (questionnaire n o 2) (Supplemental data). Correction of questionnaire n o 1 was taught by the teacher only after the students filled the entire questionnaires (1 and 2). Data collection and analysis were performed by the same investigator. Results of questionnaire n o 1 were compared between virtual and traditional classroom in total group and in subgroups (each trimester).
Dental and Craniofacial Bionetwork for Image Analysis method The Dental and Craniofacial Bionetwork for Image Analysis (DCBIA)  [18]  group developed the historical procedure to perform voxel-based 3D superimposition of craniofacial structures  [8]. This process relies on a combination of two open-source software. The first one, ITK-Snap  [19] , is used for visualization and semi-automatic segmentation of the region of reference. The second one, 3D Slicer [20] is used to register the images on the aforementioned structures and to evaluate the results. To learn how to conduct this method, clinicians and researchers are invited to watch freelyaccessible YouTube video tutorials developed by the research team  [18]. A series of about 20 videos explains the handling of the two software and the main steps to perform 3D superimposition (figure 2, online).
Commercially-available software methods In the last ten years, several commercially-available software allowing voxel-based 3D superimposition were developed. At least 4 software are now available: Dolphin Imaging (Dolphin Imaging and Management Solutions, Chatswoth, CA, USA), InVivo Dental (Anatomage, San Jose, CA, USA), Maxilim (Medicim NV, Mechelen, Belgium) and OnDemand3D (Cybermed, Seoul, Korea)  [8]. General superimpositions have been shown to be reliable for adult patients in Maxilim software  [22] , and for both adult and growing patients in Dolphin Imaging software  [21, 23]. OnDemand3D method has been positively evaluated both for adults and growing patients in general  [24, 25]  as well as regional  [26, 27]  superimpositions. These software are user-friendly, do not require extensive training of the operators and perform superimpositions in a few seconds or minutes.
For example, the OnDemand3D procedure is the following: (1) import of T1 and T2 scans in Digital Imaging and Communication of Medicine (DICOM) format (2) approximate manual registration of the T2 image on the T1 image; (3) selection of the region of reference; (4) algorithm launch; (5) evaluation of results  [28]. This process is shown in Additional file Movie S1 (figure  3 ), which has been recorded in realtime and illustrates the use of OnDemand3D software to superimpose two maxillary CBCT images of patient #2 (see further for case details).
Patient #1, alveolar bone grafting in cleft lip and palate (DCBIA open-source method) A 7-year-old patient with unilateral cleft lip and palate got an alveolar bone graft after orthodontic maxillary expansion. In order to perform a regional maxillary superimposition, we retrieved pre-expansion T1 CBCT and post-surgery T2 CBCT which were acquired two years apart. We followed the DCBIA procedure using open source ITKSnap and 3D Slicer software, using the region of reference previously described in the Material & Methods section. Regional superimposition results can be evaluated in ITKSnap software by navigating in the axial slices. Here, a very good stability and volume of the bone graft can be confirmed (figure  4  and additional file movie S2). Additional evaluation of the results can be made using the 3D surface models of the T1 and T2 images and transparent overlays in 3D Slicer software (figure  5 ).
In order to perform a regional maxillary superimposition, we retrieved the pre-treatment T1 CBCT and post-intrusion T2 CBCT which were acquired three months apart. We used OnDemand3D software to perform the superimposition, as shown in additional file movie S1. All the bone above the teeth's apexes was selected as stable structure because the two images were acquired within a short period of time to each other. Measurements of the displacements can be performed directly on the sagittal slices, providing a quantitative evaluation of the clinical results. As shown in figure  7 , we could confirm that the main displacement of the teeth was proclination through uncontrolled tipping and slight intrusion of teeth #11 and #21.
For example, it is possible to evaluate the osseous displacement on sagittal views as shown in figure 9. To visualize the overall results, we generated a 3D colour-coded mapping of the displacements, which displays the Euclidean distances between the two images through a colour scale (figure  10 ). To this aim, we segmented the T1 and T2 superimposed images and exported the resulting 3D surface model STL files in 3D Slicer software. Then, we used the ShapePopulationViewer extension to compute the colour-coded maps. As expected, the main displacement was found around the chin region and the incisal edges of maxillary incisors.
Conclusion If a CBCT examination is performed, the available 3D data should be exploited entirely for the benefit of the patient. Craniofacial three-dimensional voxel-based superimpositions have been proposed nearly 15 years ago as a convincing method to objectively monitor over time dentofacial treatment outcomes as well as growth changes. However, this approach remains barely used in daily clinical practice. This article aimed to make 3D superimposition accessible to the clinician, whether through a commercially-available software or through a combination of open source programs. -Additional file 2: Movie S2 (. mp4): Evaluation of bone grafting results in patient #1 by navigating in axial slices of T1 and T2 superimposed 3D dataset.
Material and methods This retrospective multicentric institutional review-board (IRB) and ethics committee approved (Groupe Sarcome Français GSF-GETO and Rare Cancer Network RCN) study included all eCHS treated between 1985 and 2015. Data were collected on the secured encrypted website www. easy-crf. com. Base of skull and other intracranial CHS, palliative cases or unresectable / inoperable tumors were excluded. Treatments were discussed on a multidisciplinary sarcoma board. All surgical and RT treatment techniques were allowed. Tumors were centrally reviewed by expert pathologists (RREPS et RESOS) and all histological CHS subtypes were included. Analyses were first conducted considering all histologic subtypes and secondly after extraskeletal myxoid chondrosarcoma (EMC) exclusion, knowing their recent reclassification  [23].
Parameters with a p-value less than 0. 1 in bivariate analysis were selected for the multivariate Fine-Gray model. A simplification of this full model was done with a bootstrap-model selection procedure  [11] , and backward selection. The same process was performed to investigate prognostic factors of DFS and OS by using the Cox proportional-hazards model and results were expressed with their hazard ratio (HR) and 95% confidence intervals. Exploratory subgroup analyses on DFS were performed to identify subgroups of patients who would have the greatest benefit from poRT by investigating the interaction between poRT and major prognostic factors. Results were illustrated by a forest plot. All statistical analyses were performed using SAS software, v9. 4 (SAS Institute Inc. , Cary, NC 25513). P-values <0.
Moreover, adjuvant chemotherapy was administered in highgrade CHS and was consequently associated with a higher risk of death in this series in bivariate analysis (Table  4 ). Despite such observation, poRT remained beneficial on DFS for the entire cohort. Our study has some limitations. Firstly, its retrospective design could limit its broad applicability but the rarity of eCHS prevents efficient prospective assessment of poRT benefit. Secondly, our study included data collected on a long time span. Although potential changes in modalities of surgery, RT practice and systematic molecular analyses (impact of which remains to be demonstrated on radiation response) may have taken place, if a shorter time interval had been decided to limit the heterogeneity of these parameters, the sample size would probably not have been sufficient to conduct such an analysis.
The oral cavity, an essential part of the upper aerodigestive tract, is believed to play an important role in the pathogenicity and transmission of SARS-CoV-2. The identification of targeted antiviral mouth rinses to reduce salivary viral load would contribute to reducing the COVID-19 pandemic. While awaiting the results of significant clinical studies, which to date do not exist, the commercial availability of mouth rinses leads us to search among them for reagents that would have specific antiviral properties with respect to SARS-CoV-2. The challenges facing this target were examined for 7 reagents found in commercially available mouth rinses and listed on the ClinicalTrials. gov website: povidone-iodine, chlorhexidine, hydrogen peroxide, cyclodextrin, Citrox, cetylpyridinium chloride, and essential oils.
2020; Herrera et al. 2020). Many articles have recommended the use of a mouth rinse to prevent the spread of SARS-CoV-2. However, to date (July 30), only 12 clinical protocols testing the effect of mouth rinse on SARS-CoV-2 are listed in ClinicalTrials. gov (Find Trials 2020; Fig. 1 ). One study used mouth rinse exclusively, 2 studies combined it with nasal swab sticks, and 1 study combined mouth rinse with a sinus rinse. Seven studies used mouth rinses as a gargle with or without nasal lavage, nasal spray, or nasal gel. Most of these trials evaluated PVP-I. The reduction of the salivary viral load, quantified using a polymerase chain reaction (PCR) technique, is a minority research objective. Indeed, only 3 studies had this objective. The focus of the other trials was mainly on the potential interaction of the viral load between the naso-and oropharynx with the combined use of gargle and nasal applications.
Mouth Rinses Containing H 2 O 2 H 2 O 2 is a chemical compound. It is a widely used antimicrobial, and its efficacy has been demonstrated on several human viruses, among which coronavirus and influenza viruses were found to be most sensitive (Table  2 ;  Kumar et al. 2020 ). H 2 O 2 targets the viral lipid envelope of these viruses and, more particularly, of SARS-CoV-2 (O'Donnell et al. 2020). It liberates oxygen-free radicals and disrupts the lipid membrane  (Peng et al. 2020 ). H 2 O 2 presents the advantage of being safe for  The electronic research was organized in the PubMed database. The following MeSH and non-MeSH search terms were used: ("Chlorhexidine" [MeSH terms] OR ("Cetylpyridinium chloride" [All fields] OR "essential oils" [All fields] OR "hydrogen peroxide" [All fields] OR "Povidone-iodine" [All fields] OR ("Citrox" [All fields] OR "Cyclodextrin" [All fields] AND ("Virucidal" [MeSH terms] OR ("Antiviral" [All fields]).
5% Avrio Health L. P. , USA This table is a synthesisof data obtained from electronic research organized in the databases ClinicalTrials. gov, Drug Information Portal (National Institutes of Health), National Drug Code List, and PubMed. The following MeSH and non-MeSH search terms were used to encompass every type of over-the-counter (OTC) mouthrinse or mouthwash: ("mouth rinse" [MeSH terms] OR "mouthwashes" [All fields]) AND ("Chlorhexidine" [MeSH terms] OR ("Cetylpyridinium chloride" [All fields] OR "essential oils" [All fields] OR "hydrogen peroxide" [All fields] OR "Povidone-iodine" [All fields] OR ("Citrox" [All fields] OR "Cyclodextrin" [All fields]). a Number of clinical studies identified in ClinicalTrials. gov. b Twenty-four OTC drugs use the same package name. The list of manufacturers' names is available at https://ndclist.
Acknowledgements COST action TD 1305:  IPROMEDAI-Improved Protection of Medical Devices Against Infection. The following are also acknowledged for their contribution in the discussions:  Reto Luginbuehl ,  University of Bern, Bern, Switzerland ;  Moter Annette ,  Charité-Universitätsmedizin Berlin, Germany ;  Thevissen Karin ,  KU, Leuven, Belgium; Furtos Gabriel, Raluca Ripan Institute of Research in Chemistry, Babes-Bolyai, University, Romania ;  Gameiro Paula ,  Faculdade de Ciências da Universidade do Porto , Portugal;  Katsikogianni Maria ,  Richmond Building. Department of Chemistry and Biosciences. RKT Centre, Advanced Materials Engineering, University of Bradford, UK; Locs Janis, Rudolfs Cimdins Riga, Biomaterials Innovations and Development Centre, Riga Technical University, Riga, Latvia; Miskovic Stankovic Vesna, Department of Physical Chemistry and Electrochemistry, University of Belgrade, Faculty of Technology and Metallurgy, Belgrade; Chakraborti Soumyananda, Malopolska Centre of Biotechnology Krakow, Poland; C ¸imeno glu Huseyin, Istanbul Technical University, Istanbul, Turkey ;  Farzaneh Moghtader ,  Zanjan University of Medical Sciences, Turkey; Albu Kaya Amadalina, INCDTP -Division ICPI, Collagen Department, Bucharest, Romania; Pavilan Cornelia, University of Basel, Switzerland; Bakopoulou Athina, Department of Prosthodontics, School of Dentistry, Aristotle University of Thessaloniki, Greece, Bousnaki Maria, Department of Prosthodontics, School of Dentistry, Aristotle University of Thessaloniki, Greece.
The spectral range of the analysis was from 600 to 1750 cm À 1 and the acquisition time for each spectrum was 2 times 20 s. Eleven acquisitions were recorded every 2 mm along the length on the polymerized and their opposite sides for three composite samples of each group. All experiments were performed in an air-conditioned room with a constant temperature of 21 � C. Spectral pre-processing was performed using Labspec 6 software (Horiba Jobin Yvon, Villeneuve d'Ascq, France). A normal variate correction and polynomial smoothing with size 9 and degree 6 was used. A polynomial type baseline correction with 8 � and maximum point of 33 was realized on all spectrum. In methacrylate based composites, the aliphatic C--C stretching mode (1640 cm À 1 ) peak allowed evaluation of the polymerization degree and it was correlated with the aromatic C--C stretching mode (1610 cm À 1 ) peak, which was taken as an internal reference  (Acquaviva et al.
Statistical analyses All statistical analyses were performed with RStudio software (version 1. 2. 5001). Results were exploited using a mixed linear model because our test protocol included multilevel data. Micro-Raman spectral data, the influence of irradiation time, method of polymerization, irradiated side and composite, were considered as fixed effect covariables and their involvement were verified by a sequential introduction into the model. The measurements made on each point and the sample parameters were considered random effect variables to account for the correlation inter-specimen and inter-measuring points data. Variations of these terms in intercepts and slopes within the model were characterised. The restricted maximum likelihood method was used to calculate the model coefficients.
Acknowledgements The authors would like to thank  Pr Marc ENGELS-DEUTSCH  and  Pr Boussad ABBES. They would like to thank  GC Corporation  ( Tokyo, Japan ) for curing-light loan,  Dentsply De Trey GmbH (Konstanz, Germany ) and  3M ESPE (St. Paul, MN, USA)  for composite donation. The authors thank the  Reims PICT Platform  for instrument facilities.
Data collection. Every complication occuring in the 6 months following surgery was documented. Antibiotic type, duration of treatment, surgical drainage and patient's evolution were recorded. The initial SSI severity was defined by the following presentations: cellulitic reaction treated with oral antibiotics, local collection requiring surgical drainage under local anaesthesia, and extensive cellulitis needing surgical drainage under general anesthesia. The evolution of SSI was classified according to the following categories: complete recovery, plate loosening or pain requiring hardware removal, and long-term complications (osteomyelitis or pseudarthrosis). The diagnosis of osteomyelitis was based on clinical history, sampling of the bone and histopathological characteristics  13. Statistical analysis.
MMP2 RNA, ENE, PNI and stage were independent prognostic factors To identify clinical and biological parameters significant in multivariate analysis, we performed two Cox proportional hazards models. Model 1 included all the 145 patients and all clinical and biological variables significant in univariate analysis, except PNI and VE, because of missing values in 21 patients (14%), whereas Model 2 included all significant variables, but was restricted to the 124 patients with complete data (Fig 3A, Table  S5 ). In both models MMP2high was an independent prognostic factor for DSS and DFS (Model 1 DSS: p = 0. 001, DFS: p = 0. 006, Model 2 DSS: p = 0. 034, DFS: p = 0. 016). For DSS, ENE status (p = 0. 006) and PNI (p = 0. 020) were also significant in Model 1 and 2, respectively. For DFS, ENE status was also significant in Model 1 (p = 0.
A database for healthy body fluids proteome was created in 2008, highlighting the general interest for such approach  (18). Here, we cannot exclude that tissue handling, although limited to the minimum in our protocol, may have induced or enhanced the production of some proteins, but this limitation was partially overcome by the comparison with paired juxtatumor supernatant. By the mean of an ultrafiltration catheter, interstitial fluid from a single HNSCC patient was analyzed and revealed 525 proteins by mass spectrometry, but the method was not applicable to juxtatumor tissue, which limited the potential to identify candidate biomarkers  (19). Another difficulty is that tumor secretome needs to be produced prospectively using fresh tumor samples, which limits the access to large cohorts with sufficient follow-up in order to identify prognostic biomarkers.