dataesr/scientific-paragraphs-categorization huggingface dataset:
The collected data were analyzed with Sigma Plot (release 11. 2, Systat Software, Inc. , San Jose, CA, USA). Mann-Whitney rank sum test was applied for the comparisons, first, of the open tubule diameters with or without rubbing the phosphoric acid, and second, of the Ca mass percentages for the enamel and dentin after etching with or without rubbing. c 2 test was applied to compare the proportions of open dentinal tubules in etched dentin with or without rubbing. A significant level at α = 0. 05 was adopted for all tests.
6B ), in line with the protein data in Fig. 6A. To assess the possible effects of NOTCH3 L1519P on PDGFRB expression and also further downstream in the PDGFRB signaling cascade, we monitored the levels of PDGFRB autophosphorylation and phosphorylation of the downstream effectors AKT and MAPK (p42 and p44 MAPK). Upon treatment of cells expressing wild-type NOTCH3 or NOTCH3 L1519P with PDGF-BB ligand, we observed an increased level of PDGFRB autophosphorylation in the NOTCH3 L1519P -expressing cells as well as increased AKT phosphorylation (Fig. 6C ). p42/44 MAPK phosphorylation was likewise augmented in the NOTCH3 L1519P -expressing cells compared to control cells, but this was not the case for the NOTCH3 L1519P -expressing cells (Fig. 6C ). Collectively, these results suggest that NOTCH3 L1519P elicits elevated PDGFRB downstream signaling, and, in line with this notion, there was also an increase in cell proliferation [as judged by increased Ki67 (MKI67) expression] in the PDGF-BB-stimulated NOTCH3 L1519P -expressing cells but not the wild-type NOTCH3-expressing cells (Fig.
We next analyzed the phosphorylation of tyrosine residues 751, 771, 1009 and 1021, and, in all cases, phosphorylation was enhanced in the PDGFRB R561C and PDGFRB P660T mutants compared to wild-type PDGFRB (Fig. 7B ). Finally, activation of downstream signaling events was analyzed for the various PDGFRB mutants. Increased phosphorylation of 42/44 MAPK and AKT was observed in cells transfected with the PDGFRB R561C and PDGFRB P660T mutants (Fig. 7C ). These data are in agreement with a previous report indicating that the PDGFRB mutations found in IMF patients are gain-of-function mutations  (Mudry et al. , 2017). Together, these data indicate that NOTCH3 L1519P upregulates expression of PDGFRB and that PDGFRB IMF mutations are gain-of-function mutations.
Immunocytochemistry and confocal microscopy Cells were plated on glass coverslips for 24 h, then fixed for 10 min at room temperature with 4% paraformaldehyde. Cells were permeabilized with 0. 1% Triton X-100 in PBS followed by blocking with 0. 1% Triton X-100 and 2% BSA in PBS for 1 h. Primary antibodies were incubated at 4°C overnight, and, after washes in PBS, samples were incubated with secondary antibodies for 1 h at room temperature and mounted with Vectashield medium with DAPI (Vector Laboratories). Images were captured by confocal microscopy (LSM 880 META, Carl Zeiss AG). Image analysis was carried out using ImageJ (National Institutes of Health) and Adobe Photoshop software. Antibodies are listed in Table  S3.
| Data collection and analysis Data were instantly collected and processed by the LimeSurvey software. Data were recorded in a slideshow, whose statistics were modified after each new answer. Questions with forced-choice or multiple allowable answers were presented in the form of graphs. Open-ended questions with qualitative variables were analysed according to the participants' words. The answers were analysed by topics when possible ("Free comments" section) and with a word cloud generation (www. nuage sdemo ts. fr) in which the most cited words appeared in larger size and the least cited in smaller size.
Study design and patient population The design, methods and results of the primary analysis of this phase 2, international, multicenter, open-label study (NCT00680992) have been published  [11]. Briefly, eligible patients were adults and skeletally mature adolescents at least 12 years of age with pathologically confirmed GCTB and measurable active disease within 1 year of enrollment. Patients had Eastern Cooperative Oncology Group Performance Status score ≤ 2, no current use of alternative GCTB therapies, or known or suspected diagnosis of sarcoma, non-GCTB giant cell-rich tumors, brown cell tumor of bone, or Paget disease. Patients received 120 mg denosumab subcutaneously once every 4 weeks, with loading doses on study days 8 and 15. The study was approved by each site's independent ethics committee (Additional file 1), and all adult patients provided written informed consent.
Introduction: Meningeal solitary brous tumors (SFT), like all SFT, are de ned by NAB2-STAT6 fusion and share clinicopathologic similarities with meningiomas, the most frequent meningeal tumors. Our aim is to establish the molecular identity of meningeal SFT and seek molecular prognostic factors. Methods: RNA sequencing and whole exome sequencing (WES) were performed in STAT6-positive SFT and grade 2-3 meningiomas, and data concerning other soft tissues tumors was obtained from the local database. Uniform manifold approximation and projection (UMAP), individual gene expression and Gene Set Enrichment Analysis (GSEA) were performed. Results: RNA clustering shows that SFT share a common molecular signature, different from any other type of tumoral tissue. Meningeal SFT aggregate with other SFT, with no clinical or histological subgroup.
Patients and samples Frozen tumors samples were collected from patients operated at the Pitié Salpêtrière hospital (Paris, France) between 2004 and 2018 for grade 1 or 3 CNS-SFT, including patients with a pair of primitive grade 1 and a recurrent grade 3 CNS-SFT, as already described  [9]  (cf. sup. table1). All histological samples were immunopositive for STAT6 nuclear staining and grading was reassessed according to the 2016 WHO classi cation  [3, 24]. Clinical data were collected in the medical le. Meningioma frozen samples were provided by APHM Biobank (CRB-TBM authorization AC2018-31053; CRB BB-0033-00097)  [25]. RNA sequencing data concerning other types of tumors was obtained from the local Institut Curie database for SFT and meningiomas samples, among a larger collection of soft tissues tumors (AFNOR NF S 96900 2009/33837B; data available on demand).
Molecular analyses Total RNA was extracted from frozen tumor tissues using Trizol-chloroform method (Invitrogen). The RNA integrity was veri ed using TapeStation 4200 (Agilent Technologies). RNA sequencing was performed with TruSeq Stranded mRNA Prep kit (Illumina) according to the manufacturer's protocol, and libraries sequenced with the illumina NextSeq500 pair-end 150pb. Gene expression values were estimated from the RNA-seq data using Salmon (v0. 13. 1) in TPM (Transcript Per Million) The pairedend transcriptome sequencing reads were aligned to the human reference genome (GRCh37/hg19) with StarAligner. We analyzed expressed mutation with HaplotypeCaller and Mutect2 from GATK4). Gene fusion were analysed from FASTQ data fusion nder tools (FusionMap from Oshell (v10. 0. 1. 50), Starfusion (v2.
5), FusionCatcher (v1. 0), Defuse (v0. 6. 2)). Gene expression datas allow a comparison between samples by supervised clustering using distance calculation and Pearson correlation. With the list of genes of 5% internal quantile range (IQR) variation, we looked for enrichment of pathways (GSEA, Gene Set Enrichment Analysis open access software GSEA, Broad Institute, USA) with gene sets v. 7. 1 and genes annotations Human_Illumina_HumanHT_12_v3_MSigDB. v7. 1. chip. Using 100 permutations, we analyzed gene sets with a False Discovery Rate < 25%. Literature analysis was performed on several gene databases  [26, 27]. GSEA was performed for SFT versus meningiomas and for SFT subgroups identi ed in the unsupervised RNA clustering. We compared gene expression of SFT and meningiomas within a panel of well-characterized samples: small round cells tumors, soft tissues sarcoma (with or without fusion transcript), and, brain tumors corresponding to 258 cases in total.
Physicochemical Characterization The prepared composite was characterized by X-ray diffraction (XRD) using a X'pert 3  Powder Smart Lab diffractometer (Malvern Panalytical, Malvern, UK) with Cu Kα radiation (λ = 1. 540593 Å). Data were collected in the 2θ range of 20 up to 70 • (2 • /min). A Fourier transform infrared (FTIR) analysis was conducted using a Nicolet 5700 spectrometer (ThermoElectron, Waltham, MA, USA) in the range of 400 to 4000 cm -1 at a resolution of 4 cm -1. A small amount of the sample powder (1 wt%) was mixed with KBr powder and then palletized onto pallets for analysis. The microstructure of the specimens was evaluated via scanning electron microscopy (SEM) on a TESCAN VEGA3 microscope (TESCAN, Brno, Czech Republic) and the porosimetry on a Poresizer Micromeritics (Pore Sizer 9310, Micromeritics, Norcross, GA, USA).
The peaks of the CSM polymer are not detected in the HA-CSM diffractograms; this could be attributed to the small amount of polymer introduced in the matrix. It is noted that there was no marked difference with the XRD patterns of the composite containing low molecular weight chitosan (data not shown), indicating that the polymer molecular weight does not affect the composite structure. The crystallinity degree of the HA-CSM 2. 5% and HA-CSM 5% composites and the HA apatite was determined using the formula: β 002 × 3 X C = K A , (1) where β 002 ( • ) and X C are the width peak at the half intensity of (002) reflection and crystallinity degree, the constant K A is set at 0. 24  [12]. The addition of the CS polymer in the composite matrix has a slight effect on the composite crystallinity. Thus, the highest value of the crystallinity index is observed for the HA (0.
Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and the intestinal microbiota that has rarely been described in human infections. Besides its role in halitosis and oral infections, S. moorei is considered to be an opportunistic pathogen causing mainly bloodstream and surgical wound infections. We performed a retrospective study of 27 cases of infections involving S. moorei in two French university hospitals between 2006 and 2021 with the aim of increasing our knowledge of this unrecognized opportunistic pathogen. We also reviewed all the data available in the literature and in genetic and metagenomic sequence databases. In addition to previously reported infections, S. moorei had been isolated from various sites and involved in intraabdominal, osteoarticular, and cerebral infections more rarely or not previously reported.
Although mostly involved in polymicrobial infections, in seven cases, it was the only pathogen recovered. Not included in all mass spectrometry databases, its identification can require 16S rRNA gene sequencing. High susceptibility to antibiotics (apart from rifampicin, moxifloxacin, and clindamycin; 91. 3%, 11. 8%, and 4. 3% of resistant strains, respectively) has been noted. Our global search strategy revealed S. moorei to be human-associated, widely distributed in the human microbiota, including the vaginal and skin microbiota, which may be other sources for infection in addition to the oral and gut microbiota.
Review of S. moorei in the Literature and Databases A PubMed search with the terms "Solobacterium" or "Solobacterium moorei" or "Bulleidia moorei" was conducted on 9 March 2021. We then reviewed all articles published in the English language and involving humans. The NCBI (National Center for Biotechnology Information) database was searched on the same date, for the sequences of S. moorei using two approaches that were crossed to ascertain representativeness of the selection. On one hand, we reviewed all the se-quences available in the nucleotide database (https://www. ncbi. nlm. nih. gov/nucleotide/, accessed on 9 March 2021) with the same search terms, and on the other hand, we performed a BLAST (Basic Local Alignment Search Tool) analysis of the 16S rRNA gene sequence of the S. moorei type strain JCM 10645 T (GenBank accession number NR_115130) with selection of the sequences with the highest sequence identity.
These latter were analyzed with Blast2GO software available at http://www. blast2go. de (accessed on 9 March 2021)  [13]  and sequences ≥98. 65% identical to the sequence of S. moorei were selected. This percentage corresponds to the current threshold delineating a species as established by  Kim et al. on the basis of Average Nucleotide Index and 16S rRNA gene sequence similarities comparison  [14]. Finally, metagenomic databases were searched using the Integrated Microbial Next Generation Sequencing (IGMNGS) platform, a comprehensive open source tool for processing 16S rRNA microbial profiles for ecology and diversity studies (https://www. imngs. org/, accessed on 16 March 2021)  [15]. The 16S rRNA gene sequence of the S. moorei type strain was used at the 99% similarity threshold level proposed to represent the species for the search.
S. moorei Isolation Characteristics and Antimicrobial Susceptibility From 2006 to 2021, a total of 27 S. moorei isolates had been detected in clinical specimens obtained from 27 patients in both centers. Isolates were Gram-positive, obligatorily anaerobic, non-sporulated bacilli that grew on Brucella blood agar supplemented with hemin and vitamin K1 after 2-5 days of incubation. Anaerobic Gram-positive bacilli are a heterogeneous group of bacteria, difficult to identify in clinical microbiology laboratories before the era of mass spectrometry. The development of MALDI-TOF technologies has increased the performance in identifying anaerobes but may still be unsuccessful at identifying certain species. Indeed, major differences still exist between databases of currently available mass spectrometry systems, particularly regarding anaerobes.
S. moorei is one example of this, being included in the Bruker MS system database (Bruker)  [16] , whereas it is absent from that of the VITEK ® MS system (bioMérieux) used in our two laboratories. Consequently, all 27 isolates in this study were identified by 16S rRNA gene sequencing, revealing that all of them belonged to the species S. moorei (>99% of sequence identity only with that of S. moorei type strain). S. moorei was identified in 17 male and 10 female patients, with a mean age of 59. 5 years (range: 25-93 years). This species was mainly identified in mixed aerobic-anaerobic cultures, as observed for numerous cases of infections involving anaerobes (Table  1 ). Indeed, these infections are mostly endogenous and favored by damaged mucosal/cutaneous barriers, which allow the penetration of anaerobic species into normally sterile tissues, often together with aerobic/facultative anaerobic bacteria  [17].
Lessons from the Analysis of the GenBank Database Because sequences deposited in the GenBank database may or may not be associated with published studies, and because sequences originating from metagenomic studies may be associated with published studies not retrieved by using the bacterial name as a keyword for the search unless associated with the main results of the study, we reviewed the sequences present in the database with the aim of obtaining sufficient information about sources of recovery for S. moorei. On 9 March 2021, 938 entries corresponded to the search for "Solobacterium moorei" and 1151 to the search for "Solobacterium" in the NCBI nucleotide database. Most entries corresponded to Whole Genome Sequences, either as scaffold or contig sequences-for example, for strain F024 from the human oral microbiome  [24]  and strain DSM 22971 T (=JCM10645 T = RCA59-74 T ), the type strain of S.
• Digestive tract-related sequences Sequences related to the digestive tract represented 33% (n = 110) of the human sequences and originated either from the esophagus (n = 16) or gut/feces (n = 94). Human gut sequences were identified from stool and mucosal biopsy specimens (duodenal, colon, cecum) in both healthy  [25]  and diseased subjects with inflammatory bowel diseases, including Crohn's disease  [26] [27] [28] [29]  (Supplementary Table  S1 ). Sequences were identified in adults and children and one sequence corresponded to an uncultured Solobacterium sp. clone (clone OTU124/accession number KJ527533) from the stools of preterm infants with extremely low birthweights. The analysis suggested an early implantation of the species in the human gut.
• Respiratory tract-related sequences Probably in relation to the aforementioned presence in the oral cavity, S. moorei sequences were also identified in the respiratory tract (n = 27). This included uncultured clones from bronchoalveolar lavage fluid, human lungs, the biofilm of extubated endotracheal tube of ICU patients  [33] , sputum from cystic fibrosis (CF) patients (S. moorei strain C1107/JF803577)  [34] , sputum samples of patients suffering from hospital-acquired lower respiratory tract infection (Solobacterium sp. uncultured clone V3 DCM-SHRJH/GU737675), and pneumonia patients with pulmonary emphysema (uncultured bacterium clones KY51_PHKY51_B01_003 and KY51_PHKY51_D05_007 with accession numbers LC260797. 1 and LC260830. 1, respectively) (Supplementary Table  S1 ). Nevertheless, a pathogenic role of S.
Lessons from the Metagenomic Database Screening The presence of 16S rRNA gene sequences displaying close identity to that of the S. moorei type strain was found in 55 types of metagenomes for which associated information was available, albeit imprecise for some of them. The analysis was split into humanassociated metagenomes (based on "human" or "Homo sapiens" in the designation of the metagenome) and non-human-associated metagenomes. The presence of S. moorei-related sequences was overwhelmingly observed in human-associated metagenomes, confirming observations drawn from the analysis of individual NCBI sequences. Regarding anatomical sites, metagenomes that most often contained S. moorei sequences were of tracheal and oral origin, with 17. 3% and 16. 4% of positive samples, respectively (Figure  3 ).
1, but also confirm that other human microbiota may also be suspected in certain cases unrelated to any oral or digestive comorbidity. Skin and the reproductive tract are shown to represent alternate portals of entry for S. moorei that may have been considered in previous cases of S. moorei infection in patients with intravenous drug abuse  [21, 41]  or cervical cancer  [19]. In our study, S. moorei may have originated from the skin microbiota in at least two cases (subcutaneous ear collection and bacteremia in a 52-year-old patient with diabetes and a recent toe amputation). In contrast to human metagenomes, S. moorei was occasionally identified in various non-human metagenomes, of either animal, environmental, or other origin (Table  2 ). This low representation of S. moorei-related sequences in non-human metagenomes ties in with the rare, non-human sequences demonstrated in the first part of sequence database analysis of this study and previously shown in Figure  2  with a roughly similar, non-human source distribution (animal, environment, others).
However, although all previous results suggested that S. moorei was a human-associated species, atypical observations were made during the metagenome database analysis for pig gut and invertebrate gut metagenomes. These results were therefore more thoroughly analyzed, showing that they should be considered with caution as they probably result from the following biases: invertebrate gut metagenome data originated from very few samples (n = 32) resulting from a single study of gut metagenomes in the leech, Hirudo nipponica, revealing three S. moorei-positive samples. Similarly, 322 of the 325 positive samples from the pig gut metagenome (sequence read archive accession numbers comprised between ERR2739626 and ERR2740414) originated from a single study performing a longitudinal assessment of the gut microbiome in piglets from birth up to weaning.
Conclusions Taking S. moorei as an example, lessons from the GenBank and metagenome databases' screening are in favor of their usefulness for complementing commonly performed reviews of the literature. Indeed, published data only poorly reflect the growing amount of data available from cultivation-independent studies and sequences deposited in databases. In addition, it is highly probable that most microbiologists did not report the S. moorei strains and corresponding cases identified in their institutions as our 'only' bicentric, retrospective study doubled the number of cases currently reported in the literature. Our combined strategy, analyzing data from the routine practice of medical microbiology and different databases, allows us to increase the current knowledge on S. moorei, an anaerobic opportunistic pathogen in humans.
This resulted in low (scores 0 and 1) and high (scores 2 and 3) groups for CD8, CD20 and CD163; and present (score 0) or absent (score 1-3) for PD-L1+ immune cells  [17, 18]. Quantification of the number of CD34+ and MECA-79+ blood vessels (vascular density) was performed on 5 high power 20× (1 mm 2 ) fields per section, and these were counted and averaged, as previously proposed  [19]  while their median value was used as a cut-off for the classification into two groups. Data were analyzed using StatView software (Abacus Concepts, Berkley, CA, USA). We used the χ 2 test to explore any relationship between two groups for categorical data, and factorial analysis of variances (ANOVAs) to consider the effect of at least one factor on a continuous parameter studied. Simple regression analysis was used to explore a possible relationship between two continuous parameters.
MATERIAL AND METHODS Slurries were prepared using alumina powders (CT1200SG; Almatis). The powders were dried for 1 hour at 90 C in an oven (Beschickung loading model 100-800; Memmert). The powders were incorporated into a photosensitive (l=350-400 nm) acrylic resin (C1alumina; CryoBeryl Software) to obtain 80% (w/w) dry matter content slurries that were homogenized at 150 rpm by planetary milling for 30 minutes (PM100; Retsch). The rectangular parallelepipedal specimens were designed using a CAD software program (Catia; Dassault Systèmes). Their dimensions were 1. 3×4×22 mm for the evaluation of density, 3-point flexural strength, Weibull modulus, hardness, fracture toughness by indentation and microstructure assays and 3×4×40 mm for the evaluation of fracture toughness by the SEVNBe3point bend test (Fig.
Clinical Implications SLA dental ceramics fabricated with the layers perpendicular to the occlusal surface had the best properties. This will help technicians fabricate suitable and reliable SLA crown frameworks. anisotropic shrinkage that occurs during the thermal treatment of SLA alumina. 6 The specimens were then sliced (layer thickness=50 mm) (Creation Workshop software; Datatree3D), and the data were transferred to an SLA software program (CryoCeram; CryoBeryl Software) and equipment (CryoCeram Printer; CryoBeryl Software) for additive manufacturing (polymerization energy=10 mW. cm -2 , resolution=50 mm). The entire surface of a layer was polymerized at once using a dynamic mask of digital micromirror devices. The support platform was then moved down into the slurry. The pillars were hand sectioned after the manufacturing phase.
5 mm/min on the dark gray face of the specimens (Fig. 1B ). The distance between the lower supports was 20 mm. The 3-point flexural strength in MPa (s) was (equation 1) as fol- lows: s = ð3 × F × LÞ =ð2 × W × H 2 Þ, where F is the maximum force to failure (N), L is the distance between the lower supports (mm), W is the specimen width (mm), and H is the specimen height (mm). A Weibull  distribution analysis using 3-point flexural strength data was used to assess the structural reliability of the ceramics (n=30/group). The Weibull modulus (m) was P f = 1 -exp ½ -ðs=s 0 Þ m , where P f is the probability of failure between 0 and 1, s is the 3-point flexural strength in MPa, and s 0 is the characteristic strength in MPa. A Vickers indentation hardness test (ZHU 0. 2, Zwick) was performed (ISO 14705:2016) (n=15/group).