dataesr/scientific-paragraphs-categorization huggingface dataset:
When the rigidity modulus of the tested material is very weak compared to that of the indenter, it is calculated as * = /(1 -). During the indentation testing, the penetration depth was continually recorded according to the applied load. After each test, a series of data pairs ( , ℎ) was generated, from which one would be able to identify the characteristics of the material tested using formula (1). In log-log plotting, this formula becomes: ln( ) =. $% (&) + ln (. * ) (4) The aim was thus to identify the parameters of a linear function. Figure  3  presents a test on a calibration sample: the determination of the contact point (Figure  3A ) allows shifting the origin of the loading curve (Figure  3B ). The reduced Young's modulus (E*) was calculated both at the start and end of the loading curve to evaluate the influence of data analysis on measurement.
Observation of bacterial inocula by fluorescence microscopy, flow cytometry and Scanning Electron Microscopy (SEM). The coating efficiency of biofilms on microbeads was first studied by fluorescence microscopy (LEICA MM AF microscope, objective X63). Biofilms formed on microbeads by the mCherry-SH1000 strain were observed before and after passing through the 34G injection needle. For flow cytometry analysis, samples of each type of inocula were studied with a FACSAria Fusion SORP (BD BioSciences) equipped with FACSDIVA 8 software (BD Sciences). A 100 μm nozzle and a 1. 5 neutral density filter were used. Excitation sources were 488 and 561 nm lasers. Emission of mCherry fluorescence was collected with a set of 600nm Long Pass and 610/20 nm Band Pass filters. All signals were collected and analysed on logarithmic scales.
The images shown represent the Z-projected maximal intensity signal of a reconstituted image of the ear tissue for the EGFP channel. Images were then analysed, as previously described  [25]. Images and videos acquired on the SD with the 10X objective lens were first stitched using ZEN software. Images shown correspond to the Z-projected maximum intensity signal for each channel. Time-lapse videos at 20X and 10X were analysed with Imaris software as previously described, to analyse two different parameters (average speed and straightness) of immune cell dynamics  [25]. Statistical analysis. Data generated were analysed with Prism 5 software (GraphPad Software, Inc. ) and a non-parametric Mann-Whitney two-tailed statistical test. p�0. 05 was considered statistically significant (symbols: ���� p�0.
At both time points, EGFP+ cells were recruited in infected mice (Fig 4A  -4C ), with a highly significant increase between early and late time points, and no significant difference between the "Planktonic bacteria & microbead" group and the "Biofilm-coated microbead" group at late time points. At early time-points, the EGFP signal wads statistically significant only for the biofilm group (Fig  4D ). The inflammatory response was further analysed at the cellular level at early time points (4 to 6h post-infection) using the intravital imaging approach and the previously devised confocal acquisition protocol. The aim of this second set of experiments was to study the impact of the presence of microbeads on the dynamics of innate immune responses against S. aureus biofilms by comparing the results with our previous data  [25].
These results illustrate two major characteristics of biofilm physiology: the notion that biofilms represent a physical barrier for phagocytes  [31]  and that consequently phagocytosis is ineffective  [36]. Our new ear skin model finally enabled us to quantify the motility parameters (speed, straightness) of EGFP+ recruited phagocytes at the injection site through a maximum thickness of around 150 μm. The analysis was performed at the tissue injection site taking into account technical parameters such as fluorescence intensity of cells, cell location and cell number  [25]. For each cell, the trajectory calculated by the Imaris software was checked manually point by point. Continuous movements of each cell were also followed throughout the acquisition time to ensure that there were no automatic assignment errors by the software.
Acknowledgments We wish to thank  Alexander R. Horswill  ( Department of Immunology and Microbiology, University of Colorado, Denver, USA ) for pAH9 plasmid,  Ivo Boneca  ( Bacteria-Cell Interactions Unit, Pasteur Institute, Paris, France ) for the LysM-EGFP transgenic mouse line,  Michael Givskov  and  Youg-Tae Chang  for the CDy11b probe,  Caroline Vachias  and  Pierre Pouchin.
Acknowledgements We thank  ESRF  for granting beamtime to the scanning proposal (ES151, DC) and the  Knut and Alice Wallenberg Foundation  for funding (Wallenberg Scholarship, PEA). We appreciate the helpful comments from  Abigail Tucker ,  Qingming Qu ,  Jan Stundl ,  Rolf Ericsson ,  John Long ,  Zerina Johanson  and two anonymous reviewers.
Data availability All synchrotron scan and segmentation data are available through the ESRF paleontology database. http://paleo. esrf. fr/picture. php?/5267/category/2933. Please note that free registration is required to access the data. The following dataset was generated: Author(s) Year Dataset title Dataset URL Database and Identifier Chen D, Blom H, Sanchez S, Tafforeau P, Ma ¨rss T, Ahlberg PE 2020 Lophosteus superbus, marginal jawbone (GIT 760-12) http://paleo. esrf. fr/picture. php?/5267/category/2933 ESRF heritage database for palaeontology, evolutionary biology and archaeology, 5267/category/2933.
2. 4) Deflection measurements A Digital Image Correlation (DIC) device was used. Two cameras filmed both the sample and the loading rod over the tests. The correlation was made thanks to spray-painted speckles on the loading rod. The speckles were not painted on the samples because their dimensions were too small, but the displacement of the rod is equal to the beam deflection as they are in direct contact. The movements which were measured by the cameras were calibrated with pictures of a standard speckles grid. In order to control the validity of the method, the displacements measured with DIC were also compared to those of the ZwickRoell machine. For every sample and stiffness, data appeared to be the same and all the more trustable.
5) Conclusion In the present study, the accuracy of a theoretical model to predict the yield stress of dental composites was evaluated. Based on the experimental data we obtained, we showed that the Turcsányi model initially proposed for tensile yield stress could be adapted to the conventional 3-point bending test. Correlation between the theoretical flexural yield stress and the experimental points is good. But some bias can make the model differ, especially for high-filled composites. These results are promising in order to have an easy and less expensive method to predict the yield stress of dental composites. It would be interesting to check whether the parameter 7 varies in accordance with the theory when the interface strength decreases, for instance because of an accelerated aging protocol.
This treatment is well known to be more effective than artificial saliva for enhancing salivary and lachrymal secretion in patients with pSS  [15]. To date, pilocarpine's impact on SG is still assessed by SSF or USSF. Xerostomia is a subjective clinical symptom and even if the evaluation of disease activity is a main issue in sicca syndrome, few studies published data on imaging technique and treatment management in this syndrome. The use of SGUS in sicca syndrome except for pSS patients is not yet spread. However, evaluation of the echostructural changes and vascularization of major SG could be an interesting marker and ultrasound has not been yet validated in this condition. To respond to this question, we conducted a pilot study (ECHOpilo study). The main objective was to evaluate ultrasound SG echostructure and vascular changes in sicca patients treated during 3 months by pilocarpine.
CONCLUSIONS To conclude, this pilot study is the first attempt to set forth preliminary results about response to treatment by means of SGUS. Pilocarpine improved SSF and USF measurements in our sicca syndrome population without any structural or vascular US changes. Compliance with Ethics Guidelines. The study obtained an IRB approval committee for the protection of persons Ouest VI  (16. Data Availability. The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. Open Access. This article is licensed under a Creative Commons Attribution-NonCommercial 4. 0 International License, which permits any non-commercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
ACKNOWLEDGEMENTS We would like to thank all patients participating in the study. Funding. No funding or sponsorship was received for this study or publication of this article. Authorship. All named authors meet the International Committee of Medical Journal Editors (ICMJE) criteria for authorship for this article, take responsibility for the integrity of the work as a whole, and have given their approval for this version to be published. Disclosures. Alain Saraux  is an editorial board member for Rheumatology and Therapy, but has nothing else to disclose. None of the remaining authors ( Thibaud Depinoy ,  Jacques-Olivier Pers ,  Sylvie Boisrame ,  Divi Cornec ,  Thierry Marhadour ,  Dewi Guellec ,  Valerie Devauchelle-Pensec ,  Luc Bressollette ,  Sandrine Jousse-Joulin ) have anything to disclose.
Micromilling experiments The micromilling experiments were performed on a CNC Mini-Mill/GX from Minitech Machinery using 500 µm uncoated carbide square-end-mills with 2 flutes (Mitsubishi Materials -MS2SSD0050). The microtools were analyzed under a Zeiss scanning electron microscope, model DSM 940. The measurements yielded the cutting edge radius r β of 2-2. 5 µm, corner radius of 10 µm and helix angle of 26 • as can be seen in Fig. 4. For force measurements, it was used the Kistler dynamometer MiniDyn 9256C2, the Kistler charge amplifier 5070A10100 and the data acquisition board USB 6251 from National Instruments. Figure  5  shows the axis configuration of force measurements in relation to the workpiece. The resultant force was calculated using the three orthogonal measured components from the dynamometer.
To be able to compare 3D surface models of follow-up CBCT-scans, the 3D-data sets need to be aligned and 3D surface models of the condyles need to be created in an accurate and reproducible way. 4  The alignment of follow-up scans is most accurately performed by voxel-based registration (VBR). 5, 6 Algorithms match voxels with the same grayscale values that are included in an operator-defined volume. Ideally, a volume of interest for registration is selected that has a stable position in relation to the mandibular condyle. However, the condylar segmentation based on CBCTdata remains challenging. Low bone density of the condyle, connected soft tissues, a close relationship with the glenoid fossa, conical shape of the CBCT beam, the high density petrous part of the temporal bone and an intrinsic low contrast resolution of the CBCT-data are hurdles for automated segmentation algorithms.
Part 1-image registration Study data: For the VBR, 10 patients were randomly selected out of the LORTHOG-database containing data from a cohort observational study which evaluates patients having orthognathic surgery at the Department of Oral and Maxillofacial Surgery of the University Hospitals of Leuven. All selected patients had a bilateral sagittal split osteotomy of the mandible. These patients received a CBCT-scan for pre-operative evaluation and virtual surgery planning. Follow-up CBCTscans were acquired for post-operative evaluation of the osteotomy sites, hard tissue remodeling and skeletal stability. CBCT-scans were obtained at the 1 week (1w) and 6 months (6m) follow-up visits according to the department's clinical practice protocol with the patients seated in the natural head positioning with a thin wax bite keeping them in centric relation.
The Newtom VGi evo device (QR Verona, Verona, Italy) was used with the scanning parameters of field of view (FOV) 24 × 19 cm, voxel size 0. 3 mm 3 , 110 kVp and 4. 3 mA. The DICOM files of these scans were extracted and anonymized. Registration was performed using the left ramus of each patient. Registration method: To align the 6 m CBCT with the 1w CBCT, VBR was performed in the Amira software (v. 6. 7. 0, Thermo Fischer Scientific, Merignac, France). Both DICOM series were loaded in the software and a programmed wizard was used for the procedure. After importing the DICOM files, a common and stable volume of interest was delineated in both scans by the operator. This volume of interest was used to transform the 6 m CBCT-scan towards the 1w CBCTscan, so the gray values of the voxels included in the volume of interest are matched.
8 The rigid transformation consists out of translation values (displacement on the x-, y-and z-axis) as well as rotational values (displacement by pitch, roll, and yaw) that define the movement of the 6 m CBCT Registration validation: The voxel-based registration was performed on the 10 randomly selected patients independently by two operators after initial calibration on how to delineate the modified rami. The first operator performed the registration a second time after a 2-week interval. This was done for both MR1 as MR2. Data were analyzed using MedCalc statistical software (v. 12,0, Ostend, Belgium). A two-way model intraclass correlation coefficient (ICC) for absolute agreement was applied for assessing inter-and intraoperator agreement regarding the translation and rotational values of the transformation matrices.
Segmentation validation: To assess reproducibility of the method, two operators created surface models of all cadaver condyles out of the CBCT-scans using the aforementioned method (P1 & F1). The first operator did this twice with a 2-week interval (P1 & P2). All surface models of a given condyle (P1, P2, F1) were subsequently loaded into the 3D analytical and design software 3-Matic (v. 13. 0, Materialise, Leuven, Belgium). Since every operator worked on the same DICOM data, surface models should overlap and differences in the surface could be regarded as operator differences. The caudal border of all condyles was determined by an analytical sphere, created in 3-Matic, as performed by Nicolielo et al in a previous study on this topic. 9 To create this analytical sphere, the superior pole of the P1 condyle served as a midpoint and the radius was set to 20 cm.
3D follow-up of condylar remodeling Verhelst et al a plane through the lateral and medial pole of the P1 condyle parallel through the horizontal reference plane and a midplane perpendicular on this first plane. For accuracy evaluation, MCT-scans of the isolated rami were aligned with their respective CBCT-scans. Next, 3D surface models were constructed out of the MCT-data using mere thresholding. These served as the golden standard. The P1 models were compared with the MCT models by evaluating volumes and closest point distance mapping between surfaces. All data were analyzed using MedCalc Statistical software (v. 12. 0, Ostend, Belgium). For the evaluation of the reproducibility, a two-way model intraclass correlation coefficient (ICC) for absolute agreement was applied for assessing inter-and intraoperator agreement of the volumes.
Isolation and growth conditions In April 2016 we isolated in a stool sample from a Nigerian child with marasmus a bacterial strain that could not be identified by MALDI-TOF MS. The screening was performed on a Microflex LT spectrometer (Bruker Daltonics, Bremen, Germany), as previously reported  [7]. The spectra obtained (Fig. 1 ) were imported and analysed using the Biotyper 3. 0 software against the Bruker database, which was continually incremented with the laboratory MEPHI database. The strain was isolated on 5% sheep's blood-enriched Columbia agar (bioMérieux, Marcy l'Etoile, France) at 37°C in an anaerobic atmosphere (anaer-oGEN; Oxoid, Dardilly, France) after a 15-day preincubation in an anaerobic bottle containing a Brucella medium. The study was approved by the ethics committee of the Institut Federatif de Recherche 48 under reference 2016-010.
Strain identification To classify this bacterium, the 16S ribosomal RNA (rRNA) gene was amplified using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequenced using the Big Dye Terminator v1. 1 Cycle Sequencing Kit and 3500xLGenetic Analyzer capillary sequencer (Thermo-Fisher, Saint-Aubin, France), as previously described  [8]. The 16S rRNA nucleotide sequence was assembled and corrected by CodonCode Aligner software (https://www. codoncode. com/). Strain Marseille-P3557 T exhibited a 97. 6% 16S rRNA similarity with Anaerococcus prevotii strain 20548 (GenBank accession no. NR_074575. 1), the phylogenetically closest species with standing in nomenclature (Fig. 3 ). We consequently proposed to classify strain Marseille-P3557 T as a new species within the genus Anaerococcus in the phylum Firmicutes.
Genome sequencing Genomic DNA was extracted using the EZ1 biorobot with the EZ1 DNA tissue kit (Qiagen, Hilden, Germany) and then sequenced on a MiSeq sequencer (Illumina, San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT Paired End (Illumina), as previously described  [9]. The assembly was performed using a pipeline containing several different software packages (Velvet  [10] , Spades  [11]  and Soap Denovo  [12] ) and trimmed (MiSeq and Trimmomatic  [13]  software) or untrimmed data (only MiSeq software). GapCloser was used to reduce assembly gaps. Scaffolds of <800 bp and scaffolds with a depth value < 25% of the mean depth were removed. The best assembly was selected using different criteria (number of scaffolds, N50, number of N). The genome of strain Marseille-P3557 T was 2 130 060 bp long with a 35.
4 mol% G + C content. The degree of genomic similarity of strain Marseille-P3557 T with closely related species was estimated using the OrthoANI software  [14]. OrthoANI values among closely related species (Fig. 4 ) ranged from 62. 55% between Anaerococcus marasmi and Anaerosphaera aminiphila to 96. 47% between Anaerococcus obesiensis and Anaerococcus vaginalis. When A. marasmi was compared to these closely related species, values ranged from 62. 55% with Anaerosphaera aminiphila to 77. 73% with A. prevotii.
Acknowledgements Funded by the  Méditerranée-Infection foundation  and the  French National Research Agency  under the  programme 'Investissements d'Avenir,' reference   ANR-10-IAHU-03. This research was also supported by a grant from the  Institut Universitaire de France (IUF, Paris, France , to AL). The authors thank  A. Caputo  for submitting the genomic sequence to GenBank. We also thank  T. Irie ,  K. Imai ,  S. Matsubara ,  T. Sakazume ,  Y. Ominami ,  H. Akiko  and the  Hitachi team of Japan (Hitachi High-Technologies Corporation, Science & Medical Systems Business Group   24-14 ,  Tokyo, Japan ) for the collaborative study conducted together with the  IHU Méditerranée Infection  and for the installation of a TM4000 microscope at the  IHU Méditerranée Infection.
Histological and immunofluorescence analyses Half of the sections were immersed for 10 min in PFA before being rinsed and stained for 5 min in alizarin red (Sigma-Aldrich). Slides were mounted using DAKO mounting medium prior to examination under microscope (RM 2145 DMRB microscope, Leica, Rueil-Malmaison, France). Other half sections were dipped 10 min in PFA before being rinsed and stained for 5 min in 200 nM DAPI solution (Sigma-Aldrich) to stain cell nuclei. Sections were then mounted and examined under fluorescence microscope. The immunofluorescent calcein staining was followed using fluorescent microscope (RM 2145 DMRB microscope, Leica, Rueil-Malmaison, France). The circumference of neo-bone area was marked and measured by Olympus cellSens Entry imaging software. At least 3 samples per mouse were considered for each condition.
Both peptides contain a single glutamine (Q) and no asparagines (N). Horse specimens from Quinçay (Equid1) and La Ferrassie (Equid2) derive from the Châtelperronian layers (layer Ej and layer 6, respectively). Equid3 and the Homo sp. bone specimen derive from the re-excavated archaeological deposits associated with the Neanderthal type specimen from the Kleine Feldhofer Grotte (Germany). All specimens likely date to between 40 and 50 ka BP. The base map was generated using public domain data from http://www. naturalearthdata. com/. An equid (Equid3, ZooMS specimen number F-35) and a hominin specimen (ZooMS specimen number F-15) were selected randomly from the identified specimens. Here, the only criterion for selection was the presence of a MALDI-TOF MS spectrum allowing taxonomic identification.
Buffer A was milliQ water, and the peptides were separated with increasing buffer B (80% ACN and 0. 1% formic acid), going from 5% to 30% in 50 min, 30% to 45% in 10 min, 45% to 80% in 2 min, held at 80% for 5 min before dropping back down to 5% in 5 min and held for 5 min. Flow rate was 250 nl/min. The column temperature was kept at 40 °C with an integrated oven. The Q-Exactive HF-X was operated in data dependent top 10 mode. Spray voltage was 3. 7 kV, S-lens RF level was 40, and capillary was heated at 320 °C. Full scan mass spectra were recorded at a resolution of 120,000 at m/z 200 over the m/z range 350-1400 with a target value of 3e6 and a maximum injection time of 25 ms. MS/MS HCD-generated product ions were recorded with a maximum ion injection time set to 108 ms and a target value set to 2e5 and recorded at a resolution of 60,000.
MaxQuant database searching Raw mass spectrometry data were searched in MaxQuant (version 1. 6. 3. 4) against the horse (UP000002281) and human (UP000005640) proteomes (downloaded from UniProt on 07/07/2018 and 11/09/ 2018, respectively). Sequences of common protein contaminants were added to the database search in MaxQuant. For the Equidae, searches were performed separately for each protease. For the hominin, a single search was performed including all data files, grouped per protease. Injection replicates were kept separate during MQ data analysis. Each search was performed twice, once using semi-specific proteolysis mode and once using specific proteolysis mode. For each search, default settings of 20 ppm for the first search and 4. 5 ppm for the final search were used, and a fragment mass tolerance of 20 ppm.
The UniProt accession numbers of protein groups considered possible contaminants and those present with at least two unique+razor peptides across all negative controls can be found in Table  S2. These, alongside reverse protein entries, were removed from subsequent analysis. Sample-level deamidation rates were calculated for all remaining protein groups together using 1000 bootstraps  [43]. Presented Venn diagrams were created using http://bioinformatics. psb. ugent. be/ webtools/Venn/. The raw proteomic data files as well as MaxQuant search results are available in ProteomeXchange under accession number PXD018264  [44].