dataesr/scientific-paragraphs-categorization huggingface dataset:
2(b)). The second church (Fig. 2(c, d )) is built between 1150 and 1180 AD, the roman style Abbey was devastated during the War of the Peasants (1525) and by two fires, in 1542 and 1572  (Koehl and Grussenmeyer, 2008). The documentation records the prototype of the building, including the compositing structure by different shapes of structures. And the geometric model has been obtained in the former works using Autodesk Inventor  (Diethrich, 2017)  and SketchUp  (Koehl and Grussenmeyer, 2008) , respectively. Then data are analysed and organised for feeding into the BIM environment according to the following BIM modelling process.
Modelling from geometric primitives On the base of "Family" creation, the building modelling process is conducted by Autodesk Dynamo. Dynamo, an open source visual programming application, has become a built-in plugin to Revit based on Revit Application Programming Interface (API). It can interact with Revit to extend its parametric capabilities to the Revit project level and provides an environment to create customized packages using CPython and its self-defined scripting and sharing it with other users  (Asl et al. , 2015; Yang et al. , 2017). As for the HBIM related application, Dynamo can provide following advantages: (i) possible to manipulate the Revit elements by programming, which benefits for block processing and reduce manual processing; (ii) powerful option for creating graphical representations of complex geometries (iii) supportive of mesh geometry, which can directly import the mesh geometry into Revit and create the corresponding Revit Family; (iv) potential of connection with ontology knowledge, which currently connects the Revit geometry model and external database together.
In the project, based on the function nodes provided in Dynamo, the specific visual programming mainly includes three kinds of modules (Fig. 4 ): (i) "Host" elements generation based on coordinates (Green part in Fig. 4 ). Based on the parametric "Family", the instance, including floor, wall, roof, stair, column, etc. , can be created in the right position based on the coordinates. That is, the original point and reference levels are initially defined. And the floor is located at the original point. As for the similar structure, the list function can be utilized. (ii) "Host Based" elements generation based on the relative relationship with the "Host" elements (Blue part in Fig. 4 ). The door and window are created based on the relative position in the wall. (iii) Parameter modification (Orange part in Fig.
Connection with ontology BIM approach includes information directly related to the object or parts (both tangible and intangible such as material, dating, deterioration), yet it lacks a large amount of semantics about different context aspects (for example historical context, social information, environmental resources, other heritage artefacts information, etc. )  (Simeone et al. , 2015). In the field of built heritage, BIM model is integrated with ontology semantic relational system to enhance the representation of heritage knowledge and semantic reasoning. The integration can be an adhoc development based on BIM software  (Acierno et al. , 2017) , and a two-step modelling process by migrating IFC files to ontology environment for semantics richness  (Quattrini et al. , 2017; Pauwels et al.
Full kinematic field measurement Images in the visible domain were acquired at a frequency of 25 Hz with an IDS camera equipped with a 55 mm telecentric objective. The displacement field at the sample surface was determined using the DIC technique. This consists in correlating the grey levels between two different images of a given zone, each image corresponding to a different strain level. In order to improve image contrast, black paint was sprayed onto the surface before testing the samples. This leads to a random grey field. Uniform lighting of the sample surface was ensured by a LED lamp. The software used for the correlation process was SeptD  (Vacher et al. , 1999). For the image correlation process, the zone containing the crack is initially removed from the Region of Interest (ROI, defined in the undeformed state).
Furthermore, the SeptD software takes into account the finite deformation framework and aspects linked to the geometrical transformation of the Zones of Interest (ZOI). The charge-coupled device (CCD) of the camera has 1920×1200 joined pixels. The camera was fixed on a multidirectional adjustable support and the distance between the sample and the CCD matrix was about 100 cm. In this configuration, an area of 16. 8×11. 2 mm 2 in the sample plane was observed by the digital camera. The spatial resolution of the displacement maps, defined as the smallest distance between two independent measurement points, was set to 10 pixels (the ZOI size) corresponding to 0. 35 mm.
Acknowledgements The authors thank the  National Center for Scientific Research (MRCT-CNRS  and  MI-CNRS ),  Rennes Metropole  and  Region Bretagne  for financially supporting this work. Authors also thank  Dr Mathieu Miroir ,  Dr Eric Robin ,  Mr Vincent Burgaud  and  Mr Micka ël Lefur  for having designed the biaxial tensile machine, and  Dr Pierre-Olivier Bussiere  for the chemical analyses. The authors also thank the  Campus des M étiers et des Qualifications "Design ,  Mat ériaux & Innovation " for supporting this work.
Observations All observations were part of the SPHERE consortium guaranteed time programme (SPHERE High-Contrast Imaging Survey for Exoplanets and SPHERE Disk Survey). The Infra-Red Dualbeam Imager and Spectrograph (IRDIS,  Dohlen et al. 2008)  and Integral Field Spectrograph (IFS,  Claudi et al. 2008)  were used. The first RY Lup datasets were recorded on 16 April 2016 with the IRDIFS instrumental configuration, where observations are simultaneously carried out with the IRDIS subsystem dual-band imaging (DBI) mode using H2,H3 filters respectively centred at 1. 59 and 1. 67 µm  (Vigan et al. 2010) , and the Integral Field Spectrometer operating in YJ bands (0. 95 -1. 35 µm) with a spectral resolution of 42 in Y band to 40 in J Band. Following the discovery of the disk in intensity, we obtained Dual-band Polarimetric Imaging (DPI,  Langlois et al.
2010)  observations in field stabilized mode on 27 May 2016. IRDIS provides a 10-12 square field of view (1500-1800 square au, given the star's distance 151 pc, using 12. 25 mas/pixel platescale i. e. 1. 85 au per pixel). The IFS dataset consists of 21000 spectra each spread over 5. 1 x 41 pixels on the detector. After extraction, the FoV is 1. 7 square and the spaxel size is 7. 46 x 7. 46 mas, i. e. 1. 13 au per pixel. We used an apodized Lyot coronagraph  (Soummer 2005; Boccaletti et al. 2008; Carbillet et al. 2011; Guerri et al. 2011) , including a 185 mas focal mask, as well as a pupil mask (N-ALC-YJH-S). The IRDIFS observations were performed in pupil stabilized mode in order to perform Angular Differential Imaging (ADI) post-processing  (Marois et al. 2006). The field rotation for this set of data is 73 degrees.
Finally, the true north (TN) and pixel plate scales were measured using the astrometric calibrator NGC3603  (Khorrami et al. 2016 ) observed as part of the standard SPHERE calibration routines performed for the Guaranteed Time Observations (GTO) survey  (Maire et al. 2016). More details on the datasets are presented in Table  1. The observing conditions were very good for all observing sequences. The Strehl ratio estimation provided in Table  1  is based on an extrapolation of the phase variance deduced from the reconstruction of the SPHERE Adaptive Optics system open-loop data using deformable mirror and tip-tilt voltages, and wavefront sensor closed-loop data  (Fusco et al. 2004 ). The observing conditions and the different data reduction methods for each dataset are described in more detail in Sects.
Intensity images using IRDIS-DBI (H2,H3 bands) and IFS (YJ band) The IRDIS data were first corrected for cosmetics and sky background using the SPHERE Data Reduction and Handling (DRH) pipeline  (Pavlov et al. 2008 ) implemented at the SPHERE Data Centre. The outputs include cubes of left and right images recentred onto a common origin (the centre of the field rotation) using the satellite spots. This preprocessing also includes background subtraction, bad-pixel interpolation, flat-field correction, distortion correction, and wavelength calibration (for IFS). After these first steps, the best frames were selected according to their quality, leading to the use of 72 frames out of 80 for IRDIS and of all the available frames for IFS. The IRDIS frame selection criteria is based on the central coronagraphic spot flux being within a ±2 σ deviation from the median value of the full sequence.
IRDIS-DPI (BBH band) The IRDIS-DPI observations of RY Lup were carried out on 27 May 2016 with the BBH filter (1. 625 µm, width= 290 nm) using the same apodized pupil Lyot coronagraph (N-ALC-YJH-S) as for the IRDIFS observations. Sixty-four polarimetric cycles were taken, each consisting of one data cube for each of the four half wave plate (HWP) positions (0, 45, 22. 5, 67. 5 degrees). Dedicated coronagraphic images were taken at the beginning and at the end of the science sequence to determine accurately the star centre behind the coronagraph using the four crosswise faint replicas created by the deformable mirror. The IRDIS data were first corrected for cosmetics using the DRH pipeline implemented at the SPHERE Data Centre and following the same steps as the DBI data. The outputs include cubes of left and right images (parallel and perpendicular polarized beams, respectively) recentred onto a common origin.
(2011). Since the RY Lup disk is inclined, the A&A proofs: manuscript no. 31624corr  )). This method also enables the use of any set of frames with incomplete polarimetric cycles. The method is based on an optimization using the electric field (Jones Matrix) rather than the intensity (Mueller matrix) and relies on the inverse approach (i. e. fitting a model of the data to the observed dataset) which is significantly less biased and more efficient at minimizing instrumental artefacts. No assumptions about the angle of linear polarization of the source are made to correct for the instrumental polarization. The method is based on the use of an instrumental model describing the effect of the instrument on the incident electromagnetic field. The electric field is divided into non-polarized and polarized components, I k = v k 2 ρ + | v k , m | 2 + noise, where I k is the flux measured on the detector, ρ is the nonpolarized intensity (unknown), m is the electric field linearly polarized (unknown), and v describes the effect of the instru-ment/telescope for a given half wave plate polarizer position.
Results We obtained a very clear detection of the RY Lup disk in all datasets presented in this paper. The analysis of the morphology of the detected disk primarily focuses on the IRDIS and IFS intensity images and IRDIS-DPI (see Sects. 2. 2 and 2. 3). Furthermore, the cADI IFS and IRDIS images are used to search for point-sources focusing on non-polarized companions because the intensity images reach higher contrast (Sect. 3. 2). Our physical modelling of the polarimetric and total intensity images allows a qualitative analysis of the disk, and is presented in Sect. 4.
Disk properties The IRDIS and IFS datasets reveal clearly the inclined disk around RY Lup as seen in Fig. 1  in intensity and in Fig. 2  in polarimetry. Figure  1  for IFS is a median image over wavelength range from Y to J band. In our images, the disk appears as a dominating double-arch structure in the SE-NW direction extending to 0. 53 (80 au) in radius. Our observations support a high disk inclination with respect to the line of sight, with a position angle of 107 ±1 degrees. The position angle was estimated by considering the brightest parts of the disk. In addition to these bright components the images reveal the presence of two fainter spiral-like features on the SE direction as seen on the display of the Q ϕ image (Fig. 2 ). A spiral-like feature is also visible on the opposite side of the disk along its major axis.
D'Alessio et al. 1998). This results in detailed profiles of the density and temperature structure with vertical height and disk radius. Thus, it allows us to determine the 3D temperature structure of the disk at each step of the planet-disk interaction processes. More precisely, the initial 3D dataset, before adding the planet, is determined from a set of 1D vertical structure models for a given accretion rate (which will result in the desired total disk mass). Thus, the dynamical viscous evolution in the 3D radiation hydro simulation of the disk will not significantly alter the initial global gas distribution, but any development of structure in the 3D simulations is the result of the torques exerted by the planet. We make sure that the 1D and 3D models use the same parameters including the dust opacities and alpha viscosity.
Radiative transfer models The resulting 3D disk density and temperature structure presented in Sect. 4. 1 is subsequently fed into the Monte Carlo (MC) radiative transfer code RADMC-3D developed by  Dullemond et al. (2012)   1. To convert the gas density to the dust density used in the radiative transfer calculations, we adopt a gas-todust ratio of 50, which is lower than the canonical ISM value as suggested by the ALMA Lupus survey of  Ansdell et al. (2016). For the dust opacity calculation we consider a species mixture of silicate (60%), carbonaceous (10%), and icy (30%) material, where the optical constants are taken from Draine (2003);  Zubko et al. (1996) ;  Warren & Brandt (2008). We assume two differ-  ent grain size populations, small (0. 01-1 µm) and large (1 µm-1 mm) grains, where each size distribution is a smooth power law with exponent -3.
Spectral energy distribution The SED model based on our hydrodynamical simulation compared to the observed photometry is shown in Fig. 12. The stellar spectrum is taken from the Castelli-Kurucz atlas  (Castelli & Kurucz 2004 ), choosing the model for a stellar type of G8V (T eff = 5500 K), and a surface gravity of log g = 4. 5. The flux measurements from the VLT Interferometer (VLTI)/PIONIER, SPHERE/IRDIS/IFS, 2MASS, IRAS, WISE, and AKARI hint at a strong NIR and mid-IR (MIR) excess expected for a disk around a young star. Although our model lies within the measurement uncertainties of the SPHERE data points, there is a clear trend that it underestimates the fluxes between ∼5 and ∼50 µm. The explanation is that our model only considers the dust disk from our hydrodynamical simulations with a radial grid starting at R in = 18 au.
Acknowledgements. We acknowledge our anonymous reviewers for the very careful reading and constructive suggestions that contributed to improving this paper. SPHERE is an instrument designed and built by a consortium consisting of  IPAG (Grenoble, France ),  MPIA (Heidelberg, Germany) ,  LAM (Marseille, France), LESIA (Paris, France), Laboratoire Lagrange (Nice, France) ,  INAF -Osservatorio di Padova (Italy) ,  Observatoire astronomique de l'universite de Geneve (Switzerland) ,  ETH Zurich (Switzerland) ,  NOVA (Netherlands), ON-ERA (France) , and  ASTRON (Netherlands)  in collaboration with  ESO. SPHERE was funded by  ESO , with additional contributions from  CNRS (France) ,  MPIA (Germany) ,  INAF (Italy) ,  FINES (Switzerland) , and  NOVA (Netherlands). SPHERE also received funding from the  European Commission Sixth and Seventh Framework Programmes as part of the Optical Infrared Coordination Network for Astronomy (OPTICON)  under grant number  RII3-Ct-2004-001566  for FP6 (2004)(2005)(2006)(2007)(2008), grant number  226604  for FP7 (2009)(2010)(2011)(2012), and grant number  312430  for FP7 (2013)(2014)(2015)(2016).
This work was supported by the  Programme National de Planétologie (PNP)  and the  Programme National de Physique Stellaire (PNPS)  of  CNRS-INSU  co-funded by  CNES. This work has also been supported by a grant from the  French Labex   OSUG2020  (Investissements d'avenir - ANR10 LABX56 ) and by the  ANR  grant  ANR-14-CE33-0018  (GIPSE). This work has made use of the SPHERE Data Centre, jointly operated by  OSUG/IPAG (Grenoble), PYTHEAS /LAM/CeSAM (Marseille) ,  OCA/Lagrange (Nice) , and  Observatoire de Paris/LESIA (Paris). This research has made use of the VizieR catalogue access tool,  CDS, Strasbourg, France. Q. Kral also acknowledges support from  STFC  (consolidated grant) via the institute of Asronomy, Cambridge.
Consequently, these species are of particular interest in advancing the field of comparative epigenetics in teleost fish. Indeed, while fish genomes and their gene expression have been and continue to be well-studied (Figure  3A-B ), the study of regulatory molecular epigenetic mechanisms (Figure  3C ), specifically histone modifications (Figure  3D ), DNA methylation (Figure  3E ), and miRNAs (Figure  3F ), are only beginning to be investigated in teleost fish. In the first section of this review, we use available, NCBI-deposited genome sequence datasets (https://www. ncbi. nlm. nih. gov/genome) to comparatively describe the presence and function of genes representative of three major molecular epigenetic pathways of histone modifications, DNA methylation, and miRNAs in zebrafish (ID 50), rainbow trout  (ID 196) , Atlantic salmon (ID 369) and the rat, Rattus norvegicus  (ID 73).
ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T 20 mutational analysis, and mapped these identified AA onto specific predicted protein sequences from the sequenced teleost genomes in an effort to predict possible functional differences between salmoniform paralogues. Secondly, we utilized a recently developed comparative fish-specific gene expression atlas termed Phylofish  (Pasquier et al. , 2016)  to identify possible differential expression of paralogues between tissues. This approach revealed specific differences in AA critically involved in miRNA binding between salmoniform XPO5 paralogues (Figure  17A ), which are furthermore differentially expressed in different rainbow trout tissues (Figure  17B ). While a possible subfunctionalization in this pathway needs experimental validation, this example serves to illustrate the point that functional differences in the miRNA biogenesis pathway may exist between specific teleost species and mammals.
, 2011). These gene expression changes may have been driven through histone modifications, which were equally identified as being enriched in the transcriptomic dataset  (Pierron et al. , 2011). A study conducted in European eels, Anguilla anguilla, which investigated environmental contaminants such as cadmium, mercury, polychlorinated bisphenyls (PCBs) and organochloride pesticides in a laboratory setting and compared transcriptomic responses to a wild population may serve as cautionary example, as laboratory housing, rather than contaminants, identified an enrichment of histone modification in the transcriptome  (Baillon et al. , 2016). This study therefore underlines that care must be applied when.
(Okada et al. , 2009; Wang et al. , 2011)  are identified as being divergent between salmoniform paralogues (red colour), conserved within fish but different from mammals (green colour) or conserved between fish and mammals (yellow colour) (A). In silico determination of differential tissue expression levels of xpo5 paralogues in rainbow trout based on next generation sequencing data from the Phylofish database  (Pasquier et al. , 2016 ) (B). Ts3R ) is indicated by the first red line, while salmoniform species underwent an additional, subsequent lineage-specific genome duplication event (Ss4R). Similarity of paralogues was established based on available synteny and predicted protein sequence information. C C E P T E D M A N U S C R I P T A C C E P T E D M A N U S C.
may utilize this technique to achieve better specificity. With regard to temporal aspects of epigenetic regulation in teleost fish, current studies generally link epigenetic marks and gene expression profiles at a single time point, which may reduce correlations between specific epigenetic marks and gene expression by ignoring the temporal relationships of epigenetic marks and gene expression. Therefore, similar to a previous suggestion to resolve observed discrepancies between mRNA and protein abundance in teleost fish tissues sampled at single timepoints (Popesku et al. , 2010) , detailed time-series experiments are therefore warranted for epigenetic marks. Since cost likely represents a limiting factor, the identification of consistently altered mRNA abundance of specific targets in response to experimental conditions may be identified from deposited transcriptomic time-series datasets, allowing pre-screening of specific genes for subsequent determination of epigenetic marks.
As of May 2017, the AGP included microbial sequence data from 15,096 samples from 11,336 human participants, totaling over 467 million  (48, 599  unique) 16S rRNA V4 gene fragments (abbreviated 16S). Our project informs citizen-scientist participants about their own microbiomes by providing a standard report (Fig. 1A ) and deposits all deidentified data into the public domain on an ongoing basis without access restric-tions (see Table  S1  in the supplemental material). This reference database characterizes the diversity of the industrialized human gut microbiome on an unprecedented scale; reveals novel relationships with health, lifestyle, and dietary factors; and establishes the AGP resource and infrastructure as a living platform for discovery.
cs. mcgill. ca/colonyb/). The forum, called Gut Instinct (http://gutinstinct. ucsd. edu), enables participants to share lifestylebased insights with one another. Participants also have the option to share their AGP sample barcodes, which will help us uncover novel contextual knowledge. Gut Instinct now has over 1,050 participants who have collectively created over 250 questions. Participants will soon design and run their own investigations using controlled experiments to further understand their own lifestyle and the AGP data. A living data set. The AGP is dynamic, with samples arriving from around the world daily. This allows a living analysis, similar to continuous molecular identification and annotation revision in the Global Natural Products Molecular Networking (GNPS) database  (34).
DISCUSSION The AGP provides an example of a successful crowdfunded citizen science project that facilitates human microbiome hypothesis generation and testing on an unprecedented scale, provides a free data resource derived from over 10,000 human-associated microbial samples, and both recaptures known microbiome results and yields new ones. Ongoing living data efforts, such as the AGP, will allow researchers to document and potentially mitigate the effects of a slow but steady global homogenization driven by increased travel, life spans, and access to similar diets and therapies, including antibiotics. Because the AGP is a subproject of the EMP (1), all samples were processed using the publicly available and widely used EMP protocols to facilitate meta-analyses, as highlighted above. Further examples of applications include assessing the stability of AGP runs over time and comparing the AGP population to fecal samples collected from a fecal transplant study  (48)  and an infant microbiome time series  (49) , the latter using different DNA sequencing technology, to highlight how this context can provide insight  (50).