dataesr/scientific-paragraphs-categorization huggingface dataset:
There is a wide variety of MHD instabilities in tokamak plasmas, some of which can reduce or limit the operational capabilities of the machine. 0] [11] [12] [13] [14]  In order to study, understand, and predict these instabilities, non-linear MHD simulations are performed using numerical codes such as JOREK,  15, 16  M3D-C1,  17, 18  NIMROD, 19,20 XTOR,  21  BOUTþþ, 22,23 MEGA,  24, 25  and HALO. 7 revious studies of MHD instabilities with the JOREK code relied on a reduction of the full-MHD system. This reduction, known as reduced MHD, assumes that the toroidal magnetic field is constant in time and that the perpendicular velocity (perpendicular with respect to the magnetic field) is approximately poloidal. 26, 27 The latter assumption is mostly kept for simplicity in formulating the equations.
A. Numerical methods Before introducing the physics model, some of the key numerical methods of the JOREK code are presented. These methods are the same as in previous publications,  16, 32  but they are repeated here to point out their role in the numerical stability of the full-MHD model. JOREK uses a finite-element grid in the poloidal plane, with finite Fourier series in the toroidal direction. The finite elements are quadrangular bi-cubic Bezier elements using a nodal formulation that ensures continuity of variables and their derivatives across elements (commonly defined as C1-or G1 continuity). 32 This is also valid for the poloidal space coordinates (R,Z) such that the elements are isoparametric. The Fourier series used in the toroidal direction can be chosen with arbitrary toroidal periodicity, meaning that with three Fourier modes and a toroidal periodicity of 4, the physical toroidal mode numbers simulated would be n ¼ 4, 8, and 12.
B. Where reduced-MHD fails The internal kink mode at finite-b is a good example to illustrate why full-MHD is absolutely necessary for the modeling of some tokamak instabilities, particularly core MHD, which is highly relevant to disruptions, one of the main focuses of current research and experiments. In this benchmark, the results of the linear calculation of an n ¼ m ¼ 1 internal kink instability obtained by the reduced-MHD model of JOREK, the full-MHD model of JOREK, and the linear full-MHD code CASTOR3D  59, 60   Note that the viscosity here was used only for the JOREK runs, while it is zero for CASTOR3D. As shown in Fig. 3 , the full-MHD model of JOREK and CASTOR3D agrees well on the linear growth rates, while the reduced-MHD model fails to reproduce these results at finite values of b.
Plot (a) shows a poloidal snap-shot of the whole plasma, with the zoom-box inside which the slices of plot (b) were obtained. [Associated dataset available at https://doi. org/10. 5281/zenodo. 3971940 (Ref. 58). ] model. Of course, further developments of the model will now be required in the near future to address specific tokamak instabilities such as disruptions, detachment, and ELM burn-through, which requires neutral and impurity physics. However, it is not expected that these additional physics effects will deteriorate the numerical stability of the model since they enter the system as terms that were already included and tested here (mainly density sources and temperature sinks). Another important aspect of future developments will be to address more elaborate boundary conditions, with wall-extended grids as in Ref.
ACKNOWLEDGMENTS This work was performed with the support of the JOREK Team (see https://www. jorek. eu for the present list of team members). This work was carried out within the framework of the EUROfusion Consortium and received funding from the Euratom research and training programme 2014-2018 and 2019-2020 under Grant Agreement No. 633053 and from the RCUK Energy Programme (Grant No. EP/I501045). To obtain further information on the data and models underlying this paper, please contact PublicationsManager@ccfe. ac. uk. The views and opinions expressed herein do not necessarily reflect those of the European Commission or the ITER Organization. The MARCONI computer at CINECA in Italy was used for simulations. The support from the EUROfusion Researcher Fellowship programme under the task Agreement No.
68G. 9. Simulation of an MGI-triggered disruption in JET. Columns from left to right: electron temperature T e , electron density n e , toroidal magnetic potential A / , and a Poincare plot of the magnetic field. Rows from top to bottom: time lapse of the simulation, at t ¼ 0 ms, t ¼ 2:8 ms, t ¼ 4:2 ms, and t ¼ 5:7 ms. Despite a very simplified MGI model lacking neutral physics, core-MHD is triggered and a thermalquench is obtained, demonstrating that the new full-MHD model is ready for simulations of disruption physics at the same level as the reduced-MHD model in previous studies. 68[Associateddatasetavailable at https://doi. org/10. 5281/zenodo. 3971940(Ref. 58). ].
The hybrid planar-polygonal texture provides the possibility of forming an image (the PUF tag) when it is embedded in a polygon-textured matrix, producing a specific optical response (the PUF pattern), which has to be recorded in a list of PUF keys (a database). An assembly of cells carries an additional level of PUF since the relative positions, sizes and optical patterns of cells are unique, not clonable and unpredictable. C. gloriosa may display information and hide in the background. Therefore, the comparable role of artificial tags and biological patterns brings an additional criterion to the biomimetic nature of the present biomimetic samples in terms of physical functions. By using CLC oligomers we have engineered a single-layer material mimicking the striped cuticle of the scarab beetle C.
Output signals were recorded in real time with a high-resolution oscilloscope (LeCroy, HDO4034, 4096 vertical 100 resolution) and averaged for 120 laser shots (repetition rate ~1 Hz). We observed a small time-dependent variation in transmittance even when no precursor was introduced into the reactor. To compensate for this effect, which was caused by the optics and the photolysis laser pulse, we recorded background traces without adding the precursor before and after each set of experiments. The reported data are after background subtraction. All reactant gas flows were controlled by calibrated mass-flow controllers (Brooks: 5850E, 5800E and Bronkhorst: EL-105 FLOW prestige) and mixed before entering the reactor. Reactant concentrations were determined prior to mixing of the reactant flows by UV absorption spectroscopy in two separate absorption cells for either DMS (absorption path length 90.
026 except for CH 2 OO (0. 042), suggest that the calculations are not affected by strong multi-reference character in intermediates or transition states. The molecular characteristics thus obtained were used in canonical transition state theory (CTST) calculations to derive the temperature-dependent rate coefficient k(T)  (Truhlar et al. , 1996). All calculations were performed using the Gaussian-09 software suite  (Frisch et al. , 2010). The supporting information discusses additional calculations. O 2 (R2) (k O2 = 1. 410 12 cm 3 s 1 (Eskola et al. , 2006); [O 2 ] = 3. 3  10 17 cm 3 ). The subsequent decay in absorption is due to the consumption of CH 2 OO either through reaction with DMS or through other reaction processes, e. g. , bimolecular reactions with radical byproducts like I atoms, wall loss, etc.
Acknowledgements This work is supported by  Academia Sinica and Ministry of Science and Technology, Taiwan  ( MOST 106-2113-M-001-270 026-MY3 ;  108-2911-I-001-501 ( Orchid project )) and  French Ministry of Europe and Foreign Affairs  through the  PHC Orchid  project no. 40930 YC. LV is indebted to the  Max Planck Graduate Center  with the  Johannes Gutenberg-Universität Mainz (MPGC) ,  Germany.
For Co-Immunoprecipitation assay, immunoprecipitated proteins were detected using VeriBlot for IP Detection Reagents (Abcam) without being contaminated by IgG heavy and light chains from the precipitated-antibodies. The signals were visualized using Amersham TM ECL Select Western Blotting Detection Reagent (GE Healthcare) according to the manufacturer's instructions and recorded via UVP BioSpectrum Image system (UVP). Data were analyzed using Vision Works LS software (UVP).
However, all reports of ultrasound-induced apoptosis in brain were analyzed by TUNEL assay, which was designed to detect apoptotic cells that undergo DNA fragmentation at late stages of apoptosis, but cannot detect early apoptosis and pro-apoptosis stage. More safety assessments are thus needed to explore the effects of FUS on apoptosis. On the other hand, shockwave did not significantly generate ROS in our preliminary experiments (data not shown) when compared with FUS, probably due to its short pulses and scarce iterations. This observation is beneficial for acoustically induced BBB opening in clinical applications. A previous study also shows that shockwave treatment did not induce the expression of oxidized proteins, NOX-1 and NOX-2 (oxidative stress indicators) in the brain  [67]. One of the limitation of this study is that we only use inhibitors or agonist to analyze the related signal pathways.
Acknowledgments This work was supported by grant  105-2923-B-002 -001 -MY3  and  106-2314-B-002 -168 -MY3  from the  Ministry of Science and Technology (MOST) ,  NTUH. 107-004075  from the  National Taiwan University Hospital  and  BN-107-PP-03  from the  National Health Research Institutes (NHRI). We thank  Ai-Ling Hour  for statistical analysis and the staff of the  Biomedical Resource Core  and imaging core at the  First Core Laboratories, National Taiwan University College of Medicine , for technical assistance.
This approach, along with developmental studies on larvae raised in low-calcification-substrate conditions (e. g. De Wit et al. , 2018; Ramesh et al. , 2019)  is significantly increasing knowledge of putative biomineralization genes. These approaches are particularly powerful when combined with analyses of expression modules and gene networks, such as correlative weighted gene co-expression network analysis (WGCNA) and programs such as the algorithm for the reconstruction of accurate cellular networks (ARACNe) (e. g. De Biological Reviews 95 (2020) 1812-1837 © 2020 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society. Wit et al. , 2018; Sleight et al. , 2020). These in silico techniques visualize gene interactions and provide major progress towards defining biochemical pathways in non-model species.
2) Mollusc genomes and comparative genomics In 2012, a landmark paper in molluscan genomics described the first draft of the C. gigas genome  (Zhang et al. , 2012). Since then, despite molluscs being amongst the most diverse and speciose phyla, they remain poorly represented in genome databases [e. g. the Genomes OnLine Database (GOLD; https://gold. jgi. doe. gov/index) and EnsemblMetazoa database (http://metazoa. ensembl. org/index. html)]. However, this situation should change soon with the Earth Biogenome Project (https://www. earthbiogenome. org/), which has the ambitious aim to sequence all eukaryotic species in the next decade and also programmes such as the Darwin Tree of Life (https://www. darwintreeoflife. org/). Until then mollusc genomes can be accessed far more easily than previously via transcriptomes and there is now a specific mollusc database of genomes and transcriptomes in 'ensembl' easy access format (https://molluscdb.
XI. ACKNOWLEDGEMENTS This manuscript was partly funded by the  European Union Seventh Framework Programme  [ FP7] ITN project  ' CACHE: Calcium in a Changing Environment ' (www. cache-itn. eu)under REA grant agreement  605051. The authors thank everyone involved in this project including  Mark Blaxter ,  Xushuai Zhang ,  Yan Wang-Duffort ,  Nina Fox ,  Rita Pereira ,  Nicola Munro ,  Elaina Ford ,  Lucy Gonzalez ,  Christina Chatzela ,  Rachel Ramirez , our  EU  Project Officer  Giuliana Donini  and  EU Mid-Term Review Expert Guy Duke. Also, many thanks to our Project Partners: the  Association of Scottish Shellfish Growers , specifically  Nick Lake ,  Janet Brown  and  Walter Speirs ,  Coastal Research and Management, Kiel especially Peter Krost , and our External Experts  Professor Catherine Boyen ,  Station Biologique de Roscoff  and  Professor Mike Thorndyke.
Powder angle-dispersive XRD measurements at HP were performed at room temperature in the BL04-MSPD beamline at ALBA synchrotron facility. 91 This beamline is equipped with Kirkpatrick-Baez mirrors to focus the monochromatic beam and a Rayonix CCD detector with a 165 mm diameter active area. The XRD measurements were performed with monochromatic xrays with a wavelength of 0. 4246 Å, as determined from the absorption K-edge of Sn (29. 2 keV). The sample was loaded with a 4:1 methanol-ethanol mixture in a membrane-type diamond anvil cell (DAC) with diamond culets of 400 m in diameter. The applied pressure was determined with the EoS of copper. 92 The associate error to the pressure determination, including the pressure gradients inside the DAC, is lower than 0. 5 GPa. The sample to detector distance (240 mm), along with various detector geometrical parameters of the experiment, were calibrated with the DIOPTAS software  93  using diffraction data from LaB6 measured in the same conditions as the sample.
The structural analyses were performed with the program TOPAS 4. 2. For the lowpressure (LP) cubic phase, Rietveld refinements to the XRD patterns were carried out, whereas for the HP phases the lattice parameters were obtained with Pawley/Le Bail whole pattern fittings. Figure  S1  in the Supplementary Information (SI) shows selected examples of calculated and difference profiles as obtained from the profile refinements. Room-temperature unpolarized HP-RS measurements were excited with the 532-nm line of a solid state laser. For these experiments, micron-size fragments without well-known orientation were obtained from the single crystals. Inelastically-scattered light was collected with a Horiba Jobin Yvon LabRAM HR UV spectrometer equipped with an edge filter that cuts Raman signals below ∼50 cm -1 and a thermoelectrically cooled multichannel CCD detector enabling a spectral resolution better than 2 cm -1.
3. -First-principles calculations Ab initio total-energy calculations at 0 K for the C-, B-, and A-type phases of Tb2O3 (and also for other SOs) were performed within the framework of density functional theory (DFT)  95  with the Vienna Ab-initio Simulation Package (VASP),  96  using the pseudopotential method and the projector augmented waves (PAW) scheme. 97, 98 In this work, the generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) parametrization  99  was used for the exchange and correlation energy, after evaluating calculations performed also with its extension to the solid state (PBEsol). 100 A dense Monkhorst-Pack grid  101  of special k-points (6×6×6 for the C phase and 4×4×4 for the A and B phases) and a plane-wave basis set with energy cutoffs of 530 eV were used.
This is consistent with the smaller pressure coefficient of the Eg 2 mode in Tb2O3 at 11 GPa than those found in Sm2O3, Nd2O3 and La2O3 at 0 GPa or close to 0 GPa. Our calculations have allowed us to represent the atomic vibrations of the Raman-active modes of A-type Tb2O3 using the J-ICE software. 137 We have clearly observed that the classification of the two low-frequency and the two high-frequency Raman-active modes as pure bending and stretching modes is not correct. First of all, we have to note that there are no pure stretching nor pure bending modes. In all vibrations O(I) atoms are immobile. The low-frequency Eg 1 mode corresponds to a mixture of bending and stretching modes where Ln atoms vibrate in the hexagonal a-b plane with a small vibration of the O(II) atoms (see Figure  S12a  in the SI).
The tensor has been obtained with the finite Eulerian approximation as implemented in the Win_Strain package [42]. The change of the  monoclinic angle (always perpendicular to the b axis) with pressure implies that, in this monoclinic compound, the direction of the a axis changes with pressure assuming both b and c axis constant. Furthermore, the departure of this monoclinic angle from 90º indicates that the direction of maximum compressibility is not exactly that of the a axis. Therefore, in order to evaluate the direction of maximum compressibility as a function of pressure we have calculated and diagonalized the experimental and theoretical isothermal compressibility tensor, ij, at different pressures. The experimental and theoretical elements of this tensor at different pressures are reported in Tables  S9  and S10 , up to 11.
Acknowledgements Authors thank the financial support of  Generalitat Valenciana  under Project  PROMETEO 2018/123-EFIMAT  and of the  Spanish Ministerio de Economía y Competitividad  under Projects  MAT2015-71035-R ,  MAT2016-75586-C4-2/3/4-P ,  FIS2017-2017-83295-P , as well as through MALTA  Consolider Team research network  under project  RED2018-102612-T. J. A. S. also acknowledges the  Ramón y Cajal program  for funding support through  RYC-2015-17482. A. M. and P. R. -H. acknowledge computing time provided by  Red Española de Supercomputación (RES)  and the  MALTA  Consolider Team cluster. HP-XRD experiments were performed at MPSD beamline of  Alba Synchrotron  (experiment no. 2016071772). We would like to thank  Oriol Blázquez  ( Universitat de Barcelona ) for his contribution to the Raman measurements.
CONCLUSION We surveyed 20 advanced many-electron techniques on precisely defined realistic Hamiltonians for transition metal systems. For a given basis set, we achieved ∼ 1 mHa agreement on the total energy between high accuracy methods, which provides a total energy benchmark for many-body methods. To our knowledge, such an agreement is unprecedented for first principles calculations of transition metal systems. Our accurate reference energies should enable the development of approximate, but more computationally efficient, many-body techniques as well as better density functionals, without the necessity of experimental reference values. These systems are also a useful test for future quantum comput- ing algorithms. To enable such comparisons, we include pyscf scripts that can execute the benchmark for any density functional available in libxc  [70] , and can export the one-and two-body integrals needed for testing manybody methods.
B. Configuration interaction Configuration interaction with singles and doubles excitations (CISD) was used as implemented in the PySCF package. CISD approximates the many-body wave function as a sum of Slater determinants, constructed from a reference Slater determinant, which was taken from restricted open shell Hartree-Fock. In CISD, the wave function is given as |Ψ CISD = (c 0 + ij,σ C (s) ai c † a,σ c i,σ + ijkl,σ,σ C (d) abij,σ,σ c † a,σ c † b,σ c i,σ c jσ )|Ψ HF , where c † and c are creation/destruction operators, respectively, a, b refer to virtual orbitals, i, j refer to occupied orbitals, and all C parameters are variationally optimized. CISD scales approximately as O(N 6 e ) and is known to not arXiv:1910. 00045v2 [cond-mat. mtrl-sci] 5 Oct 2019 TABLE I. Calculations in the database.
This will result in series of tensor contractions involving one and two electron integrals (stemming from Ĥ0 and V ), and RDMs up to fourth order. The application of the Wick's theorem to the strings of operators is done with the "Second Quantization Algebra" symbolic algebra Python library [? ], which we modified to fit our needs. The scripts also automate the generation of the C code used to solve the resulting equations and to calculate the energies E 2 and E 3.
5. A small improvement in accuracy was implemented after this version. Should be "new" for all calculations • method: a string representing the method used for the calculation. example "PBE" • totalenergy: total energy in Hartrees • totalenergy-stocherr : Stochastic error estimate • totalenergy-syserr : Systematic error estimate, if available A script called 'gather. py' retrieves all data from all directories. Further scripts handle plotting and error estimation.
Measurement Methods Conductivity measurements were carried out from -40 • C to 80 • C using a Multichannel Conductivity Meter, based on frequency response analyser (MCS 10, Bio-Logic, Clermont-Ferrand, France). Measurements were carried out using sealed cells with Pt parallel-plate-electrodes, to protect the samples from air exposure. Prior to any measurements, conductivity cells were calibrated using aqueous KCl solution (standard conductivity solutions; 147 µS•cm -1 , 1413 µS•cm -1 , and 12. 88 mS•cm -1 ) at 25 • C. Density and viscosity measurements were performed as a function of the temperature using a digital vibrating tube densimeter (mode 60/602, Anton Parr and a rolling-ball viscometer (Lovis 2000 M/ME, Anton Parr, Craz, Republik Österreich), respectively. Data acquisitions were realized at thermal equilibrium with successive increments of 5 • C within the range of 5 • C to 80 • C.
Decomposition temperatures reported from TGA data are the onset, as determined from the step tangent. Electrochemical measurements including operating voltage experiments, floating tests and Electrochemical Stability Windows (ESW) studies, were carried out on a Versatile Multichannel Potentiostat (VMP3, Bio-Logic) piloted by an EC Lab interface. To determine operating voltages, cyclic voltammetry (CV) measurements were carried out applying a scan rate of 10 mV•s -1 and gradually increasing the potential limit. The cell operating voltage was determined for a potential whose coulombic efficiency of the CV is greater than 98. 5%. Floating tests were performed at 23 • C in a temperature-controlled room. These tests consist of following steps; (i) charging the device with a constant current density of 1 A•g -1 until the potential limit is reached, (ii) maintaining this potential limit value for 12 h, and (iii) discharging the device to 0 V with a current density of -1 A•g -1.
Calculation Methods Calculations of the sigma surface and structure descriptors, such as the COSMO volume, HOMO and LUMO energies, were completed using the Turbomole 7. 0 programme package  [36]. Before being able to visualize the 3D structure of each species using TmoleX (version 4. 1. 1), all structures were optimized in the gas phase with a convergence criterion of 10 -8 Hartree, using HF-6 311G**++ basis set, followed by DFT calculations combining the resolution of identity (RI) approximation,  [37, 38]  within the Turbomole 7. 0 programme package using the B3LYP function with the def2-TZVPD basis set  [39, 40]. The resulting optimized structures were then used as inputs in the COSMOconfX programme (version 4. 0) to generate the conformers of each species using the BP-TZVPD-COSMO+GAS basis set.
The COSMO volume (Å 3 ), the sigma profile and the sigma surface of each species were then determined and viewed using the COSMOthermX software, which is based on the COSMO-RS (COnductor-like Screening MOdel) computation technique. The combination of TmoleX and COSMOthermX software (version 19. 0. 5) was then used to understand the differences in structure, charge distribution and volume of the three solvents, EmimTFSI and Et 4 NBF 4 investigated during this study and to understand the specific cation-solvent interactions in solution as a function of the number of solvent molecules in the first solvation shell by following the methodology previously described by our group  [33, 41, 42].
Acknowledgments: The authors would like thank  Sébastien Rose  and AXYNTIS for supplying the samples of phenyl-acetonitrile for this work and also for his supporting to the projects. Furthermore, F. I. , J. J. and F. G. kindly thank the  CEA le Ripault  and more particularly  Corinne Marcel ,  Agnes Biller  and  Jean-Paul Aubin  for their helps within flash point measurements. The authors would also like to thank " Le Studium Loire Valley Institute for Advanced Studies" and Région Centre Val de Loire  for financial support to the researchers involved in this study.