dataesr/scientific-paragraphs-categorization huggingface dataset:
Reverse Transcriptase-qPCR Immediately following a 24-or 48-h infection, RNA was isolated from Mø in 12-well plates. RNA isolation was performed using NZY Total RNA Isolation kit (NZYTech), following the manufacturer's instructions. Total RNA measuring 200 ng was used for cDNA synthesis with NZY First-Strand cDNA Synthesis Kit (NZYTech), according to the manufacturer's instructions. qPCR was performed using NZY qPCR Green Master Mix (NZYTech) with the different sets of primers (Table  1 ) (Eurofins Genomics) at a final concentration of 0. 5 mM. The PCR proceeded as follows: 1 cycle of 95°C for 10 min, followed by 40 cycles of 95°C for 15 s, 60°C for 30 s, and 72°C for 30 s. The qPCR was performed using a QuantStudio ™ 7 Flex System (Thermo Fisher). The data were analyzed using the DDCt method in the Applied Biosystems ™ Analysis Software.
The mRNA expression profiles were normalized with respect to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) housekeeping gene and finally calculated relative to noninfected samples. For each condition, three biological replicates were tested; and for every biological replicate, two technical replicates were performed. Statistical analysis was performed by ANOVA two-parameter. Gene expression heatmaps were generated using TM4 MultiExperiment Viewer software.
No signal was detected in non-infected cells, confirming that the red fluorescence detected in the cytosol corresponds to virus-encoded Gag protein. ImageJ software analysis of the images showed that about 80% of cells expose to HIV particles internalized the virus. Most cells displayed small numbers of dots in the cytoplasm. A large number of cells tend to concentrate them at the nuclear region. This finding is in accordance with previous results showing viral capsid concentration in nuclear region before retrotranscription  (45)  and with viral staining of Gag visualized by confocal microscopy 6 h p. i in cytosol and in perinuclear region of Mø  (46). Since one of the steps of virus replication cycle is the integration of the retroviral DNA into the host genome, a nested PCR (Figure  1C ) revealed an amplicon of 391 bp, thus further confirming HIV infection of Mø.
ACKNOWLEDGMENTS ADEIM-FFUL (Associacão para o Ensino e a Investigacão em Microbiologia); to the  Instituto Portugueŝ do Sangue  for providing human blood samples; to BEI resources (and  Colorado State Univ. , USA)  for proteins and strains; and to  Instituto Nacional de Saude Ricardo Jorge  for clinical strains and their antibiotic susceptibility determination.
Procedure for unblinding if needed {17b} The lifting the blind will then be able to be carried out by the resident or the practitioner who treats the patient. 7 Data collection and management 7. 1 Plans for assessment and collection of outcomes LSPI only be used once per patient during the bonding appointment. It will be read with a periodontal probe on the 4 sides of each tooth from 16 to 26 (12 teeth so 48 measurements in total per patient). Then, to evaluate the plaque control, the MOP will be used at each appointment. Its evaluation is done on 3 intra-oral photographs in occlusion after removal of the orthodontic archwires. They will be calibrated using a spreader with green marks to have the same magni cation. The camera used is a Nikon D7000 model with an AF-S Micro Nikkor 60mm lens.
Plans to promote participant retention and complete follow-up {18b} Subjects may withdraw their consent and request to exit the study at any time and for any reason. Data prior to this withdrawal of consent will be collected unless the participant objects in writing. The investigator may temporarily or permanently interrupt the participation of a subject in the study for any reason that would best serve the subject's interests. In the event of premature exit, the investigator must document the reasons as completely as possible. Leaving a participant's study should not change their usual care in relation to their illness. In the event of a subject lost to follow-up, the investigator will make every effort to resume contact with the person.
management {19} and Con {27} All clinical data will be collected in anonym / individual case report form (CRF). The data will then be compiled in an Excel spreadsheet meeting the requirements of the FDPA (French Data Protection Authority). The Excel le including the anonymized data and that of the correspondence table will be protected by a password and saved on the secure server of the Rennes hospital. They will not be transmitted outside the establishment. The les will be accessible only to the investigators and examiners. Photo shoots will be kept in the patient's CRF. 7. 4 Plans for collection, laboratory evaluation and storage of biological specimens for genetic or molecular analysis in this trial/future use {33} Not applicable 8 Statistical methods.
It was therefore decided in agreement with the patient, his parents and the surgical and prosthetic teams, to use mini-implants. Four OBI ® (Eurotechnika, Sallanches, France) of a diameter of 2. 7 mm type mini-implants were placed after avulsion of tooth 22. The OBI ® implants length ranged from 9 to 15 mm. An optical and a Cone Beam Computed Tomography (CBCT) impression were made to plan the surgery and print a surgical guide from the 3Shape Implant Studio software (Straumann, Basel, Switzerland) (Figures  9  and 10 ). The implantation planning allowed to optimize the drilling axis of the mini implants according to the residual bone volume. After implant placement (Figures  11 12 13 14 ), an orthodontic arch with four incisors was set up as a temporary solution (Figure  15 ).
Images were acquired on a spinning disc from Perkin Elmer with the CSU-X1 scan head. The biofilms were observed using a 40× water immersion objective (Fluor 40×/0. 8W, Nikon). The biofilm image stacks were obtained at 499 × 500 pixels (two HAMAMATSU C9100-13 EMCCD cameras) in three different areas of each surface analysed. 3D reconstructions were created by ImageJ software.
| Data management and statistical analysis We used Excel 2007 (Microsoft Inc. ) to create a database with appropriate checks to identify errors and a commercially available statistical software package (SPSS V27) for analyses. Descriptive statistics were computed for all study variables. Univariate and multivariate regression mixed-effect models, if indicated, were developed to evaluate possible associations between the predictor variable and the outcome variables. Cox proportional hazard modeling was used to identify patients at risk for PME within 6 months after OSM-MWFILB. To assess the univariate models, candidate variables with p ≤. 15 were considered statistically significant. These eligible candidate variables were then further analyzed using the multivariate model with the statistical levels of significance, p ≤.
Literature Search Methodology Two independent reviewers (G. S. , C. Z. ) performed a comprehensive literature search to identify related studies in PubMed, Scopus, Web of Science, and Cochrane Library databases, between 1 January 2010 and 15 May 2021. The following search strategy was used to find relevant studies: (bioceramic sealer OR bioceramic root canal sealer) OR (hydraulic sealer OR hydraulic root canal sealer) OR (calcium silicate-based sealer OR calcium silicate-based root canal sealer) AND (root canal OR endodontics OR root canal treatment) OR (root canal filling OR root canal obturation). The references list of the included studies and previously published reviews were searched. Laboratory and clinical studies investigating at least one of the CSBS' properties/outcome were included in the review.
The plates were washed twice with PBST and imaged in an Operetta High Content Imaging System (Perkin Elmer) using a 20 × magnification objective. Five images were acquired per well and analyzed using Harmony software (Perkin Elmer), version 3. 5. 2. Image analysis consisted of identifying and counting the Vero E6 cells based on the nuclear segmentation, viral infection, and cytoplasmic staining detected by the immunofluorescence assay  27. Clinical trial design and oversight. This triple-blind randomized controlled trial was conducted in accordance with the principles of the Declaration of Helsinki and ethical standards of human experimentation with the approval of the Human Research Ethics Committee of Bauru School of Dentistry of the University of Sao Paulo, Brazil (CAAE 34,070,620. 6. 0000.
An EXCEL ® database was created from these numbered packages and used for randomization. After randomiza-(  1 ) Reduction (%) = [(B -A)/B] × 100. tion, packages with mouthwash bottles and oral care kits were delivered to the hospitalized patients. This study was considered triple-blind because the patients, the examiner and the statistician were blinded to the treatment groups. Mouthwash intervention. The eligible participants were randomly assigned to one of the following groups: AM or NAM. The patients were instructed to use 5 mL of the mouthwash and to switch between gargling/rinsing for 1 min up to 5 times a day: upon awakening, after breakfast, after lunch, after dinner and before bedtime  14, 15. Each patient followed this adjunctive therapeutic protocol until the outcome associated with COVID-19 medicine treatment was recorded.
Outcome measures. The primary outcome was the time to clinical improvement, defined as the length of stay in the hospital (patients did not need oxygen therapy support for more than 24 h and no longer showed any symptoms). Secondary outcomes were clinical evolution, need for care in the ICU and death. The criteria for the transfer of a patient to the ICU was the presence of respiratory effort requiring the use of O 2 above 8. 0 L/min, which is the initial graduation of nonremovable masks. The mouthwash protocol was also verified regarding the conditions of use and side effects  14, 15. Statistical analysis. Statistical analysis was conducted using R (R Core Team) and SAS® software version 3. 8 (SAS Institute Inc). Descriptive and exploratory data analyses were performed. A Mann-Whitney U nonparametric test was used to compare the groups regarding age, number of comorbidities, and duration of symptoms prior to hospitalization.
Results In vitro cytotoxicity and antiviral activity. In the optical microscopy observations, APD demonstrated cytotoxicity only at the initial dilution (2. 0 mg/mL, the most concentrated stock solution) since Vero CCL-81 cell monolayer integrity was observed after treatment with all the other dilutions. The integrity of the cell monolayer was observed under a microscope after treatment with APD at dilutions ranging from 1:2 (1. 0 mg/mL) to 1:64 (1. 56 × 10 -2 mg/mL); these results were confirmed by cell fixation and staining with Naphthol Blue Black. The data for both the cell cytotoxicity and antiviral activity of APD were also confirmed by indirect immunofluorescence (IIF) (Fig. 1  and supplementary material). The real-time RT-PCR results showed a significant reduction in viral load when compared to the positive control at the 1:2 (99.
770 FDA drugs extracted from the DrugBank database (https:// www. drugb ank. ca/) was carried out by a team of researchers  21  which recently proposed phthalocyanine, hypericin, TMC-647055 and quarfloxin derivatives as the potentially most effective drugs for the treatment of COVID-19. All four molecules are known to have antiviral properties, but the results indicated that their high affinity for the inner cavity of the spike glycoprotein in the prefusion conformation could block the HR1 region, thus preventing the conformational changes necessary for SARS-CoV-2 entry into target cells. In other words, these molecules are potential spike glycoprotein fusion inhibitors able to prevent docking and thus infection of host cells by coronavirus. The main interaction responsible for this fusion inhibition effect of phthalocyanine is hydrophobic, but very significant polar interactions, including hydrogen bonds, seem to be responsible for this effect of hypericin, the second most potent molecule.
However, these patient data were used for statistical analysis in intention-to-treat (ITT) for secondary objectives, which assessed the total displacement of the maxillary canine until Class I occlusion was reached and measured the speed at which the canines reached Class I occlusion on both sides. Regarding the remaining secondary objective, which was to compare the pain levels on both sides of the maxilla using the VAS during the first 3 days of wearing Class II elastics, 32 patients were evaluated with the VAS at day 1 (D1) and D2. Nine of the patients did not complete the questionnaire on these dates. For the VAS at D3, only 31 people were evaluated because 10 patients did not complete the questionnaire by D3. Despite randomization at the beginning of the study at D0, the mean distance between the maxillary and mandibular canine tips was statistically greater at a threshold of 9% on the irradiated side than on the placebo side, with a mean of -1.
Before measurement the powder was outgassed at 100 °C. Raman analyses were carried out using a confocal Raman microscope Horiba Labram HR 800 Jobin Yvon. The samples were exposed to a continuous laser radiation provided by an Argon diode laser at 532 nm (8 mW). A macrospot module was used to obtain a spot size of 100x100 µm. Raman spectra were acquired through a grating of 1800 lines per mm (spectral resolution of 1 cm -1 ) with a quantum well detector cooled to -60 ° C (Synapse CCD). Each spectrum was recorded between 900-1100 cm - 1 (integration time of 240 s, 3 accumulations). A certified silicon standard allowed frequency equipment to be calibrated using the silicon line at 520. 7 cm -1. A baseline correction and fitting processing were realized using Labspec 5 software (Horiba Jobin Yvon) by varying parameters (position and width of phosphate bands) to provide the best curve fit.
Acknowledgements M. P. G. acknowledges the support provided by the  Spanish Government  through Project  MAT2015-65601-R  ( MINECO/FEDER, UE) , and the  "Generalitat de Catalunya " for the 2017  SGR11-65  and the  Icrea Academia Award. M. E. acknowledges the  Serra Hunter Fellowship. This project was supported by  Inca-Cancéropôle GSO  under the  DOXOSARCOME  project.
More research to further explain this stronger association between diabetes and dental caries in younger adults is required. The large representative sample and the stratification by age and sex are clear strengths of the present analyses. However, findings must be interpreted in light of the study limitations. First, diabetes, dental caries, and control variables were self-reported and thus subjected to reporting and recall bias, while the use of clinical and biological data would have allowed more detailed analyses. Second, the type of diabetes was not reported, and it is possible that differing associations may be observed for type 1, type 2, and gestational diabetes. As a matter of fact, these types of diabetes affect different populations, and one may hypothesize that these populations do not share the same risk for dental caries.
Real-Time Monitoring Spheroid proliferation was also determined using real-time monitoring with an In-cuCyte Live Cell Analysis System (Incucyte ZOOM, Essen Bioscience, West Wickham Kent BR4 OPH, UK). Spheroid diameters were measured using the IncuCyte software. Spheroid cell death induced by radiation and/or DIMATE treatment was monitored in real-time using the IncuCyte. Irradiated and/or DIMATE-treated spheroids were incubated with 50 µL of Cytotox Green reagent (4633, Essen Bioscience) in phenol red-free medium according to the manufacturer's instructions and placed under the 20× objective lens of the IncuCyte Live Cell Analysis System over a period of 48 h. The evolution of Cytotox Green fluorescence intensity was then analyzed with the IncuCyte software.
Self-Renewal Self-renewal of the chordoma spheroids was assessed by colony formation assays and spheroid size assays. After irradiation and/or DIMATE treatment, the spheroids were maintained 24 h in culture before being dissociated using the TryPLE reagent (5 min, 37 • C, Thermofisher, Illkirch, France) followed by gentle pipetting to obtain single cell suspensions. Two thousand or five thousand cells were seeded onto 6-well plates and were allowed to form colonies for 5 doubling times (2 weeks for CH22, 5 weeks for U-CH12, and 7 weeks for U-CH1). The colonies were counterstained with a solution of ethanol 75% crystal violet (Sigma, V5265) and counted using the ImageJ software. To perform a spheroid size assay, 200 single cells were seeded in ULA 96-well plates and were allowed to form spheres for 15 days.
Aldefluor Assay ALDH enzymatic activity was measured using the Aldefluor kit (Stem Cell Technologies). The cells suspended in Aldefluor assay buffer were incubated with an ALDH enzyme substrate for 40 min at 37 • C. As a control for baseline fluorescence, the cells were also treated with ALDH inhibitor diethylaminobenzaldehyde (DEAB). The cells were washed and stained with viability dye (Miltenyi Biotec, Paris, France) at 1:1000. Fluorescence was detected using a BD Bioscience LSR Fortessa flow cytometer and analyzed using the FACSDiva software (BD Biosciences, San Jose, CA, USA).
Twelve libraries were pooled at a concentration of 4 nM each, together with 1% PhiX. Sequencing was performed (paired end, 2 × 75 cycles) using NextSeq 500/550 High Output V2 kit on a NextSeq 500 machine (Illumina). Alignments were performed using STAR on the GRCh38 version of the human reference genome. The number of duplicate reads were assessed using PICARD tools. No sample was discarded from the analysis (number of unique reads above 10 million). The expression values were extracted using Kallisto version 0. 42. 5 tool17 with GENECODE release 23-genome annotation based on the GRCh38 genome reference. The Kallisto TPM expression values were transformed in log2(TPM+2), and all samples were normalized together using the quantile method from the R limma package within R (version 3. 1. 1) environment.
Here are the steps in the CAMBRA CRA process for the 0-6 year age group: 1. From the medical, dental and social histories reported, compile relevant data to record in the CRA form (  Biological risk factors contribute directly to the initiation or progression of dental caries (both the caries disease and caries lesions). They include an assessment of factors that have been established as most important (Table  1 ). The risk factors utilized in this CRA form are: 1. Frequent snacking on fermentable carbohydrates, at least three times daily outside of mealtimes. Frequent carbohydrate intake results in a prolonged acidic environment in the plaque that dissolves the tooth mineral and can act as a driving force to reinforce the overgrowth of cariogenic bacteria and the suppression of oral commensal (beneficial) bacteria, leading to future caries development  [26].
Acknowledgements The authors thank the HCWs of the medical unit for their investment and participation in this study. English-language editing services were provided by cookietrad@gmail. com. Funded in part by  ANR-15-CE36-0004-01  entitled  MediHand-Trace (MHT)  and  Agence Nationale de la Recherche (ANR) ,  IHU Mediterranée Infection   10-IAHU-03.
AFM imaging and force measurements. To analyze the surface topography of biofilms from each L. lactis strain, AFM images of an area of 50 µm × 50 µm (JPK Instruments, Bruker, USA) were recorded in contact mode in PBS at room temperature. MLCT cantilevers (Bruker, USA, nominal spring constant of ~ 0. 01 N/m, as determined using the thermal noise method  50  ) were used with a scanning rate of 1 Hz and a resolution of 128 × 128 pixels. The images acquired were analyzed using the Data Processing software from JPK Instruments (Bruker, USA). Mechanical properties of the different L. lactis biofilms were measured in force spectroscopy experiments by recording a grid map of 16-by-16 force curves on an area of 50 µm × 50 µm in PBS. For that, AFM colloidal probes were used and prepared using the protocol described in  51.
5 µm. To measure the adhesion forces between single cells and biofilms, AFM colloidal probes were first immersed for 1 h in 50 µL of PBS (1X) containing 4 mg/mL of dopamine hydrochloride (99%, Sigma), rinsed in PBS and used directly for cell probes preparation. For that, single-cells from 50 µL of diluted bacterial suspension (×100) were immobilized on the colloidal probes. Cell probes were then used to measure cells-biofilm interaction forces. All the force curves obtained were analyzed using Data Processing software from JPK Instruments (Bruker, USA). Adhesion force histograms were obtained by calculating the maximum adhesion force of the last peak for each curve. For each strain, experiments were repeated at least three times with cells coming from independent cultures.
Step 1: creating the virtual preoperative 3D model of the patient's oral anatomy Preoperatively, a CT scan or a cone-beam was performed. In order to have well detailed dental cusps and patient occlusion, an intraoral 3D scan is secondly undertaken. The 3D intraoral mesh and the bone reconstruction obtained from the CT scan were fused to generate a detailed preoperative 3D model using a rigid transformation between the two-point clouds and a semi-automatic alignment done. First, an initial transformation matrix was manually obtained. Second, the Iterative Closest Point (ICP) algorithm is run to refine the transformation by automatically minimising the quadratic distance between the two-point clouds  [16]. The segmentation of the relevant anatomical structure is then made during surgical planning with the open-source software 3D Slicer.
Rheological Characterization of Formulations All the rheological studies were carried out on an Anton Paar MCR102 Rheometer (Graz, Austria). The geometry chosen was a stainless steel cone/plate equipped with a solvent trap (diameter 50 mm, angle 1 • and truncation 100 µm) providing a homogeneous shear of the samples. All the data obtained were analyzed using the Anton Paar RheoCom-pass™ software version 1. 25 (Graz, Austria) associated to the rheometer. All experiments were performed in triplicate and all data are expressed as the mean ± standard deviation.
Measurement of the Adhesive and Mucoadhesive Forces The adhesive and mucoadhesive behavior of formulations presenting different mucoadhesive agents (Carbopol C971P (carbomer), Protanal LF 10/60 FT (sodium alginate) and Satiaxane (xanthan gum)) were evaluated by measuring the force and the work required to detach the corresponding formulation from the upper plate of the rheometer in a tensile test. This test was carried out with an Anton Paar MCR102 Rheometer and the raw data were analyzed using the Anton PaarRheoCompass software. The geometry chosen to perform all the experiments was a stainless-steel plate/plate (diameter = 50 mm). For adhesion experiments, the hydrogel was carefully loaded on the lower plate of the rheometer and heated at 37 • C for ensuring the gelation of the system. After that, the upper plate was lowered until contact with the sample (100 µm).
An equal amount of DMA complexed with HP-β-CD in solution (10 µg/mL) was placed in the release media directly as a control sample of the complete release of DMA from hydrogel formulations. The cumulative release (%) of DMA from hydrogels was calculated by dividing the DMA amount released from the hydrogel formulation by the measured amount of released DMA from the control solution. To compare dissolution profiles, the difference factor (ƒ 1 ) and similarity factor (ƒ 2 ) were determined for each hydrogel formulation release profile, comparing them to the free mucoadhesive dissolution profile  [73, 74]. The ƒ 1 and ƒ 2 factors provide an independentmodel method for data analysis to measure the similarity between two release profiles. The factor ƒ 1 is the percentage of difference between two dissolution profiles at each time point and is calculated using the following expression: f 1 = {[SH|R t -T t |]/SHR t } × 100 (6) where R t is the amount of released drug on the reference formulation and T t is the amount of released drug on the test formulation.