dataesr/scientific-paragraphs-categorization huggingface dataset:
Moreover, the biofilm images captured after 48 and 72 h revealed the absence of C. albicans cells (Figure  9b, c ). To characterize the structure and spatial distribution of the live cells in the biofilm on the different surfaces (Ti, PDMS, HAp-PDMS, Zn:HAp-PDMS and Ag:HAp-PDMS) at 24, 48 and 72 h 3D composite images were analyzed using Image J software (Figure  10 ). The 3D image was made up of several biofilm layers along the y-axis. Given the thickness of the biofilm, by Image J software we could obtain automatically the dimensions of the xand y-axis. On the other hand, the z-axis measures the fluorescence intensity of live (red color) cells. In the pictures shown in Figure  10  is illustrated the spatial distribution of the live (red color) cells in the C. albicans biofilm along horizontal (coverage) and vertical (thickness) distributions on the different substrate (Ti, PDMS, HAp-PDMS, Zn:HAp-PDMS and Ag:HAp-PDMS) at different time intervals (24, 48 and 72 h) as indicated by the fluorescence intensity.
The results revealed that the C. albicans biofilm structure and composition were similar on Ti substrate (considered as a control), PDMS and HAp-PDMS composite layers regardless of the studied time interval. Nevertheless, live cells (red color) are no longer dominant in the biofilm formed on the surface of Zn:HAp-PDMS composite layer. One can also notice that the evolution of C. albicans biofilm on Ti substrate coated with Zn:HAp-PDMS composite layer was slightly diminished over time (Figure  10e, f ). The fungicidal effect  [71]  of the surface Ag:HAp-PDMS composite layer on biofilm formation and development was shown against C. albicans (Figure  10a-c ). of several biofilm layers along the y-axis. Given the thickness of the biofilm, by Image J software we could obtain automatically the dimensions of the x-and y-axis.
Acknowledgments: We are grateful to  Mariana Chifiriuc  ( Microbiology Department, Faculty of Biology, University of Bucharest ) for their technical help on evaluation of antifungal activity of complex layers against C. albicans biofilm. We also thank  George A. Stanciu  and  Radu Hristu  ( Center for Microscopy-Microanalysis and Information Processing, University Politehnica of Bucharest ) for their technical support to providing the CLSM images. This work was supported by  Romanian Ministry of Education , through the  Core program  PN  16-48  ( MS-FISCOMAT ) and  Core program  PN  16-47-01 02/2016  (contract  4N/09. 03. 2016 ). In addition, this work was supported by contract  STAR no. 53/20. 11. 2013  financed by  Romanian Space Agency. Mihai Ganciu performed experiments. Daniela Predoi  and  Andreea Groza  analyzed the results and wrote the paper.
The advent of culture-independent methods has greatly improved the detection of microorganisms, many of which cannot yet be grown in culture. 57 The most common culture-independent technique to analyse the microbiome is based on 16S ribosomal RNA (16S rRNA) gene community profiling. 57 The 16S rRNA gene is present in all prokaryotes and contains variable regions that are unique between microorganisms and that can be used as a means of identification. 16S rRNA genes can be extracted from heterogeneous samples, amplified and sequenced, and then compared with databases such as the Human Oral Microbiome Database,  37  a publically available online resource that links sequence data with phenotypic, phylogenetic, clinical and bibliographic information of microorganisms found in the oral cavity. If a match for the sequence is found on the database, the microorganism can be identified; if there is no matching entry on the database, the sequence can be added as a record for a previously unknown phylotype.
Characterization of Plasma Polymerized Coatings X-ray Photoelectron Spectroscopy The chemical composition was analyzed by XPS with a SPECS (Germany) using an Al non monocromatic source XR50 (200W and 14 kV) with an analyzer Phoibos 150 MCD-9 with pass energy of 25eV, high resolution steps of 0. 1eV, chamber pressure of 5. 10 9 mbar and using a Flood gun FG15/40. Peak deconvolution was performed with CasaXPS software.
ACKNOWLEDGEMENTS Authors acknowledge the  Spanish Government  for financial support through Project  MAT2012-38438-C03-01 , co-funded by the  EU through European Regional Development Funds, and Ramon y Cajal fellowship of CC. Support for the research of MPG was received through the '' ICREA Academia '' prize for excellence in research, funded by the  Generalitat de Catalunya. The  European Commission  is acknowledged for support through Cost Action  MP1101  and the  University Pierre et Marie Curie  for the PhD scholarship.
qPCR was performed using SYBR Green PCR Master Mix (Applied Biosystems) and different sets of primers (Table  1 ) (Eurofins Genomics) at a final concentration of 0. 5 μ M. The PCR reaction 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 sec and, 72 °C for 30 sec. The mRNA expression profiles were normalized with respect to GAPDH (Glyceraldehyde 3-phosphate dehydrogenase). The qPCR was performed using a QuantStudio ™ 7 Flex System (ThermoFischer). Relative gene expression was obtained using the instruments software (relative quantity = 2 -∆∆Ct ). The mean of five non-stimulated and uninfected donor samples was taken and used to produce log 2 ratios with respect to the normalized data from stimulated and/or infected cells. Gene expression heatmaps were generated using TM 4 MultiExperiment Viewer software and hierarchichal clustering for the gene tree.
Gene silencing was measured by qPCR. Statistical Analysis. Data are presented as mean ± standard deviation. Statistical analysis was made using SigmaPlot 12. Multiple group comparisons were made using ANOVA one parameter tests followed by pairwise comparisons of the groups using Holm-Sidak test. Two group comparisons were made using Student's t-test. All the prerequisites of the tests were verified. The considered nominal alpha criterion level was 0. 05 below which differences between samples were deemed significant.
Acknowledgements We acknowledge  Gareth Griffiths  ( Oslo University ) for critical reading of the manuscript and to  Jonathon Blake  ( EMBL-Heidelberg ) for support on gene expression heatmaps generated using TM 4 MultiExperiment Viewer software. To  Instituto Português do Sangue  for providing blood samples; to BEI resources (and  Colorado State Univ. , USA)  for proteins and strains; to the  Centre for AIDS Reagents, NIBSC (United Kingdom)  for providing IFNγ. This work was funded by  FCT -Fundação para a Ciência e Tecnologia  with the support from the fellowship  SFRH/BD/63747/2009  to DP and project grants  PIC/IC/82859/2007 ,  PTDC/BIA-BCM/102123/2008 ,  PTDC/ SAU-MII/098024/2008  to EA.
The structural elements shown above the alignment were generated using the native α-1-antitrypsin structure (PDB ID: 1QLP) sequence invariant residues between sequences are typed red on a white background and residues conserved within each group are displayed as white letters on a red background. Underlined sequences represent the predicted hinge region (blue) and reactive center loop (yellow). The predicted cleavage site is marked with a double vertical line. P1 and P1′ residues are labeled weight of nearly 44 and 46 kDa close to the theoretically expected one (Fig. 2b, d ). These results were confirmed by mass spectrometry analysis which proved the correspondence of these protein species to Siropin 1 and 2 (data not shown). These data demonstrate the molecular cloning and the expression of the E.
DNA manipulation and PCR Chromosomal DNA was isolated from E. siraeum DSM 15702 using the Wizard ® Genomic DNA Purification kit (Promega). Preparation of plasmid DNA and separation of fragments by agarose gel electrophoresis were performed as described by Sambrook et al. [38]. To amplify the genes encoding for Siropins, we used gene-specific and universal primer pairs in a 1∶4 ratio to generate the attachment binding sites (underlined) attb1 and attb2 in the final constructs. Based on the E. siraeum complete genomic sequence available in the NCBI Databank (ID: FP929044. 1), we designed the specific oligonucleotide sequences F-SP1 5′GTACAAAAAAGCAGGCTTCAC AGGCATCAAAGCCGCAAGCC3′ and R-SP1 5′CAAG AAAGCTGGGTCTCATATACCTGTATACACGCC3′ for Siropin 1.
Subsequently, blots were incubated with primary antibody (with 1/10,000 dilution of mouse anti-polyHistidine monoclonal antibody, Sigma) at room temperature for 1 h. Treated membranes were washed three times with the phosphate-buffered saline solution and incubated with goat anti-mouse HRP (Bio-Rad) during 1 h. Blot signals were detected using chemiluminescent substrate and ChemiDoc ™ MP System (Bio-Rad). The multiple alignment of the Serpin amino-acid sequence was done using the program ClustalW  [40]  and the figure rendering was done using the ESPript sequence analysis server  [41]. The 3D homology model of Siropin 1 and 2 was generated using the Geno3D server, and images were rendered by using VIEWERLITE ™ 5. 0.
Samples were eluted in 50 μl, dried in a speed vacuum centrifuge and dissolved in 10 μl of reconstitution buffer (96:4 water/acetonitrile and 0. 1% formic acid) and analyzed by LC-MS/MS. For this analysis, peptides were separated using the nanoAcquity UPLC system (Waters) fitted with a trapping (nanoAcquity Symmetry C 18 , 5 μm, 180 μm × 20 mm) and analytical column (nanoAcquity BEH C 18 , 1. 7 μm, 75 μm × 200 mm) coupled directly to an linear trap quadropole (LTQ) OrbitrapVelos (Thermo Fisher Scientific) with a Proxeonnanospray source. The peptides were introduced into the mass spectrometer (OrbitrapVelos Pro, Thermo) and a spray of 2. 2 kV was applied. Peptides analysis was performed using MaxQuant Software (version 1. 0. 13. 13). The data were searched against a species-specific (E. siraeum) Uniprot database with a list of common contaminants appended.
Acknowledgements The authors would like to express their gratitude to  A. SLIMI  for his help with figure treatment and Anaxem platform for animal handling. HM, NA and AG were supported by the project  CMCU-PHC Utique (n°14G0816 )-Campus France (n°30666QM). Part of the project relates to SerpinGuTarget  ANR-14-CE-16-0018. We would like to thank  A. L. Abraham ,  A. Bolotin ,  V. Rossi  and  N. Thielens  for the discussion on microbial serpins. We are also grateful for  S. D. Ehrlich  and  F. Haimet  to allow this collaboration.
Neutron beams are very penetrating and non-destructive. The great penetrating power permits up to 1 cm sections of bone to be examined. To our knowledge, there are no data available about the qualitative changes of HAP crystals in the OA subchondral bone as assessed by PND. The aim of this study was to evaluate HAP changes in subchondral trabecular bone from human femoral heads in relation to OA without homogenizing the bone samples. For this purpose, from the same individuals, areas with full thickness loss of the cartilage (considered to be as the latest stage of the disease) were compared with subchondral trabecular bone in areas surrounded by the normal cartilage (considered to be normal bone). For that, the following techniques were using: FTIR spectroscopy and PND.
4 For FTIR spectroscopy, fragments of the sample were the crushed particles sieved before making the, KBr pellets and analyzed with a Brucker® IFS25 spectrometer as previously described  [92]. Data were collected in the absorption mode between 4000 and 400 cm -1 with a resolution of 4 cm -1. The carbonate ratio (CR) of HAP was defined as the ratio between the intensity of the ν 2 ν 3 bands of carbonate ions at 870 cm -1 and 1420 cm -1 , respectively, and the intensity of the ν 3 ν 4 bands of phosphate ions at 1035 cm -1 and 604 cm -1 , respectively. The neutron diffraction diagrams were collected on the G4. 1 two-axis multidetector powder diffractometer [93] installed on a cold-source beamline of the Orphée reactor (Saclay, France). This beamline was equipped with a two-axis powder diffractometer, with a verticalfocusing pyrolytic graphite monochromator and an 800-cell multidetector covering an 80° 2 range (step 0.
Acknowledgements We thank our other patient partners  Claire Pritchard  and  Margaret Pritchard  for their contribution to this work. Collaborators Appendix: Additional Participants of the Histopathology Workshop Group:  Rui PP de Albuquerque, Department of Oral Medicine, Birmingham Dental Hospital and School of Dentistry, University of Birmingham, UK. Rigel Allen ,  Oral Medicine, University of Manchester, Manchester, UK. Elisa Astorri, Centre for Experimental Medicine and Rheumatology, Queen Mary University of London, London, UK. Chiara Baldini, Rheumatology Unit, University of Pisa, Pisa, Italy. Rajdeep Bhabra , patient partner. Pilar Brito-Zerón ,  Department of Autoimmune Diseases, University of Barcelona, Barcelona, Spain. Preetha Chengot, Department of Histopathology, St. James's University Hospital, Leeds, UK.
FB has a senior fellowship from  Arthritis Research UK  ( 21236 ). The  Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence  was part-funded by  Arthritis Research UK  ( 20298 ); this Centre is a collaboration between the  Universities of Glasgow, Newcastle and Birmingham. The funders did not influence the content of these recommendations. Competing interests SJB has received honoraria/consultancy fees in the field of Sjögren's syndrome in 2015-2016 for  AstraZeneca ,  Celgene ,  Glenmark ,  Eli Lilly ,  Novartis ,  Ono  and  UCB Pharmaceuticals. Roche  provided rituximab for the TRACTISS study. BAF has received honoraria/consultancy fees from  Novartis ,  Roche  and  Medimmune. FB has received honoraria/consultancy fees from  Roche ,  GlaxoSmithKline ,  Glenmark  and  Medimmune , and research funding from  UCB.
10, 11 Recently, we reported on a large family with 14 members affected by PDB, four of whom developed GCT at single or multiple pagetic skeletal sites. 12 We excluded the presence of mutations in SQSTM1 or in other genes known to be associated with PDB-related syndromes (TNFRSF11A [MIM: 603499], TNFRSF11B [MIM: 602643], VCP [MIM: 601023], and identified multiple chromosomal regions, potentially housing the causative mutation. 12, 13 e now report the identification of a heterozygous missense mutation in ZNF687 (MIM: 6010568) in all affected members of the family and in seven additional unrelated individuals with GCT/PDB. The same mutation (c. 2810C>G) and one additional mutation (c. 725G>T) in ZNF687 (GenBank: NM_020832. 2) were also detected in two families and in some severe PDB cases (with earlier onset and an increased number of affected skeletal sites) from two cohorts of pagetic individuals with different genetic backgrounds and previously analyzed for SQSTM1 mutations.
Whole-Exome Sequencing Strategy Genomic DNA samples from four family members belonging to the extended pedigree were tested with the NimbleGen SeqCap EZ ExomeTM capture kits (Roche), and the resultant fragments were sequenced on an Illumina GAIIx (Illumina) with 90 bp paired-end reads. Reads were obtained and aligned to the human reference genomic sequence (UCSC Genome Browser GRCh37/ hg19) with MAQ7 and NextGENe software v. 2. 0. We adopted a prioritization scheme, described in Table  S3 , to identify the pathogenic mutation in each individual, similar to the approach (C) A portion of the amino acid sequence of ZNF687 from diverse mammal species. (D) The ancestral haplotype with rare variants in SV2A-rs149735232 (t minor-allele frequency ¼ 1. 5%), SETDB1-rs138864506 (t minorallele frequency ¼ 0.
The proband (II-6) and all affected siblings (II-1 and II-3) of family 3 were heterozygous for the ZNF687 c. 725G>T missense mutation. This mutation was not detected in the three unaffected family members (II-2, II-4, and II-5) of family 3 (Figures  2A  and 2B ) and was not reported in the 1000 Genome and ExAC databases. The serine at the 242 position of ZNF687 is highly conserved in all species (Figure  2C ), and the p. Ser242Ile change was predicted in silico (by SIFT, PolyPhen, PMut, and Align GVGD) to be highly pathogenic, suggesting a causative role. Computational analysis strongly suggested Ser242 to be an important phosphorylation site (score of 0. 996 in NetPhos prediction). 20 Subsequently, both the c. 2810C>G and c. 725G>T mutations were screened by TaqMan assay in two cohorts of PDB-affected individuals of different ethnicity.
To further clarify ZNF687 involvement in PDB pathogenesis, we first analyzed the ChIPBase database, an integrated platform for decoding transcription factor binding sites (including 11 independent ChIP-seq experiments of NFkB transcription factor). 24 nterestingly, in all experiments, ZNF687 was detected as a genomic target of NFkB in its putative promoter (Figure  4B ). Similar to ZNF687, ZMYND8 (MIM: 615713) and ZNF592 (MIM: 613624), the other two partners of ZNF687 in the Z3 complex formation, are regulated by NFkB transcription factor, which binds their promoters (data not shown). Next, we evaluated ZNF687 expression in tumor tissues derived from five individuals with GCT/ PDB. As expected, in comparison to expression in healthy bone marrow, a dramatic increase in ZNF687 expression was observed in the RNAs extracted from tumor biopsies of these individuals, confirming the pathological role of ZNF687, whose expression resulted from the c.
Acknowledgments We thank  Dr. Monica Autiero  for helpful suggestions and manuscript editing,  Mrs. Edith Gagnon  at  Quebec Research Centre  for Sanger sequencing,  Dr. Riccardo Muscariello  at the  Department of Medicine and Surgery at Federico II University  for recruitment of PDB-affected individuals, and  Dr. Federica Scotto di Carlo  for her assistance in submitting this paper. This work was supported by  Telethon Italy  (grant no. 11119A , F. G. and L. G. ), the  European Calcified Tissue Society/AMGEN  fellowship (F. G. ), the  Italian Society for Osteoporosis, Mineral Metabolism and Skeletal Diseases (F. G. ) , the  John G. Haddad Research Award  from the  Paget Foundation  (L. G. ), and the  Italian Association for Cancer Research  (grant IG-2014 no. 15707 , F. G. ). The Short-term Mobility Program from the  Italian National Research Council  (F.
G. ) is gratefully acknowledged, as well as the  Galliera Genetic Bank  funded by  Telethon Italy  (grant no. GTB12001 ). This work is dedicated to the memory of  Dr. Giuseppe Mossetti. Received: September 15, 2015 Accepted: December 17, 2015 Published: February 4, 2016 Web Resources The URLs for data presented herein are as follows: 1000 Genomes, http://browser. 1000genomes. orgChIPBase database, http://deepbase. sysu. edu. cn/chipbase/index. php  ExAC Browser , http://exac. broadinstitute. org/GenBank, http://www. ncbi. nlm. nih. gov/genbank/NetPhos 2. 0, http://www. cbs. dtu. dk/services/NetPhos/NLStradamus, http://www. moseslab. csb. utoronto. ca/NLStradamus/OMIM, http://www. omim. org/ UCSC Genome Browser , http://genome. ucsc. edu.
In an exploratory analysis, we examined the interaction of smoking with gender. Females who smoked appeared to be at higher risk of HPV-positive OPSCC compared with female nonsmokers, but this relationship was not seen in males. However, there were very few women with HPV-positive OPSCC (n=28) in our study, and these sparse data produced imprecise estimates. There are a few limitations to our study. All oral health variables were self-reported and thus they may be considered as less valid oral health indicators than clinically-diagnosed disease. 39 However, previous studies have also found high correlation between self-reported tooth loss and a clinical examination. 40 The current study is in agreement with previous work demonstrating that routine dental visits are associated with decreased risk of developing head and neck cancers.
Subjects and study design This was an exploratory, randomized, open-label, active-controlled, 4-period, cross-over study conducted at a single center in Germany between 7 January 2014 and 21 February 2014. The study was approved by the Landesärztekammer Thüringen Ethics Committee on 28 November 2013, and performed in compliance with the Declaration of Helsinki, Good Clinical Practice Guidelines (CPMP/ICH/135/95), and the EN ISO 14155 (2011) standard for medical devices. All subjects provided written informed consent prior to study participation. The study (EUDAMED no. CIV-13-10-011648) was registered at www. clinicaltrials. gov (NCT02005328). Male and female subjects (18 years and older) were eligible if they had taken drug(s) causing salivary hypofunction/ xerostomia for at least 1 week prior to study initiation and were expected to continue without any change during the study.
Statistical analysis A sample size of 24 subjects was arbitrarily chosen. Results are regarded as exploratory in nature, and only descriptive statistics were performed. Two analysis sets were defined. The full analysis set (FAS) included all randomized subjects who received each product of their sequence group and had data available for the primary efficacy criterion for each product. The safety set comprised all randomized subjects who received at least one product application of their sequence group. The primary efficacy endpoint was the area under the curve (AUC) of the dry mouth evaluation (VAS item 4) from baseline to 4 h after the first product application. The primary analysis was performed on the FAS and was descriptive only. The adjusted AUC difference between groups and the associated 95% confidence interval (CI) were calculated using an analysis of variance, including product and period as fixed effects and subjects as random effect on the FAS.
The digital revolution is changing the world, and dentistry is no exception. The introduction of a whole range of digital devices (intraoral, extraoral, face scanners and cone beam computed tomography (CBCT) with low dose radiation) and processing software (computer-assisted-design/computer-assistedmanufacturing (CAD/CAM) prosthetic software, software for planning implant surgery), together with new aesthetic materials and powerful manufacturing and prototyping tools (milling machines and 3D printers), is radically transforming the dental profession. Classically, case history and physical examination, together with X-ray data from two-dimensional radiology (periapical, panoramic, and cephalometric radiographs), represented the necessary preparatory stages for formulating a treatment plan and for carrying out the therapy.
A better understanding of the dynamics of molecular changes occurring during the early stages of oral tumorigenesis may help refine prevention and treatment strategies. We generated genome-wide expression profiles of microdissected normal mucosa, hyperplasia, dysplasia and tumors derived from the 4-NQO mouse model of oral tumorigenesis. Genes differentially expressed between tumor and normal mucosa defined the "tumor gene set" (TGS), including 4 non-overlapping gene subsets that characterize the dynamics of gene expression changes through different stages of disease progression. The majority of gene expression changes occurred early or progressively. The relevance of these mouse gene sets to human disease was tested in multiple datasets including the TCGA and the Genomics of Drug Sensitivity in Cancer project.
The TGS was able to discriminate oral squamous cell carcinoma (OSCC) from normal oral mucosa in 3 independent datasets. The OSCC samples enriched in the mouse TGS displayed high frequency of CASP8 mutations, 11q13. 3 amplifications and low frequency of PIK3CA mutations. Early changes observed in the 4-NQO model were associated with a trend toward a shorter oral cancer-free survival in patients with oral preneoplasia that was not seen in multivariate analysis. Progressive changes observed in the 4-NQO model were associated with an increased sensitivity to 4 different MEK inhibitors in a panel of 51 squamous cell carcinoma cell lines of the aerodigestive tract. In conclusion, the dynamics of molecular changes in the 4-NQO Research Paper Oncotarget 35933 www. impactjournals. com/oncotarget model reveal that MEK inhibition may be relevant to prevention and treatment of a specific molecularly-defined subgroup of OSCC.