dataesr/scientific-paragraphs-categorization huggingface dataset:
GALILÉE-1 is the new validation and processing system for evaluated data, developed at CEA. This system can handle evaluations stored either in the ENDF-6 format or in the new General Nuclear Data (GND) format. It consists of various components respectively dedicated to read/write the evaluated data whatever the format is, to diagnose inconsistencies in the evaluated data and to provide continuous-energy and multigroup data as well as probability tables for transport and depletion codes. All these components are written in C++ language and share the same objects. This paper describes the state of progress of the various parts of the system and gives some illustrations.
Introduction GALILÉE-1 system is part of a CEA global development program dedicated to fine modelling of nuclear systems. It is carried out in synergy with the evaluation code CONRAD  [1] , and with the new generation of reactor physics codes, APOLLO3  [2] , TRIPOLI-4  [3]  and MENDEL  [4]. It can handle evaluations stored either in the ENDF-6 or in the new General Nuclear Data (GND) format.
GALILÉE-1 system consists of: • processing modules providing continuous-energy data (CE), multigroup data (MG) as well as probability tables (PT), • interface modules creating application libraries (from these processed data) for deterministic or Monte Carlo transport codes, shielding codes or depletion codes, • an automatic chain for creating these libraries. GALILÉE-1 system originality lays in its two complementary running ways: an integrated one (Fig. 1 ) with a convivial and automatic chain for creating consistent and validated libraries for the various application codes and an open way for providing application codes with processing tools (Doppler on the fly for instance in a Monte Carlo transport code). At the present, only the processing modules are under development. Cross-comparisons with other processing systems are systematically carried out at each step in order to fully master possible discrepancies.
GALILÉE-1 processing modules Three main processing modules are under development in GALILÉE-1 system, a parser dedicated to read and write evaluated and processed data in ENDF-6 or GND format, a verification/validation tool described further and a processing code TREND (Treatment and Representation of Evaluated Nuclear Data). They are written in C++ language and share common objects grouped in GBASE component. GBASE objects are completely independent from the input data (evaluation) format and the output data (processed data) format. As shown in Figure  2 , GBASE objects are initialized thanks to the Parser that reads the evaluation data. These objects are checked and eventually corrected by the Verification/Validation Tool and then processed data are created by TREND code. The objects storing processed data are also kept in GBASE and can be written on binary or character files by the Parser.
GBASE objects The GBASE object hierarchy is very close to the GND object hierarchy. For each nucleus or element, we create a data base allowing us to store, in the same object, structure data and interaction data for a given projectile. GBASE structure data contain all the information needed to verify and eventually correct the evaluated data: masses, level scheme, spins, energy, half-life, decay modes, etc. GBASE interaction data contain the list of products that can be created by the interaction, all the information given by an evaluation (JEFF-3. 2, ENDF/B-VII. 1, JENDL4. 0,…) but organized in such a way that processing is easier and processed data (CE data, PT, MG data, …).
Verification / Validation One of the goals of GALILÉE-1 system is to test the consistency and the validity of nuclear data evaluations. We plan to perform a complete assessment of evaluated files before any treatment. Some checks can be performed by comparing data with the ones contained in structure databases, e. g. NUBASE or ENSDF. This is the case for: • the masses of the nuclides, given in terms of neutron mass, • the energies of the excited states reached in the inelastic scattering, • gamma decay schemes of the excited states. Some additional tests are designed to check the coherence between the data given in an evaluation: • coherence between thresholds considered for various data of the same reaction, • energy balance for reaction products, • spin/parity of resonance parameters, • normalization of distributions.
TREND TREND code aims at replacing NJOY99 and CALENDF codes in CEA application library production. It consists of three main parts, TREND_CE corresponding to NJOY RECONR, BROADR, UNRESR, THERMR and HEATR modules, TREND_PT corresponding to CALENDF treatment and TREND_ MG corresponding to NJOY GROUPR module. At the present RECONR and TREND_PT functionalities are developed, BROADR /THERMR functionalities are under progress. In order to validate TREND reconstruction at 0 Kelvin in the resolved resonance range, crosscomparisons with NJOY99 were carried out for all JEFF-3. 2 nuclei (~ 470). In case of discrepancies, additional comparisons were made with NJOY2012 and PREPRO2015. About 25 nuclei show relative reconstruction discrepancies larger than 1. E-5, between NJOY99 and TREND, for MT1, MT2, MT102 and MT18 when it exists.
A monochromatic light source (Polychrome V, TILL photonics (FEI), Hillsboro, OR) was used to measure the activity spectrum of ReaChR. We used 300-ms light flashes ranging from 650 to 400 nm (25 nm steps; interstimulus interval 1. 5 s) at a constant light intensity of 1. 2 × 10 16 photons cm À2 s À1. The monochromatic light source was also used to generate light pulses at different frequencies in order determine the temporal response properties of ReaChR. Stimuli were generated using custom-written software in LabVIEW (National Instruments, Austin, TX). Output light intensities were calibrated (10 12 À10 18 photons cm À2 s À1 ) by using a spectrophotometer (USB2000+, Ocean Optics, Dunedin, FL).
Multi-electrode array recordings and data analysis All multi-electrode array recordings were performed on a 252 channel multi-electrode array system (USB-MEA256-System, Multi Channel Systems, Reutlingen, Germany), and data were acquired using the MC_Rack software  (MC_Rack v4. 5, Multi Channel Systems). Ex vivo isolated flat-mounted retinae of ReaChR-treated rd1 mice aged 2 months or older as well as ReaChR-treated primate ex vivo retinal explants in tissue culture were tested. Mice were euthanized as described above and post-dissection, the retinae were placed on a cellulose membrane soaked overnight in poly-L-lysine (Sigma-Aldrich) and superfused in oxygenated Ames medium (A1420, Sigma-Aldrich) containing sodium bicarbonate (Sigma-Aldrich) at 34°C, with the RGC side gently pressed against a 60-lm electrode spacing multi-electrode array chip (256MEA60/10iR, Multi Channel Systems).
A flicker stimulus consisting of light at 550-nm blinking at frequencies ranging from 1 to 100 Hz (intensity: 1. 59 × 10 16 photons cm À2 s À1 ) was presented to the retinae to measure the temporal dynamics of ReaChR's light response in ReaChR-treated blind mice. RGC activity was then amplified and sampled at 20 kHz. Signals were filtered with a 200 Hz high-pass filter in MC_Rack, and individual channels were spike-sorted by visualizing the waveforms' principal component analysis plots using Spike2 software v. 7 (Cambridge Electronic Design Ltd. , Cambridge, UK). Custom-written MATLAB scripts were used for plotting the responses to randomized presentations of different wavelengths (10 nm steps) of light and for analyzing the responses to flicker stimuli. For a given flicker frequency tested, a spike modulation index (M.
The multi-electrode was gently inserted into the cortex perpendicularly to the surface of the brain and 600 lm deep. Then, the tissue surface was covered with agarose (1. 2% in cortex buffer). Signals were amplified using a 16-channel amplifier from MultiChannel Systems (model ME16-FAI-lPA-System), sampled at 25 kHz, and recorded using the software MC Rack (Multi Channel Systems, Reutlingen, Germany). For spikes and for LFP, a high-pass filter at 200 Hz and a low-pass filter at 300 Hz were used, respectively. Signals were then analyzed using custom MATLAB (Mathworks, Natick, MA) scripts. For every experiment, the electrode presenting the best signal was selected and analyzed. LFPs were shown as an average of 200 repetitions, spiking events detected by a threshold set at six times the median absolute deviation of the trace and peristimulus time histograms generated with bins of 5 ms.
Their activity was recorded for 2 min followed by 2 min of illumination of the chamber (based on the protocol used in  Lagali et al, 2008). The movies were analyzed using mouse behavior phenotyping and motion tracking software Ethovision XT build 8. 0 (Noldus Information Technology, Leesburg, VA). The mouse was detected using a center of mass algorithm by adjusting the threshold to maximize the contrast between the mouse and background, in the dark and during illumination. The average velocity and trajectory of the mouse was tracked for 2 min in the dark and for 2 min after light was switched on. All behavior experiments were run during the dark phase of the mice between 18 and 21 h. These data were then analyzed and plotted in Prism 6 (GraphPad Software, La Jolla, CA). Significance was assessed using a one-tailed Student's t-test, and an a-level of P < 0.
Acknowledgements We thank  Roger Y. Tsien  for providing the ReaChR plasmids. We thank  Benjamin Taklifi  and  Céline Winckler  for technical support and  Elric Esposito  and  Stéphane Deny  for helpful discussions. We are thankful to  Noga Vardi  for critical feedback. We thank  Manuel Simonutti  in the  Plateforme Animalerie at the Institut de la Vision  for performing intravitreal AAV injections. We are grateful to  Kate Grieve  for organizing the human donor eyes. This study was supported by the  Centre National de la Recherche Scientifique (CNRS) , the  Institut National de la Santé et de la Recherche Médicale (INSERM) ,  Pierre et Marie Curie University (UPMC) , an  Agence Nationale de la Recherche  Grant (LIFESENSES:  ANR-10-LABX-65 ) and an  ERC Starting Grant  ( OPTOGENRET, Grant No 309776 ).
Furthermore, new and improved robotic devices are likely to become available soon, encouraging the expansion of robotic surgery and hopefully reducing costs. The Robotic Chest Surgeons Network will be concerned with surgeon training and quality control so as to minimize complications during learning, including in particular: (a) standardization and certification of training; (b) monitoring adverse events and developing quality performance measures; (c) holding master classes to train young thoracic surgeons in robotic skills; (d) data sharing (common database) and facilitating clinical research; and (e) fostering a climate of cooperation to encourage researchers to exchange ideas and design trials. The Network will also contribute to the development of thoracic health care policies. Few organizations concerned specifically with robotic surgery exist.
rOBOtic sUrGerY versUs vAts FOr MAJOr LUNG resectiONs: A PrOsPective rANDOMiZeD triAL A randomized trial (NCT02804893) to compare VATS with robotic surgery for lung resections to treat lung cancer is about to start recruiting. VATS is an established approach to resectable lung cancer, being associated with reduced pain, fewer complications, shorter postoperative stay, and equivalent oncological outcomes compared to thoracotomy (1, 26). Furthermore, its use is expanding rapidly: in 2015, 50% of the pulmonary lobectomies performed in the United States, and 33% of those performed in Europe employed a minimally invasive approach (27) However, because of restricted freedom of movement and poor ergonomics, VATS is demanding for thoracic surgeons and requires a long learning curve. In theory, robotic surgery overcomes many of the disadvantages of VATS, but these benefits have not been conclusively demonstrated.
A recent large retrospective comparison of the two techniques  (28)  found that for robotic lobectomy and wedge resection, costs were higher and operating times longer than for VATS, with no difference in adverse events. However, 40 robotic centers were included in the evaluation -an average of 8 robotic cases per center, suggesting that many of the surgeons may still have been learning the robotic technique. A smaller 2015 comparison  (29)  of the first 28 VATS lobectomies with the first 28 robotic lobectomies performed in a single institution reported that perioperative outcomes were similar for both techniques during the learning period but that the robotic approach was associated with better safety and fewer conversions for uncontrolled bleeding. NCT02804893 is a prospective multicentric randomized trial to compare complications and conversion rates between robotic and VATS approaches to stage I and II lung cancer.
Coping with various types of natural or man-made hazards the FP7 SECURITY CRISMA project (http://www. crismaproject. eu) has designed and developed an experimental software framework allowing building crisis management simulation application. One of the five pilot applications of CRISMA dealing with preparedness to the coastal submersions was developed and implemented using return of experience of the reference Xynthia storm surge event in the Charente Maritime County in France. The paper addresses the generic CRISMA Framework applicability to simulate mitigation effects of a coastal submersion through CRISMA-Wave implementation of a full modelling cycle. The CRISMA-Wave paradigm reflects user needs for simulation of "what-if" scenarios for short and long-term actions and the paper describes in particular its different components : *Simulation of submersion effects at a range of temporal and spatial scales, *Preparedness Planning, *Assessment of impacts depending on scenarios based on options for managing the inundation risks, *Cascading effects and *Evaluation of damages with comparison of submersion defence scenarios based on cost-benefit and multi criteria analysis.
Introduction Recently completed the EU FP7 SECURITY project CRISMA (www. crismaproject. eu) -"Modelling crisis management for improved action and preparedness" has developed a generic methodology and software framework for the implementation of simulation-based decision support systems  [1]. CRISMA targeted use cases in the preparatory phase of crisis management: short and long-term planning, desktop training and assessment in field trainings. Application prototypes cover different types of hazards (floods, snowstorms, earthquakes, forest fires, accidental pollutions, mass accidents) and illustrate how the CRISMA Framework can be used in a relatively simple but integrated manner to develop fully fledged decision support applications. A generalized workflow of a CRISMA application is depicted in the Figure  1.
CRISMA-WAVE as a solution for simulation of coastal submersion scenarios The CRISMA-WAVE prototype is based on the generic, hazard-neutral CRISMA Framework that is the result of the fundamental system developments achieved by the CRISMA Project  [4]. This framework provides all necessary building blocks in order to construct a complex crisis management system. The building blocks are generic, configurable, composable, reusable and adaptable. They are the core elements of the architecture and encapsulate the functionality of the CRISMA Framework. These functionalities can be offered by existing software components or by components developed from scratch. Several software components can meet the building blocks requirements. In this context, the developer selects the best building block configuration adapted for a specific application of a crisis management system.
org/ Evacuation model -The evacuation, agent-based model used the software Life Safety Model 2D i (LSM2D). This model allows performing different evacuation scenarios depending on a number of roads closed due to inundations, the estimated casualties on population, and the estimated impacts on buildings due to the flood. Developed by BC Hydro it was further interfaced with TELEMAC-2D and used by HR Wallingford  [9]. In addition to these components, a security layer has been deployed in order to handle user authentication in the application. Internationalization has been also introduced to support multi-language versions and as per today English and French interfaces exist.
Implementation principles On the server side of the CRISMA-WAVE infrastructure, three servers have been deployed: xWeb-based platform -this server hosts the web application and the user interaction building blocks. Node. jsj is used for the deployment of the web application. x ICCM instance -this server hosts the infrastructure building block x Web services -This server hosts the following integration building blocks : data integration (GeoServer) and simulation model integration (PyWPS) The frontend of the CRISMA-WAVE is based on HTML5, JavaScript (AngularJSk) and CSS3. The user interaction building blocks have been developed with the same components.
Illustrated example of a system exploitation In order to use this application, all the required models should exist on the area of interest and the various data used should be also available. We didn't detail the building of model and the implementation of the data. We just precise here that all the data used are stored in some database and the evolution of the local situation should be easily take in account by upgrading the concern databases. The way the use of CRISMA-WAVE is envisaged takes the form of a double loop as presented in the following workflow (Figure  9 ). The result of this large scale simulation provides two types of information: • a global overview of the potential inundated area due to the overflowing or overtopping of dikes; • an evaluation of the impact of this event on dikes which classify each segment of dike (dikes are considered in this model as a successions of elements of about 250m length) in 3 categories according to the highest probability of no failure, breach appearance or dike's total failure According to these first synoptic results, the user can decide: • to stop the process (if there are no identified risks); • to restart the process with another meteorological event boundary conditions; • to go further and make a focus on one or more local areas of interest, usually corresponding to the hot-spots identified at a large scale.
S6, ESI † ). Finally, the mean value of χ per track is distributed uniformly over the angle range 30°to 70°(Fig. S7 , ESI †), indicating that the rotating grains are evenly distributed in the diffraction patterns. In the exemplary tracks shown in Fig. 2e-g  it can be seen that the χ and q profiles can be positively or negatively correlated. A statistical analysis presented in Fig. S8  to S10 (ESI †) of the cross correlation coefficient between Δχ and Δq shows that the total number of positively correlated tracks is ∼54% and that most of the Δχ and Δq profiles are highly correlated. We further classify precursor and perovskite tracks by training two self-organizing maps (SOMs) in MATLAB (see Fig. S11  and S12, ESI †). 20 Fig. 3d  shows the results from the SOMs clustering. The Δq vs. Δχ tracks are classified by the Cartesian quadrant where they spend most of their time.
Image processing Data processing was performed using a GI-XRD MATLAB software. 24 The 390 images collected during the deposition and the annealing phases were remapped into scattering vector coordinates, as detailed in ref. 23. The scattering vector is de-fined as q = k f -k i = [q x q y q z ], where k i is the incident wave vector and k f is scattered wave vector. Here, the scattering vector q is referred to the Euclidean norm of q. Images are represented in reduced scattering vector rectangular coordinates: q z and. We also refer to scattering vector polar coordinates: azimuth χ = π/2 -atanĲq z /q xy ) in degrees and distance , which corresponds to the wavevector 2π/λ, where λ is the beam wavelength. Intensity in the diffraction patterns shown in Fig. 1  is normalized between 0 and 1. Azimuthally integrated line profiles are generated as shown in ref.
Diffraction spot tracking A spot-tracking program was written in MATLAB and integrated in the GI-XRD software. An original remapped image was treated with background removal and top hat filtering to enhance the local diffraction spots and facilitate 2D peak detection. An image processing MATLAB algorithm commonly used for tracking moving colloidal particles (J. Crocker's track. pro routine) was modified to work with the moving diffraction spots. 25 A matrix containing the (x,y) coordinates of the detected spots in each image and time (or equivalently image) index was fed into the tracking routine. As an example, in the 60 images of the deposition phase, the number of detected spots was 155 420. However only tracks lasting more than 11 images (i. e. ∼3 min) and with a maximum displacement higher than 10 pixels were selected.
Large diffraction spots with displacement above 4 pixels were not considered. Diffraction spots with excessive overlap to other diffraction spots and stationary spots were also not included. For each track and each image corresponding to the track, we generated a region of interest (ROI) having the diffraction spot coordinates at its centre. The diffraction spot was fitted with a 2D Gaussian, which was then used as a shape-preserving filter to generate a new ROI, where only the diffraction spot is visible. The image was then converted to a black and white ROI and information on the diffraction spot shape extracted, such as area, eccentricity, orientation, etc. Videos of each single track were also generated (see ESI †). Videos were checked by hand and false tracks removed from the dataset.
Acknowledgements This work was funded by the  UK Engineering and Physical Sciences Research Council  via grants  EP/M025020/1  ' High resolution mapping of performance and degradation mechanisms in printable photovoltaic devices ',  EP/J017361/1  ( Supersolar Solar Energy Hub ) and the  E-Futures Doctoral Training Centre in Interdisciplinary Energy Research   EP/G037477/1. This work was partially funded by 'The President of the  UAE 's  Distinguished Student Scholarship Program  (DSS), granted by the  Ministry of Presidential Affairs, UAE'  ( M. A. PhD  scholarship). XMaS is a mid-range facility supported by the  Engineering and Physical Sciences Research Council (EPSRC). We are grateful to all the XMaS beamline team staff for their support. We thank  Robert Masters  for performing the SEM scans.
Rhea (http://www. rhea-db. org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research. These include the first implementation of a simple hierarchical classification of reactions, improved coverage of the IUBMB Enzyme Nomenclature list and additional reactions through continuing expert curation, and the development of a new website to serve this improved dataset.