dataesr/scientific-paragraphs-categorization huggingface dataset:
Introduction to physics engines In rigid body dynamics simulations run with ODE, the state of a system consisting of N rigid bodies is described by the positions r i of their centres of mass, a quaternion representation of their orientations q i , and their linear and angular velocities v i and v i respectively. These velocities are collected in the column vector V~v 1 ,v 1 ,. v N ,v N f g T. We use the superscript T to denote the transpose of a vector or a matrix everywhere in this article. The vector L L~M MV V then collects all linear and angular momenta, where M M~m 1 1,I 1. m N 1,I N f g is a 6N|6N block diagonal matrix whose elements are the mass matrices m i 1 and inertia matrices I i of the N bodies (with 1 the 3|3 identity matrix). The Newtonian dynamics equation then reads _ L L~F F where the generalized force F F is a vector collecting forces and torques applied to the system.
As a result, no energy is stored in this effective spring, at odds with a regular spring which stores an averaged energy k B T (see below subsection ''Preliminary tests of validity and performance of the global thermostat'' along with the histograms of energy in Figure  1 ). In particular, ODE uses a powerful software called libccd  [20]  to detect collisions between two convex shapes. Whenever overlapping is detected between two rigid bodies, ODE attaches a temporary joint between them called a ''contact joint''. Defining vector c 1 (resp. c 2 ) that connects the center of mass of body 1 (resp. 2) to the contact point and denoting n the common normal to both bodies at the contact point (directed from 2 to 1), the kinematic constraint imposed by the contact joint would read n T v 1 zv 1 6c 1 ð Þ {n T v 2 zv 2 6c 2 ð Þ ~0 in the perfect case when the holonomic constraint imposed by the contact joint reads exactly d~0.
Global schemes of Langevin dynamics are designed to minimize the perturbation introduced by the thermostat on the Hamiltonian trajectory (so called ''disturbance'' as defined originally in  [36] ), hence on the dynamical properties, such as autocorrelation functions, and related quantities, such as diffusion coefficients. In these globally applied thermostats the stochastic term of the correction force acting on each particle is proportional to the momentum of that particle. Two main global algorithms have been designed so far: (a) Stochastic Velocity Rescaling methods, most notably the ''global thermostat'' introduced by Bussi and Parrinello  [19] , (b) the Nose-Hoover Langevin thermostat  [37]. Here we first show how to implement Langevin-Euler equation in the ODE software. Moreover we show that the global thermostat introduced by Bussi and Parrinello is so remarkably adapted to this implementation that it improves quite significantly the sampling efficiency with respect to local Langevin dynamics (by two orders of magnitude in typical situations), while preserving the time-dependent properties such as autocorrelation functions.
For simplicity, we choose to fix all the S ? ii to a common frequency S ?. Note that (S ? ) {1 is the relaxation time of the thermostat, i. e. the autocorrelation time of the kinetic energy (see supplementary Figure  S1 ). We then improve the sampling efficiency of this Langevin dynamics by extending the ''global thermostat'' algorithm designed by Bussi and Parinello in 2008  [10]  to physics engines. This algorithm allows faster yet correct sampling of the phase space in the canonical ensemble. However, it is designed for the translational degrees of freedom only. In order to apply it to an articulated rigid body system, we therefore have to extend it to the rotational degrees of freedom and adapt it to the ODE software. To this aim, we replace the traditional Langevin-Euler correction G G~S ? SET E 1{ 1 2bSET {1 ! Lz ffiffiffiffiffiffi ffi S ? bE s _ L L ð32Þ Eq.
Introduction 1 While much research concentrates on the challenges inherent in the creation and annotation of treebanks, there are also a number of less well-documented challenges presented when the annotated data is used in subsequent linguistic research. Search engines for unannotated corpora, or corpora annotated only at the word level (e. g. PhiloLogic 4 2 ) usually present query results in the form of a Key Word In Context (KWIC) concordance: a convenient synoptic overview which can be easily exported to a spreadsheet or sorted in a variety of ways. By way of contrast, most treebank corpus search engines return tree fragments or tree representations as their default representation of query results (e. g. CorpusSearch 3 , TigerSearch 4 , TrED 2. 0 5 ). While these preserve the syntactic annotation, enabling the user to verify that their query has returned the desired results, it can be very difficult to obtain a synoptic view of the data, and it is virtually impossible to export the results to common software environments (word-processors, spreadsheets) in a format appropriate for subsequent analysis.
The two main Old French treebanks (the MCVF corpus and the SRCMF corpus) do not contain morphological tagging beyond part-of-speech, so it is impossible to search tags for 'nominative case' or even to restrict the search to masculine nouns only. Consequently, the results returned by the search engine will include some noise, and must be checked manually. (NP-TMP (D cele) (NCPL nuit)) ( V J o t ) (CODE <milestone%%%unit="folio"%%%n="[82a]"$$>) (CODE <lb%%%n="792"$$>) (NP-ACC (ADJP (Q molt) (ADJ boen)) (NCS ostel)) (PONFP ,)) (ID YVAIN,25. 793)) In terms of providing a rapid initial answer to the research question "do most inflecting proper nouns show case inflection?", this output is of limited use, as there is no simple way of browsing the lexical form of the proper nouns returned. Moreover, the output of a local installation of CorpusSearch is similar, and while it would be in principle be possible to post-process the output file to produce results in a more readable form, the software required to do this has to the best of our knowledge not been implemented in either the MCVF or other major Penn-format corpora.
Overview The TXM platform is a powerful tool for working with large, richly annotated corpora, and is designed to form a modular and open-source framework for corpus analysis. The platform is built around four core modules:  the CQP search engine 16 , designed for high-performance lexical pattern searches on large corpora (up to a billion words) tagged at the word level;  R statistics software 17 , enabling statistical analysis of corpus queries to be carried out within the TXM platform;  a web-based or desktop GUI providing access to the CQP and R modules;  a rich Java/Groovy and XSLT based import subsystem which enables users to manage and to import their own corpora from a variety of file formats (for example, plain text Unicode, XML, XML-TEI, XML-TMX, XML-Transcriber, etc. ) while allowing application of NLP tools on the fly (like TreeTagger for example).
Adaptation of TXM for treebank corpora A similar online interface for TigerSearch queries is offered by the INESS platform (Rosén et al. 2012)   20  , although the underlying engine is a re-implementation rather than an integration of the original software. The primary objective of the INESS platform is to provide an online infrastructure for the hosting of treebanks in a variety of formats (dependency, constituency, LFG, HPSG, etc. ). However, while it offers advanced functionality for treebank queries, the platform is similar to other treebank search engines in that results are always expressed in the form of trees (with highlighted nodes) or full sentences. To the best of our knowledge, no concordance-style output has been implemented. Moreover, since the software itself is not released under an open-source licence, such functionality cannot be added by third-party developers.
29"> <variable name="#npr"idref="[. ]#w_YvainKu_5490" /> <variable name="#sj" idref="[. ]#Tom%20%-%20%1/YvainKu_03_1319815832. 29" /> </match> </matches> As with the TigerSearch default stylesheets, concordances are generated by the TXM platform by applying an XSL to this exported Tiger-XML file. However, three key innovations in the design of the export module permit a much more sophisticated treatment of the data than that offered by the default stylesheets. Firstly, the concordance XSL is sensitive to the query variable name #pivot. By identifying a single node within the query, terminal or non-terminal, as #pivot, the user is able to specify the node within on which the concordance will be centred. The XSL uses the name attribute of the <variable/> element in the exported Tiger-XML to identify this node.
Evaluation and Future Developments In the course of the development of an Old French treebank, we found that researchers wishing to use the corpus were not able to export and analyse results in such a way as to be able to answer core research questions in Old French syntax. The KNIC concordance presented in this paper is a response to this problem, providing the user with a convenient synoptic view of query results which is easy to export and analyse further in spreadsheet software. A number of recent research projects and papers based on the SRCMF corpus have relied on data presented in the form of a KNIC concordance. In addition to providing an architecture in which post-processing of TigerSearch's exported results files can easily be implemented to create these concordances, the TXM platform's corpus administration features and web interface allow Tiger treebanks to be uploaded and used online without distributing the corpus source files (if necessary).
However, currently the integration of TigerSearch and TXM remains relatively low-level. A number of key improvements are envisaged in the future:  The TigerSearch interface within TXM will be developed to include more features of the TigerSearch GUI, particularly coloured query syntax and lists of available values for each node feature.  KNIC concordances are currently available only for export, but should be integrated into the TXM's KWIC concordance GUI. This requires a higher-level integration of the Tiger module within TXM.  Higher-level integration of TigerSearch will also allow TXM's R-based statistical tools to be used on treebank query results, as it is already available for the CQP query results. This work was initially carried out as part of the 'Syntactic Reference Corpus of Medieval French (SRCMF) ' project (2009-2012), jointly funded by the ANR (France) and the DFG (Germany) with principal investigators Sophie Prévost (Lattice, CNRS & ENS) and Achim Stein (Stuttgart).
g. D 0 → Kπ and D + → Kππ) at values of transverse momentum above 1 GeV/c. At lower transverse momenta, however, the statistical significance of the measurement is insufficient for currently achievable datasets. The challenge is even greater for charm baryons. The most abundantly produced charm baryon (Λ c ) has a proper decay length (cτ ) of only 60 µm. This is lower than the impact parameter resolution of the present ITS in the transverse momentum range of the majority of Λ c daughter particles. Therefore, charm baryons are presently not measurable by ALICE in central Pb-Pb collisions. For the same reasons as outlined above, the study of beauty mesons, beauty baryons, and of hadrons with more than one heavy quark are also beyond the capability of the current detector. A crucial limitation of the present ITS detector is given by its limited read-out rate capabilities.
The ITS can run at a maximum rate of 1 kHz (with dead time close to 100 %), irrespective of the detector occupancy. For all physics channels that cannot be selected by a trigger, this rate limitation restricts ALICE to use only a small fraction of the full Pb-Pb collision rate of 8 kHz that the LHC presently can deliver and prevents the collection of required reference data in pp collisions. Clearly the present ITS is inadequate to fulfil the required rate capabilities envisaged for the ALICE long-term plans discussed in the previous section. Finally, the impossibility to access the present ITS detector for maintenance and repair interventions during the yearly LHC shutdowns represents a major limitation in sustaining high data quality. Rapid accessibility to the detector is a key priority in the design of the upgraded ITS.
Moreover, the possibility to use the information of the cluster size to identify light hyper-nuclei is being studied (see Chap. 8). • Read-out time: as mentioned in Sec. 1. 2, the present ITS features a maximum read-out rate of 1 kHz. The new detector is designed to be able to read the data related to each individual interaction up to a rate of 100 kHz for Pb-Pb collisions and 400 kHz for pp collisions, a factor two higher than the ALICE upgrade requirements. The read-out architectures that allows such rates to be achieved are presented in Chap. 6. On the basis of the above considerations, the baseline solution for the layout of the ITS upgrade is to replace the existing ITS detector in its entirety with seven concentric layers of pixel detectors. Monolithic Active Pixel Sensors (MAPS) implemented using the 0.
3 MeV/c; a magnetic field of 0. 2 T, which is planned for a run dedicated to the measurement of low-mass di-electrons, corresponds to the worst case scenario in terms of detector occupancy c including a safety factor of ten The expected radiation doses and hadron fluences for the upgraded ITS detector are computed for the following integrated luminosities, which correspond to the target statistics needed for the proposed physics studies: • 8 × 10 10 Pb-Pb inelastic collisions; • 1 × 10 11 p-Pb inelastic collisions; • 4 × 10 11 pp inelastic collisions. A conservative safety factor of ten is further applied to take into account uncertainties on the beam background, possible beam losses, inefficiency in data taking and data quality requirements. The expected radiation levels are summarised in Tab.
Single chip test Prior to mounting on the module, each chip will be tested according to a defined testprocedure. The results of each test will be recorded and stored in a commonly accessible database. The chips will be classified according to the test results and only good chips which are fully functional and meet the geometrical requirements will be used for module mounting. A detailed scheme for the classification of the chips will be defined once full size prototype chips are available and a sufficient number of chips have been tested to produce a large enough statistical sample. Every tested chip has to be traceable, either electrically or via a visual mark, throughout the different testing and assembly steps. Several techniques are under consideration, but no final choice for the chip identification has yet been taken.
The list of constantly noisy pixels can be retrieved from the data base with the corresponding noise charge. The random pixel noise is calculated based on the average pixel noise input distribution given by the Average pixel noise and the Average pixel noise sigma input parameters. First, the probability is calculated to achieve a noise larger than digitisation threshold. The digitisation threshold (∼ 100 electrons) is calculated as the product of the Threshold over noise cut input parameter and the Average pixel noise. In the second step-based on the calculated probability, the noise charge is calculated randomly above the digitisation threshold. In the third and last step of the pixel response simulation, the charge contributions from charged particle(s) and noise are summed up for each pixel and compared to the digitisation threshold (unless the pixel is marked as a dead pixel in the database and removed from the list of active pixels).
Vertex finding and track-to-vertex association The reconstruction of the interaction vertex position is one of the key tasks that the ITS has to fulfil. This is currently done with the present ITS at three different levels with different purposes: at run time, the vertex position is reconstructed for a fraction of the collected events, without performing a full reconstruction, using only the information of the two innermost layers of the ITS. This first measurement, averaging over the collected events, is recorded on the offline conditions database and is used to monitor the luminous region during the data taking and, subsequently, as an optional constraint for the vertex position in the transverse plane. The same fast vertex reconstruction is carried out offline eventby-event to have a seed of the tracking procedure in the TPC.
This is the region with the largest warming signal and also the largest uncertainties between the simulations. Therefore, improvements in the reconstruction of global ice cover and Arctic vegetation, along with improved data to evaluate the simulation of sea ice and high Arctic atmospheric and ocean temperatures, could significantly improve the simulations and allow much better constraints on total Pliocene warming. From the PlioMIP Experiment 2 simulations it appears that higher CO 2 concentrations warmed the planet and drove large surface albedo feedbacks in the high latitudes through changes in sea ice, vegetation and ice sheets. The latter two of these factors are important components of long term Earth system sensitivity, suggesting that long term response to CO 2 increases is greater than climate sensitivity  (Lunt et al.
Discussion Paper | Discussion Paper | Discussion Paper | Information Systems Laboratory (CISL), sponsored by the NSF and other agencies. W. -L. C. and A. A. -O. would like to thank the Japan Society for the Promotion of Science for financial support and R. Ohgaito for advice on setting up the MIROC4m experiments on the Earth Simulator, JAMSTEC. The source code of MRI model is provided by S. Yukimoto, O. Arakawa, and A. Kitoh in Meteorological Research Institute, Japan. Z. Z. acknowledges that the development of NorESM-L was supported by the Earth System Modelling (ESM) project funded by Statoil, Norway. Aisling Dolan is acknowledged for a beautiful title for this paper. Discussion Paper | Discussion Paper | Discussion Paper | Dowsett, H. J. , Cronin, T. M. , Poore, R. Z. , Thompson, R. S. , Whatley, R.
Acknowledgements. D. J. H. acknowledges the  Leverhulme Trust  for the award of an  Early Career Fellowship  and the  National Centre for Atmospheric Research  and the  British Geological Survey  for financial support. A. M. H. and S. J. H. acknowledge that the research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013) / ERC  grant agreement no. 278636. A. M. H. acknowledges funding received from the  Natural Environment Research Council  ( NERC  Grant  NE/I016287/1 , and  NE/G009112/1  along with D. J. L). D. J. L and F. J. B. acknowledge  NERC  grant  NE/H006273/1. D. J. L. acknowledges  Research Councils UK  for the award of an  RCUK  fellowship and the  Leverhulme Trust  for the award of a  Phillip Leverhulme Prize.
e. with a standard deviation larger than 0. 04). Lastly, the simulated global NEE fluxes are output at the daily timescale and spatially averaged from the ERA-Interim grid (0. 72 • × 0. 72 • ) to a 2. 5 • × 3. 75 • resolution (latitude, longitude). The LMDZ (Laboratoire de Météorologie Dynamique zoom) atmospheric transport model  (Hourdin et al. , 2006 ) is used at this resolution to convert these terrestrial fluxes into monthly atmospheric CO 2 concentrations, during the period 1989-2009. In order to complete the carbon balance at the planetary scale, we also transport the global oceanic and fossil net carbon fluxes respectively taken from a climatology  (Takahashi et al. , 2009)  and from the EDGAR database (Emissions Database for Global Atmospheric Research; http://edgar. jrc. ec. europa.
1c, 3a). Finally, using the multisite-optimized model overall brings a small improvement of the modelled interannual variability of C CO 2 , with a median reduction of 3. 9 % for the RMSD between modelled and measured monthly anomaly (not shown). Forty-five locations, out of the 53 used in this study, display an improvement with RMSD decreases of up to 27 %, while at the remaining 8 locations the degradation of the simulated interannual variability remains small with RMSD increases always smaller than 1. 5 % (not shown). These results suggest that despite the relative shortness (1-3 years) of most of the FluxNet data sets selected to optimize the ORCHIDEE model, the diversity of the covered weather situations gives a modest, yet consistent source of information to better reproduce interannual variations of carbon fluxes at the global scale.
Context. Constraining the gas and dust disk structure of transition disks, particularly in the inner dust cavity, is a crucial step toward understanding the link between them and planet formation. HD 135344B is an accreting (pre-) transition disk that displays the CO 4. 7 µm emission extending tens of AU inside its 30 AU dust cavity. Aims. We constrain HD 135344B's disk structure from multi-instrument gas and dust observations. Methods. We used the dust radiative transfer code MCFOST and the thermochemical code ProDiMo to derive the disk structure from the simultaneous modeling of the spectral energy distribution (SED), VLT/CRIRES CO P(10) 4. 75 µm, Herschel/PACS [O i] 63 µm, Spitzer-IRS, and JCMT 12 CO J=3-2 spectra, VLTI/PIONIER H-band visibilities, and constraints from (sub-)mm continuum interferometry and near-IR imaging.
(2011 ), Brown et al. (2009 ), and Lyo et al. (2011)  based on (sub-)mm interferometry continuum observations suggest a PA=64 • , 55 • , and 64 • respectively. As we aim to compare our model with the CO 4. 7 µm lines we employed a PA of 56 •. 2 FUSE and HST-COS spectra were obtained from DIANA protoplanetary disk observations and modeling database (http://www. dianaproject. com/). Details on the data reduction procedures will be given in  Dionatos et al. (in prep. ). 3 Recent near-IR imaging  (Muto et al. 2012; Garufi et al. 2013 ) and sub-mm interferometry  (Brown et al. 2009; Andrews et al. 2011; Pérez et al. 2014)  have revealed that the disk of HD 135344B has spiral arms and asymmetries in the dust emission. One possible reason for the discrepancy between the inclination derived from mid-IR imaging data (i.
Then the Monte-Carlo dust radiative transfer code MCFOST  (Pinte et al. 2006 (Pinte et al. , 2009) )  is used to calculate the dust's thermal and density structure, T dust (r, z), n dust (r, z), and the mean radiation field J ν (r, z). MCFOST is employed to compute a synthetic SED, and continuum images in the H band and at 870 µm for comparison with VLTI/PIONIER and SMA continuum observations. The MCFOST disk structure and radiation field is then used as input for the thermo-chemical radiative transfer code ProDiMo  (Woitke et al. 2009). ProDiMo calculates the disk chemistry, the gas and dust heating and cooling, and the energy level populations of molecules and atoms. ProDiMo computes the synthetic line fluxes and channel maps for gas emission lines from the optical to the mm using escape probability.
ProDiMo generates channel maps data cubes; i. e. , for each velocity bin, a 2D image of CO emission is generated (see  details in Bertelsen et al. in prep. ). The pixel size of the CRIRES detector in the spatial direction is 0. 086", at a distance of 140 pc that corresponds to a pixel size of ∼12 AU. We generated the ProDiMo data cubes with a pixel size of 2 AU. The ProDiMo data cubes were first convolved in the spatial direction with a Gaussian PSF of FWHM=180 mas. Then they were convolved with a Gaussian of FWHM=3. 3 km/s in the wavelength direction to simulate R=90 000 of the observations. A mask of 0. 2" (28 AU) with the correct PA was applied in each channel to mimic the slit. The fluxes were added in the direction perpendicular to the slit to generate a 2D spectrum. In the 2D spectrum the centroid of the photo center at line velocity (υ) was calculated using  (Pontoppidan et al.