dataesr/scientific-paragraphs-categorization huggingface dataset:
Interestingly, in this study only 8 out of 79 patients had bacteria isolated from microbiological culture and recorded in the CRF. However, almost all patients (77/79) were receiving systemic antibiotic treatments, indicating concomitant bacterial infections, although it was not possible to know more about the sites of bacterial infection as this information was not collected in the CRF. The median duration of IV anidulafungin in patients with intra-abdominal infections was 14 days, which was longer than the 10 days of IV anidulafungin duration described in the pooled analysis of the overall general population  [22]. In the real-world AmarCAND2 study, the median duration of antifungal therapy was 14 days for targeted therapy and 17 days for empirical therapy  [11]. Furthermore, in our population, a lower percentage of the patients (22% and 19%; data not shown) switched to oral therapy compared to that found by Kullberg et al.
Acknowledgements Data from this analysis were presented at the 55th  Interscience Conference of Antimicrobial Agents and Chemotherapy  (ICAAC) meeting, San Diego, CA, USA, 17-21 September 2015. Editorial/medical writing support, under the direction of the authors, was provided by  Neil Cockburn  of  CMC Connect , a division of  McCann Health Medical Communications Ltd. , Macclesfield, UK, funded by  Pfizer , in accordance with Good Publication Practice (GPP3) guidelines (Ann Intern Med 2015;163: 461-4 ). Research data sharing Upon request, and subject to certain criteria, conditions and exceptions (see https://www. pfizer. com/science/clinicaltrials/trial-data-and-resultsfor more information),  Pfizer  will provide access to individual de-identified participant data from  Pfizer -sponsored global interventional clinical studies conducted for medicines, vaccines and medical devices (1) for indications that have been approved in the US and/or EU or (2) in programmes that have been terminated (i.
2014 [17] invasive candidiasis A8851015 (NCT00548262) b Latin America Open-label Candidaemia and Nucci et al. 2014 [18] invasive candidiasis A8851016 (NCT00537329) b Asia Open-label Candidaemia Mootsikapun et al. 2013 [19] A8851019 (NCT00689338) c Europe and Canada Open-label Candidaemia and Ruhnke et al. 2012 [20] invasive candidiasis A8851022 (NCT00805740) USA, Canada, Europe, Double-blind, randomised Candida deep-seated Pfizer data on file Russia, Switzerland tissue infection a.
Results and discussion To test this hypothesis, we assembled and analyzed a dataset of 753 public and 182 newly sequenced saliva and stool metagenomes from 470 healthy and diseased individuals (diagnosed with rheumatoid arthritis, colorectal cancer or type-1 diabetes) from Fiji  (Brito et al. , 2016) , China  (Zhang et al. , 2015) , Luxembourg  (Heintz-Buschart et al. , 2016) , France  (Zeller et al. , 2014) , and Germany  (Voigt et al. , 2015)  (see Materials and methods, Figure  1 , and Supplementary file 1). For these samples we profiled 310 prevalent species, accounting for 99% of classifiable microbial eLife digest Trillions of bacteria and other microbes live in the human body. The mouth and the gut in particular, are microbial hot spots at either end of the digestive tract. Every day, humans swallow around 1.
, 2014; Zhang et al. , 2015). However, due to insufficient taxonomic resolution, oral provenance has so far remained impossible to distinguish from an influx of closely related but distinct strains from the environment. We therefore defined a list of disease states with putative links to oral-fecal transmission and annotated known associations in the literature to all species in our dataset (Figure  4A ; Supplementary file 2). Transmission scores were significantly increased for known opportunistic pathogens (ANOVA, p=0. 016), causative agents of dental caries (p=10 À9 ), and plaque-dwelling bacteria (p=0. 002). Likewise, species associated with periodontitis showed increased evidence for transmission (p=0. 002), though this signal was mostly due to mildly periodontic species, while core drivers, such as Tannerella forsythia, Treponema denticola and Porphyromonas gingivalis  (Socransky et al.
, 1998) , showed little or no indication of oral-fecal transmission. Endocarditis-associated species showed significantly increased transmission scores upon phylogenetic regression (p=0. 007), mostly driven by Haemophilus, Aggregatibacter and viridans Streptococci. This overall elevated transmissibility of taxa known to colonize ectopically in various habitats across the body (i. e. , opportunistic pathogens), in particular via the bloodstream and associated with inflammation (i. e. , endocarditis-or periodontitis-associated species  (Hajishengallis, 2015) ), may provide first cues to possible mechanisms of oral-fecal transmission. Our dataset included metagenomes from case-control studies for rheumatoid arthritis (RA,  (Zhang et al. , 2015) ), colorectal cancer (CRC,  (Zeller et al. , 2014) ) and type-1 diabetes (T1D,  (Heintz-Buschart et al.
Metagenomic datasets Publicly available raw sequence data was downloaded from the European Nucleotide Archive (ENA) for the FJ-CTR (FijiCOMP, project accession PRJNA217052)  (Brito et al. , 2016)  and CN-RA (PRJEB6997)  (Zhang et al. , 2015)  cohorts. Sample metadata was parsed from ENA and the respective study publications. For the LU-T1D (PRJNA289586)  (Heintz-Buschart et al. , 2016)  cohort, newly generated salivary and fecal metagenomes were added under the existing project accession. For the FR-CRC (ERP005534)  (Zeller et al. , 2014)  and DE-CTR (ERP009422)  (Voigt et al. , 2015)  cohorts, newly generated metagenomes were uploaded under project accession PRJEB28422 (samples ERS2692266-ERS2692323).
Metagenomic sequence processing Raw reads were quality trimmed and filtered against the human genome issue 19 to exclude host sequences using MOCAT2, as described previously  (Kultima et al. , 2016). For taxonomic profiling, reads were mapped against a database of 10 universal marker genes for 1753 species-level genome clusters (specI clusters,  (Mende et al. , 2013) ), using NGless  (Coelho et al. , 2018). A maximum likelihood-approximate phylogenetic tree (with the JTT model,  (Jones et al. , 1992) ) for representative genomes of the same 1753 clusters was inferred based on protein sequences of 40 near-universal marker genes  (Mende et al. , 2013)  using the ETE3 toolkit  (Huerta-Cepas et al. , 2016) , with default parameters for ClustalOmega  (Sievers et al. , 2011)  and FastTree2  (Price et al.
Taxa filtering and annotation The dataset was filtered to include taxa satisfying the following criteria in !10% of samples (see Figure 2-figure supplement 5 for details): horizontal coverage (breadth) of !0. 05; average vertical coverage (depth) !0. 25; specI cluster relative abundance of !10 À6. These criteria excluded taxa representing 0. 8 ± 1. 2% of gut and 1. 2 ± 1. 9% of oral total mapped abundance. For the remaining 310 taxa, general phenotypes (Gram stain, sporulation, motility, oxygen requirement, among others) were annotated using the PATRIC database (accessed Dec 2015)  (Wattam et al. , 2017) , and missing values were amended manually. Host and disease association phenotypes (including opportunistic pathogenicity and periodontitis association) were annotated manually, based on published literature and the MicrobeWiki website (https://microbewiki.
Similarly, we computed the log-likelihood of the least likely agreement case (L min ) per allele: L min ¼ X i min log p 1;1 i ð Þ À Á ; log p 0;0 i ð Þ À Á À Á From these values, we calculated a raw probability score (P raw ) for the observed allele agreement between a given pair of oral and gut samples: p raw ¼ L obs =L min P raw scales the likelihood of the observed agreement by the likelihood of the theoretically most extreme cases of agreement across all observed alleles. In particular, the shared observation of very rare alleles (very low f oral and f gut ) has a strong impact on P raw , whereas the shared observation of very common variants is downweighted. We computed P raw for all pairwise permutations of oral and gut samples in the dataset with observations (reads) at !20 matching positions.
All steps (data preprocessing, model building, and model evaluation) were performed using the SIAMCAT R package (https://bioconductor. org/packages/SIAMCAT, version 1. 1. 0; see also  Zeller et al. , 2014). All statistical analyses were performed in R. Analysis code is available online (see below). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Acknowledgements The authors would like to thank  Sina Klai  of the  University of Zu ¨rich, Switzerland ,  Johanna M Schmidt  and  Gereon Rieke  of the  University of Bonn, Germany , for helpful comments and discussions on this manuscript, in particular regarding the medical relevance of several of the discussed bacterial species. We thank  Katri Korpela ,  Lucas Silva ,  Thea van Rossum  and other members of the  Bork lab at EMBL, Germany , for helpful discussions. We thank  Anna M Glazek  and  Yan Ping Yuan  for bioinformatics support,  Stefanie Kandels-Lewis  of the EMBL for support on sample logistics and administration,  Rajna Hercog ,  Jan Provaznik  and  Vladimir Benes  and, in general, the  EMBL Genomics Core Facility  for sequencing support, and  Laura Lebrun of LCSB  for support with the biomolecular extraction platform.
Data and analysis code availability All generated raw sequence data has been uploaded to the European Nucleotide Archive under the project accessions PRJEB28422 (French CRC,  (Zeller et al. , 2014)  and German German healthy controls,  (Voigt et al. , 2015) ) and PRJNA289586 (Luxembourg T1D,  (Heintz-Buschart et al. , 2016) ). Sample metadata is available from Supplementary file 1. Processed data (taxonomic profiles, taxa annotations, etc. ) and full analysis code are available via a gitlab repository (https://git. embl. de/ tschmidt/oral-fecal-transmission-public; copy archived at https://github. com/elifesciences-publications/oral-fecal-transmission-public-).
Statistical analysis. Data were analyzed by means of descriptive statistics and Friedman ANOVA test. In addition, Dunn's test was used to perform pairwise comparison of the assigned scores between protocols. Intraand inter-observer reproducibility was assessed by means of Kappa statistic, taking Landis & Kock (1977) values as reference (0-0. 19, poor agreement; 0. 20-0. 39, fair agreement; 0. 40-0. 59, moderate agreement; 0. 60-0. 79, substantial agreement; 0. 80-1. 00, almost perfect agreement)  13. A commercially available software (Prism 5, GraphPad, San Diego, CA, USA) was used for data evaluation. The level of statistical significance was set at 0. 05. A statistically significant difference among protocols was revealed by the Friedman ANOVA test for all the anatomical parameters (p < 0.
X-ray measurements were acquired for the constituent monomers (Bis-GMA and TEGDMA) in isolation and containing photo-initiator to identify their contributions to the scattering signal of each blend through weighted least squares (WLS) fitting. The contribution of the X-ray beam to the measurements was assessed by conducting observations for over 30 min for the uncured and polymerized samples in the absence of light. To aid data analysis, measurements were taken for direct beam, empty sample containers, mica windows, water, and a silver behenate calibration standard to allow the scattering patterns to be corrected for background and normalization effects. Transmitted beam was recorded throughout using a beamstop mounted photodiode. In addition to in situ photopolymerization measurements and control/calibration measurements, scattering patterns were obtained for control molecules that possess structures similar to those under investigation [methacrylic acid (MA), methyl methacrylate, ethylene glycol, triethylene glycol (TEG), bisphenol A, and bisphenol A dimethacrylate (all Sigma-Aldrich, Dorset, UK)].
The data were normalized and background corrected using the DAWN software package (version 2. 8. 0, 2017, Diamond Light Source, Oxford, UK). 32, 33 Data were azimuthally integrated over 360°t o produce a 1D output and were subsequently fitted with pseudo-Voigt models to obtain the peak center and the full width at half maximum (fwhm). To confirm the observations from the I22 beam line, additional synchrotron X-ray scattering measurements were performed on the XMaS beam line (BM28) at the European Synchrotron Radiation Facility (ESRF, Grenoble, France). An incident X-ray energy of 15 keV was used corresponding to a wavelength (λ) of 0. 82 Å, with a beam size of 0. 08 × 0. 5 mm (horizontal × vertical). A similar experimental geometry was used to that described in Section 2. 3 and additional details for this experiment can be found in the Supporting Materials and Methods.
Additional spectral profiles were taken of the empty cell, mica windows, and the monomer to correct for background subtraction and intensity normalization. Data were baseline corrected using Omnic software (Omnic Specta software, version 8. 0, Thermo Fisher Scientific, Oxford, UK). Separate laboratory FT-NIR spectroscopy measurements, replicating the sample geometry and irradiance regimen described in Section 2. 3, were performed to confirm the observations of in situ observations (see Supporting Materials and Methods). 2. 4. Small-Angle Neutron Scattering. Small-angle neutron scattering (SANS) measurements were performed on the SANS2D  34  instrument at the ISIS pulsed neutron source (Rutherford Appleton Laboratories, Oxford, UK). Disc-shaped partially deuterated resin samples were sealed within aluminum foil and mounted on a cadmium sample rack.
SANS2D is a time of flight instrument which uses a wavelength range of 1-12 Å to provide a q range of 0. 004-2 Å -1. An 8 mm (diameter) beam size was used to collect SANS data in a transmission mode geometry using a 2D area detector (Ordela, 3 He-CF 4 , Oak Ridge National Laboratory, Tennessee, USA). 35 cquisition times per sample were approximately 1 h and additional measurements were also taken on samples with a hydrocarbon methacrylate functionality to serve as controls. Further measurements were taken for the direct beam, empty sample rack, sample transmission, aluminum foil, and a vanadium calibration standard to correct for background and transmission effects and to normalize the data to absolute scattering units, respectively. Data were reduced to 1D in absolute scattering units using the SANS2D plugin for the Mantidplot  36  software package (version 3.
8. 0, 2016, Oxford, UK). 2. 5. Thermal Changes during Photopolymerization. Thermal variations associated with photopolymerization were characterized and correlated with X-ray scattering data. Temperature measurements were performed at a frequency of 10 Hz using type K thermocouples with a 0. 2 mm tip and a Pico TC-08 data logger (Pico Technology, UK). Ring molds equivalent to those used for X-ray scattering measurements were filled with a 60/40 wt % Bis-GMA/TEGDMA monomer blend with either a CQ or TPO photo-initiator. The monomer blends were photopolymerized at an irradiance of ∼730 mW cm -2 using a Bluephase Style 20i LED curing light (Ivoclar Vivadent, Schaan, Liechtenstein) for 180 s. For each photo-initiator system, three measurements were conducted with the thermocouple tip placed centrally within the resin and an additional three with the tip at the sample surface.
The heating module and housed sample were orientated with the annulus of the aluminum plate normal to the path of the impinging Xrays. X-ray scattering measurements were taken at 5 °C increments, from 20 to 55 °C, to characterize structural changes as a function of temperature. X-ray scattering data were collected using a 2D area detector (Pilatus 100K) with a 487 × 195 pixel format (pixel size = 172 × 172 μm 2 ) fixed on to a two theta detector arm. The detector was placed 470 mm behind the sample and collected scattering data at angles of 2θ = 7, 13 and 22 to cover a q range of 0. 2-1. 8 Å -1 , where q = 4π sin θ/λ for each 5 °C temperature increment. Scattering data were collected with a 1 s count time and a 2. 7 ms readout time. Transmitted beam was also recorded at each angle and temperature increment using a photodiode to correct for changes to the sample density and thickness.
To aid data analysis, measurements were taken for direct beam, empty sample containers, and a silver behenate calibration standard. Scattering patterns were background corrected and normalized to the incident monitor intensity. Data were azimuthally integrated over 360°to produce a 1D output and were subsequently fit with a pseudo-Voigt model to determine peak positions of correlation lengths as a function of temperature. 2. 7. Statistical Analysis. A one tailed paired Students t-test was used to determine differences in the change in correlation length (α = 0. 05), where factors were photo-initiator chemistry, irradiance protocol, and relative differences in resin matrix viscosity. Statistical analysis was performed in the R programming (version 3. 1. 3, 2015, R Foundation).
CQ systems polymerized at irradiances of 25 mW cm -2 represent an extreme condition and it can be seen that conversion continues to rise at 300 s. Identical systems polymerized at higher irradiances typically achieve conversion values of 55-65 %. Data were obtained from I22 (Diamond Light Source). incide with similar behavior seen in the correlation length (Figure  7a, b ) and medium-range order (Figure  7c, d ) for the respective photo-initiator species despite differences in sample set up. Figure  8b  shows the change in correlation length and medium-range order as a function of temperature for a prepolymerized 60/40 wt % resin specimen. It can be seen that heating confers an almost linear extension of the correlation length at a rate of ∼0. 0016 Å °C-1 , while order decreases by approximately 1.
Data were obtained from BM28 (ESRF), see Supporting Materials and Methods. Figure  10. Normalized maximum increase in relative medium-range structural order for each resin blend (viscosity) vs polymerization rate (irradiance). Data have been normalized to the degree of reactive group conversion to determine structural order per converted CC bond. CQ-initiated resins are shown by the first four points (also inset), while the other data points refer to TPO-initiated resins. Systems polymerized at slower rates display the greatest increase in structural order for a given blend, while increasing viscosity decreases the medium-range order. Data were obtained from BM28 (ESRF), see Supporting Materials and Methods. viscosities,  38  which have been resolved here. In this study, the correlation length increases from an initial value of ∼4.
A more polymerized system will inevitably display greater structural order due to the restriction of the thermal motions and chemical bond distributions. Direct correlations between X-ray scattering data and the polymerization rate are therefore complicated by the relative differences in reactive group conversion for each polymerizing system. DC was quantified using both real-time ex situ laboratory-based FT-NIR spectroscopy and in situ measurements performed simultaneously to the acquisition of X-ray data with differences between the two measurements considered negligible. Normalizing the increase in correlation length with respect to DC resulted in a pattern of observations similar to those seen in Figure  9  (see Supporting Data, Figure  S7 ). However, Figure  10  shows that normalized structural order decreases with increasing reaction rate.
Data sources and searches We followed the PRISMA statement. The following databases were searched: Ovid MEDLINE In-Process and Other Non-Indexed Citations via Ovid SP and MEDLINE via Pubmed (1966 to present); LILACS via the Virtual Health Library search form (1982 to present); the Web of Science® via Thomson Reuters (1900 to present). Reference lists of query studies were inspected to identify any additional relevant published or unpublished data. Google Scholar was also queried to identify additional references. We sought out unpublished and on-going trials by searching the World Health Organization International Clinical Trials Registry Platform, ICTRP. There was no restriction on language of publication. We employed an iterative search strategy in order to adopt a systematic approach. This two-step process took shape as the process evolved (final search strategy detailed in Supplemental Text).
Data synthesis and analysis In order to provide a pooled estimate of the prevalence, we performed random-effects meta-analyses. Meta-analyses were carried out on the double arc cosine transformed proportions, using the inverse of the variance of the transformed proportion as the study weight. The pooled transformed proportions along with their confidence interval were back transformed to a proportion. A meta-regression was performed to determine a potential effect of the mean age and gender of patients on a prevalence increase of incidental findings. Statistics and plots were generated using R version 2. 15. 0 (libraries meta 4. 3-2 and metaphor 1. 9-8).
Description of the retrospective studies Of the 70 retrospective studies ( Table  S1  provides details, for each retrospective study, about indications of examinations, population, radiological apparatus, type of incidental findings (proportion of findings by ROI), how the CBCT was read and how the incidental findings were managed. The two most commonly used types of CBCT apparatus were the i-CAT (Imaging Sciences International, Hatfield, USA) and NewTom® (Verona, Italy) families, with 25 and 16 studies, respectively. Oral and Maxillo-Facial radiologists (OMFR) were reported to have examined the dataset in more than 45 studies. About a third of studies reported information about follow-up of patients, or the need to do it; in particular, some studies focused on incidental findings that required referral  [17, [22] [23] [24] [25] [26] [27] [28] [29] [30] [31].
Meta-analyses on prevalence data We identified 33 studies (47%) dealing with focal calcification discoveries. Proportions of Carotid Artery Calcifications (CAC) were identifiable in 23 studies and referred for an examination of the CBCT volume in the intra and/ or extracranial part of the carotid artery. Using a random effect meta-analysis, the overall proportion of CAC with 95% confidence interval (CI) was estimated at 0. 09 CI95% [0. 02;0. 21]. Proportions of extra-cranial CAC (ECAC) were identified in 18 studies, of which 10 were common with those of CAC. The overall proportion was estimated at 0. 05 CI95% [0. 02;0. 10]. The forest plot in Fig. 1a  and Fig. 1b  (upper parts) revealed a great heterogeneity among studies, as statistically confirmed by an I2 value greater than 97%, p<0. 01.
The objective of this paper is to review the current knowledge on the development of nanostructured zirconia-based ceramics and composites suitable for application in dentistry. Isi Web of Science, Science Direct, Scientific. net databases, and Google were searched electronically for the period of 1980 to the present, matching the keywords "nano" with the keywords: "Zirconia, ZrO 2 , Y-TZP, and dental, dentistry". A total of 74 papers were found, with the majority coming from Asia, indicating a more active scientific interest on the topic in this geographic area, followed by Europe, South America, and North America. The research shows, even though the scientific activity on nanostructured ceramics was intense in the last fifteen years, the development of fully dense zirconia-based nanoceramics is yet at an initial stage, most of all from the point of view of the clinical applications.