dataesr/scientific-paragraphs-categorization huggingface dataset:
Human clinical samples (blood and cardiac valves) Interestingly, Ca. Saccharibacteria were also detected in clinical samples at a low frequency. A large screening of 7,405 positive blood culture bottles from febrile patients showed that 0. 8% (63/ 7,405) were positive using standard PCR targeting Ca. Saccharibacteria (Figure  5A ). These data were confirmed by Sanger sequencing of the PCR products (Figure  3 , Table  S3 ). The most common bacterial species associated with Ca. Saccharibacteria were Escherichia coli (15%), Klebsiella pneumoniae (11%), Staphylococcus aureus (11%), Staphylococcus epidermidis (10%), Staphylococcus capitis (10%), and Enterococcus faecalis (6%). Strikingly, we also detected Ca. Saccharibacteria in the blood culture of a patient infected by the yeast Candida albicans (3%).
Discussion Until recently, CPR were overlooked within the bacterial domain and therefore in the human microbiome. Their recent Phylogenetic tree based on the amplicon sequences constructed using MEGA7. Red, amplicons from blood cultures; yellow, amplicons from urine samples; brown, amplicons from fecal samples; pink, amplicons from vaginal samples; purple, amplicons from cardiac valves; and blue, amplicons from oral samples. discovery has led to their increased detection in amplicon sequencing datasets as well as those of metagenomics, thus highlighting their non-negligible presence in the oral cavity. Here, we have carried out a preliminary study exploring the prevalence of CPR, and more specifically Ca. Saccharibacteria in various human sample types through a retrospective analysis of CPR within our inlab database of 3,550 16S amplicon datasets as well as prospective analysis of readily available human samples.
Funding This work was funded by the  IHU Mediterraneé Infection (Marseille, France)  and the  French Government  under the  Investissements d'avenir (Investments for future) program  managed by the  Agence Nationale de la Recherche (ANR , fr;  National Agency for Research)  (reference:  Mediterraneé Infection   10-IAHU-03 ). This work was also supported by the  Region Provence Alpes Cote d'Azur and European funding FEDER PRIMI.
Two to three thousand syndromes modify facial features: their screening requires the eye of an expert in dysmorphology. A widely used tool in shape characterization is geometric morphometrics based on landmarks, which are precise and reproducible anatomical points. Landmark positioning is user dependent and time consuming. Many automatic landmarking tools are currently available but do not work for children, because they have mainly been trained using photographic databases of healthy adults. Here, we developed a method for building an automatic landmarking pipeline for frontal and lateral facial photographs as well as photographs of external ears. We evaluated the algorithm on patients diagnosed with Treacher Collins (TC) syndrome as it is the most frequent mandibulofacial dysostosis in humans and is clinically recognizable although highly variable in severity.
We extracted photographs from the photographic database of the maxillofacial surgery and plastic surgery department of Hôpital Necker-Enfants Malades in Paris, France with the diagnosis of TC syndrome. The control group was built from children admitted for craniofacial trauma or skin lesions. After testing two methods of object detection by bounding boxes, a Haar Cascade-based tool and a Faster Region-based Convolutional Neural Network (Faster R-CNN)-based tool, we evaluated three different automatic annotation algorithms: the patch-based active appearance model (AAM), the holistic AAM, and the constrained local model (CLM). The final error corresponding to the distance between the points placed by automatic annotation and those placed by manual annotation was reported. We included, respectively, 1664, 2044, and 1375 manually annotated frontal, profile, and ear photographs.
| Dataset We included pictures from the photographic database of the maxillofacial surgery and plastic surgery department of Hôpital Necker Enfants Malades in Paris, France. This database contains 594,000 photographs of 22,000 patients followed in the department since 1981. The photographs were taken by a professional medical photographer using Nikon D7000 in standardized positions, that is, frontal facial pictures with neutral expression and right and left profiles along the Frankfort horizontal plane  (Hexsel et al. , 2017). We included all pictures of patients diagnosed with TC syndrome during a medical genetics consultation. Non syndromic children were selected among patients admitted for wounds, trauma, infection and various skin lesions not being part of a chronic disease. Follow-up for any type of chronic disease was considered as an exclusion criterion, as this chronic disease could be related to a genetic syndrome with a potential described or undescribed facial phenotype  (Khonsari et al.
Faster R-CNN is based on a convolution neural network (CNN) preceded by a region proposal algorithm to generate "bounding boxes" or locations of possible objects in the image  (Ren et al. , 2017). The manual annotations of the bounding boxes were performed with labelme  (Labelme, 2022). We manually annotated a total of 100 facial photographs, 100 profiles and 100 ears. Data augmentation techniques, that is, ±10 degrees of rotation and flipping, were used to increase the size of the training set  (Pawara et al. , 2017). In case of multiple detections, the bounding box with the highest probability of detection was selected. The highest weight of the Haar cascade and the best confidence score of the Faster R-CNN were selected. Intersection over union (IoU) was used to define true positives, false positives, and false negatives for the predicted bounding boxes.
The general approach is to sample a region from the image around the current estimate, project it into a reference frame and search for a combination of points, which optimized the total cost, by manipulating the shape model parameters  (Cristinacce & Cootes, 2006 , 2008). The model with the best performance in the previous step was then pretrained on public databases to find out whether the contribution of a pretrained model increases performance. Indeed, already annotated and publicly available online databases of photographs are available  (Deng et al. , 2019) , that is, Labeled Face Parts in the Wild (LFPW)  (Belhumeur et al. , 2011) , Annotated faces-on-the-wild (AFW)  (Zhu & Ramanan, 2012) , Helen  (Le et al. , 2012) , and XM2VTS  (Messer et al. , 2003)  for frontal facial pictures with a total of 3402 images; Annotated Facial Landmarks in the Wild (AFLW)  (Kostinger et al.
Assumptions of normality and homoscedasticity of errors were tested. The statistical analyses were performed on R 3. 6. 2 using the nlme  (Pinheiro et al. , 2012)  and ggplot packages  (Wickham, 2016). landmarks method  (Bookstein, 1997)  to remove the artifacts from equidistant sampling. We then performed a GPA  (Rohlf & Slice, 1990) , followed by a PCA. We kept the first components that explained more than 95% of the total variance. We used a MANOVA to determine whether these components were sufficient to classify a patient into the two groups. The significance threshold was defined as p < 0. 05. These statistical analyses were performed on R 3. 6. 2 using the geomorph package  (Baken et al. , 2021).
| Dataset In the TC syndrome group, 56% of included patients had a genetic confirmation (TCOF1 or POLR1D mutations) (Table  1 ). For frontal facial pictures (N = 1664), we included 618 photographs of patients with TC corresponding to 60 patients and 1046 photographs of control patients corresponding to 842 patients. Mean age was 8 years (±5. 5) and there were 46% of girls in the dataset of photographs. For the profile pictures (N = 2044), we included 451 photographs of patients with TC corresponding to 60 patients and 1593 photographs of control patients corresponding to 576 patients. Mean age was 7. 8 years (±5. 2) and there were 53% of girls in the dataset of photographs. For the ears (N = 1375), we included 100% photographs of control patients corresponding to 503 patients. Mean age was 7.
classification between TC patients versus controls in the validation set was performed, using either ground-truth landmarks (placed manually) or automatically placed landmarks with the best model from the previous step. For nonanatomically defined landmarks-that is, landmarks 2-16 for frontal faces; 2-11 for profiles; 2-19, 22-35, and 37-50 for ears-we used the sliding semi-F I G U R E 1 Steps for creating an automatic landmarking tool. (a). Bounding box detection. (b). Testing of three automatic annotation models. (c). Comparison of the model only trained on the data versus the model pretrained on public data. Here the examples chosen are frontal face photographs. The public photographs in Step C were extracted from the LPFW database.
A classification between TC patients versus controls in the validation set was performed, using either ground-truth landmarks (placed manually) or automatically placed landmarks with the best model from the previous step. For nonanatomically defined landmarks-that is, landmarks 2-16 for frontal faces; 2-11 for profiles; 2-19, 22-35, and 37-50 for ears-we used the sliding semi-F I G U R E 1 Steps for creating an automatic landmarking tool. (a). Bounding box detection. (b). Testing of three automatic annotation models. (c). Comparison of the model only trained on the data versus the model pretrained on public data. Here the examples chosen are frontal face photographs. The public photographs in Step C were extracted from the LPFW database.
Dataset of photographs and (B) population description. (A) Frontal Profile Ears N 1664 2044 1375 Gender Girls 770 (46%) 1093 (53%) 733 (53%) Group Treacher Collins 618 (37%) 451 (22%) 0 (0%) Controls 1046 (63%) 1593 (78%) 1375 (100%) Age (years) Mean ± SD 8. 0 ± 5. 5 7. 8 ± 5. 2 7. 5 ± 5. 1 Median 7. 4 7. 6 7. 7 Min 0 0 0 Max 27 27 22 <2 y. o 257 (16%) 326 (16%) 276 (20%) 2-8 y. o 655 (40%) 753 (37%) 450 (67%) >8 y. o 739 (45%) 949 (47%) 649 (47%) (B) Frontal Profile Ears N 902 576 503 Gender Girls 463 (51%) 303 (53%) 268 (53%) Group Treacher Collins 60 (7%) 60 (10%) 0 (0%) Controls 842 (93%) 516 (90%) 503 (53%) Age (years) Mean ± SD 6. 6 ± 4. 8 7. 5 ± 5. 9 7. 2 ± 5. 3 Median 6. 2 7. 2 7. 2 Min 0 0 0 Max 27 27 22 <2 y. o 204 (23%) 103 (18%) 102 (20%) 2-8 y. o 377 (42%) 225 (39%) 183 (36%) >8 y.
Statistical analysis Statistical analysis was performed using the BiostaTGV online platform (https://marne. u707. jussieu. fr/biostatgv/) developed by INSERM ("Institut National de la Santé et de la Recherche Médicale", Paris, France). Chi-square tests were used to compare the proportions between two groups or more. Excel software (Microsoft Office) was used to classify and analyze the data collection. A p-value lower than 0. 05 was considered statistically significant.
Results Thirteen cases of poroma with folliculo-sebaceous differentiation were studied. Clinical, histological, immunohistochemical, and molecular features of all cases are summarised in Table  1. Briefly, there were eight females and seven males. The median age at the diagnosis time was 61 years (range: 23-90). Seven tumours were located on the head and neck region, three presented on the thigh, one on the axillary area, and one on a finger (tumour site was unknown for case #13). One case arose from a preexisting sebaceous nevus (case #10). The median tumour size was 10 mm (range: 4-25 mm). Follow-up data were available in eight cases (mean duration: 11 months [2-36]) and no recurrence was observed. Microscopic features of the cases are highlighted in Table  1 , and Figures  1  and 2. All tumours were connected with the epidermis and located in the dermis with focal extension into the subcutaneous tissue in four cases.
Currently, it remains unclear which specific peptides could be appropriate for applications in different fields of dentistry. The aim of this scoping review was to scan the contemporary scientific papers related to the types, uses and applications of peptides in dentistry at the moment. Literature database searches were performed in the following databases: PubMed/MEDLINE, Scopus, Web of Science, Embase, and Scielo. A total of 133 articles involving the use of peptides in dentistry-related applications were included. The studies involved experimental designs in animals, microorganisms, or cells; clinical trials were also identified within this review. Most of the applications of peptides included caries management, implant osseointegration, guided tissue regeneration, vital pulp therapy, antimicrobial activity, enamel remineralization, periodontal therapy, the surface modification of tooth implants, and the modification of other restorative materials such as dental adhesives and denture base resins.
Information Sources and Search The literature database search was performed by two independent reviewers (RB and CECS) until September 2022. The search was carried out in the following databases: PubMed/MEDLINE, Scopus, Web of Science, Embase, and Scielo. The search strategy was first defined for the MEDLINE database using a controlled vocabulary and free keywords (Table  1 ). The MEDLINE search strategy was then adapted to other electronic databases. The reviewers also hand-searched the reference lists of the included articles to identify additional manuscripts.
Selection Process and Data Collection Process After running the search strategy, a reference management program was used (End-Note X9, Clarivate Analytics, Philadelphia, PA, USA) to store the files of all databases. Then, duplicate articles were removed, followed by manual removal after the organization of titles in alphabetical order. All studies were initially scanned for relevance by title followed by abstract using an online software program (Rayyan, Qatar Computing Research Institute, HBKU, Doha, Qatar). The titles and abstracts of the articles were screened according to the following inclusion criterium: in vitro or in vivo studies that evaluated or reported the use of peptides for dental applications. The search was carried out on documents published in any language without restrictions on their date of publication.
Reviews, case reports, case series, pilot studies, and conference abstracts were excluded. If the review authors were not sure about the eligibility of any study, it was kept for the next phase. All phases were carried out by two independent reviewers (RB and CECS) to check whether they met the inclusion criteria. The same two reviewers summarized and categorized the data using a standardized form. The information collected included the type of study, the peptide used, the application proposed and the main results.
Results This scoping review is described according to the PRISMA extension for scoping reviews guideline  [19]. After database screening and duplicate removal, a total of 6450 articles were recognized (Figure  1 ). After title and abstract screening, 156 articles remained for full-text inspection. From the 156 articles assessed for eligibility, 23 articles were excluded due to the following reasons: in 11 articles, the full text was not retrieved  [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] , 4 articles were not related to the dentistry field  [31] [32] [33] [34] , 4 studies were reviews  [6, 12, 35, 36] , 3 studies were not related to peptides  [37] [38] [39] , and 1 study was a pilot clinical trial  [40]. Thus, a total of 133 articles were included in the present review.
Acknowledgments The authors of this article would like to acknowledge  Vincent Dorcet  for the assistance in TEM experiments performed on the THEMIS platform (ScanMAT,  UAR2025  University of Rennes 1-CNRS; CPER-FEDER 2007-2014),  Loïc Joanny  ( CMEBA ) for SEM-EDS analysis, and  François Cheviré  ( ICSR, Laboratory "Glasses and Ceramics" ) for XRD analysis at the  Université de Rennes 1.
The dental technician can model the prosthesis using CAD software and then machine or print the prosthetic part. Digital impression systems eliminate the error-prone plaster modeling step of conventional impressions, and the impression can be stored as an STL file for an unlimited time. Digital technology can provide greater reliability by eliminating casting stresses and/or dimensional variations experienced by materials during curing or removal  [8]. Different capture techniques are used in intraoral scanners. The triangulation technique (for I-500, Cs3600 cameras) aims to assume the measurement of the volume of the object by calculating the difference between the incident and reflected light in contact with the object. This acquisition process requires software with significant computing power and complex algorithms capable of reconstructing the surface in three dimensions.
Conventional Impression In a second step, the impression transfers were screwed on to the maxillary working model at 5 N•cm before taking the conventional impression (Figure  1c ). This allows the spatial position of the implant to be transferred into the impression material for precise repositioning of the implant analog on the working model. The transfers were ETK Naturactis ® short transfers with S-Naturactis screws (Figure  1d ). Each of the three calibrated operators took three impressions using a custom open tray and polyether material, Impregum™ Penta™ Soft from 3M ® (Figure  1e ). The custom impression trays were created digitally using Dental System's 3D modeling software (3Shape ® ) and the digital file of the previously scanned maxillary working model and were printed with the Formlabs' Form 2 ® 3D printer.
Comparison of Digital Models The evaluation criterion for the impressions was accuracy, a combination of precision and trueness (ISO 5725-1)  [15]. Trueness is the difference between the mean value and the true value. Precision is the distribution of values around the mean that provides the reproducibility of a measurement. All STL files corresponding to the digital reference model, the 9 conventional impression models and the 36 digital impression models were saved in the same folder on the USB drive for comparison. To compare the accuracy between the conventional and digital impressions, several measurements were performed using dimensional control and metrology software Geomagic ® Control X™ (3DSYSTEM ® ). This software was used to compare two 3D digital models: a reference digital model and a model to be compared by aligning and superimposing them to calculate measurement differences (distances, angles) along a particular axis.
The distance deviations were evaluated in two ways, firstly as an absolute value, to obtain an average of the deviations for each impression, and secondly as a negative or positive raw value, to assess the direction of the deviation. The angular deviation corresponds to the angle between the reference digital model and the analyzed impression vectors. A method comparing the dispersion of the values around their mean for each impression was also applied to assess the precision. IBM SPSS version 28. 0 was used to analyze the data. The level of significance was set at p-value ≤ 0. 05. Repeated measures analyses of variance followed by Bonferroni multiple comparisons tests were applied for statistical comparisons.
The images were acquired at 60 kV and 166 µA with a rotation step of 0. 4 • using a microtome densitometer (Skyscan 1272 Bruker-source: 20-100 kV to 10 W, spot size < 5 µm) using an 11-MP camera and 14-µm resolution. The 3-D reconstruction of the tooth-abutment-elastomer film assembly was performed with NRecon v1. 7. 3. 0 software (Bruker). The images of the samples were then cleaned using a macro in the software CTan v1. 20. 8 (Bruker) and then spatially oriented with DataViewer v1. 5. 6. 2 (Bruker). Virtual visualization of the abutment-film teeth was performed in CTVox v3. 3. 1 (Bruker), a software program that enables slices to be made in the three views (coronal, sagittal, and transverse) (Fig  2e ). These slices passed through various previously identified sites (S1, S2, S3, and S4; E1/E5/E1*/E5*; E2/E4/E2*/E4*; and E3/E3*).
0] [31]  For the marginal fit, S1 corresponds to the distance between the cervical margin and the FDP margin mesially, S2 distally, S3 on the vestibular side, and S4 on the palatal side. With respect to the internal space, three sites-E1/E5/E1*/E5*; E2/E4/E2*/E4*; and E3/E3*were selected to determine the thickness between the prosthetic abutment and the underside of the FDP at the midaxial, (E1/E5/E1*/E5*), axio-occlusal (E2/E4/E2*/E4*), and centro-occlusal (E3/E3*) sites (Fig  2f, g ). Figure  2a-g  shows the steps implemented in this study. Each of the image slices was inserted into another imageprocessing software (ImageJ, Fiji) to automatically extract the values of the thickness of the marginal and internal fit using the methods proposed by Maragos et al  34  and Kimmel et al. 35  The average marginal fit was obtained by averaging the values of S1, S2, S3, and S4 of all of the abutment teeth, whereas the average internal fit was the average value of E1/E5/E1*/E5*, E2/E4/E2*/E4*, and E3/E3*.
46 The results of the study by Huang et al also appeared to show that the distance between the abutment teeth and adjacent teeth affects the accuracy of the abutment scan. 47 In intraoral scanning, when the distance between the abutment teeth and the adjacent teeth is more than 1. 5 mm, the scan error does not increase, and more accurate scan data can be obtained. In the present study, the plaster models were scanned with an extraoral scanner. This process does not alter the accuracy of the restorations  24  but instead improves the marginal and internal adaptation of the reconstructions. 23 Kernen et al reported that the precision and trueness were higher for extraoral scans than for intraoral scans. 48 These results agree with those reported by many other authors. 40, 49, 50 According to these authors,  26, 51  scanning of the stone cast or impression is the most accurate method and the best fabrication technique with the lowest marginal gaps.
Degree of conversion measurements For each resin cement tested (n = 7), 6 cylindrical specimens (diameter 6 mm x height 3 mm) were made with Teflon molds: 3 were performed in with light-activation for 60 s at 1200 mW per square cm (Valo Grande lamp, Ultradent Products Inc, South Jordan, UT, USA) immediately after mixing, and 3 were performed only in self-curing mode (mixed in the dark). All samples were then stored in the dark in distilled water at 37 °C for one week before the degree of conversion (DC) measurement. DC was determined using Fourier transformed infrared spectroscopy (FTIR) with a NicoletTM iS10 spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) in attenuated total reflectance (ATR) mode following proposed protocol from previous publications  [21]. These spectra were recorded with OMNIC software (Thermo Electron Corporation, Waltham, MA, USA).
Background: Radiotherapy and chemotherapy are frequently employed in head and neck cancer (HNC) patients causing significant side effects that impair life quality and prognosis. Photobiomodulation (PBM) has become a growing approach to managing such oral complications. Despite its proven efficacy and absence of contraindications, there is still a lack of universally accepted disease-specific PBM protocols. Objective: A narrative review was conducted to identify the current proposals relating to the use of PBM to treat complications of oncological treatments in HNC patients. Methods: An electronic search in PubMed and Scopus databases was performed with the following keywords: ("photobiomodulation" OR "PBM" OR "laser therapy" OR "LLLT" OR "laser") AND ("head and neck cancer" OR "oral cancer") AND ("mucositis" OR "oral mucositis" OR "dysgeusia" OR "oedema" OR "xerostomia" OR "dermatitis" OR "trismus") until October 2021.