dataesr/scientific-paragraphs-categorization huggingface dataset:
The extensive use of the SWG protein alignment algorithm contributes positively to its performance and sensitivity. Several unique additional SyntTax properties were instrumental for the analysis of the ygjD gene cluster. Beyond the confirmation of known interacting factors in this complex, SyntTax was able to predict the interplay between new potential partners composing this multiprotein machinery involved in the bacterial tRNA modification. The SyntTax web server is built upon the proven Absynte synteny algorithm and allows full access to complete taxonomic records for each sequenced archaea and bacteria in the NCBI database. This tool is capable of adapting rapidly to the sequencing of new genomes due to the daily automated update of its databases. The taxonomic capabilities of this web service are not available in other tools and add a new dimension to synteny analysis by providing robust results while reducing computing time.
Exhaustive access to prokaryotic lineages is not available in similar tools such as GeCont2, PSAT or GCVIEW. Although solely based on genomic sequences, annotations and taxonomic data, the accurate illustration of genomic contexts produced by SyntTax is able to provide exhaustive cutting edge predictive information on protein-protein interaction. These predictions complement adequately those provided by other tools such as STRING which uses a complex combination of genomic, post-genomic and text databases. The principles shown here demonstrated that the high number of sequenced genomes and their increasing redundancy no longer constitute a burden. This wealth of information can indeed be used effectively to target specific aspects of the evolution of prokaryotic gene clusters and to yield insights on the molecular interaction between the corresponding proteins.
Structural analysis of membrane proteins by solid-state NMR Structural analysis of membrane proteins is a prerequisite for understanding their function and biogenesis. Although membrane proteins form 30% of the proteome, they still represent only 1% of the structures in the Protein Data Bank. X-ray crystallography has been the main method used for structure determination. Typically produced in small quantities, requiring specific detergents for membrane extraction, flexible and dynamic, membrane proteins have been far fewer for yielding crystals of sufficient quality for X-ray diffraction analysis. Among alternative methods for structure determination, such as nuclear magnetic resonance (NMR) and electron microscopy (EM), solid-state NMR (ssNMR) has proven particularly powerful, providing structures of soluble and membrane proteins with equal success.
M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT 3 Important components of NMR analysis are powerful computational methods, such as ARIA or ISD, that allow structural calculations based on the distance data  (Rieping et al. , 2008 , Bardiaux et al. , 2012). Since not only biological polymers, but also membrane proteins typically exist as symmetric assemblies, the use of symmetry to calculate structures can reduce calculation complexity and cost  (Bardiaux et al. , 2012). Benjamin Bardiaux (Institut Pasteur, CNRS UMR3528, Paris, France) described the power of combining ssNMR and computational methods based on ambiguous distance restraints to solve the structure of the Yersinia adhesin A (YadA), secreted via the type V pathway  (Leyton et al. , 2012). YadA belongs to a class of type V secretion systems called autotransporters, which cross the inner membrane of Gram-negative bacteria via the Sec system.
MD-2 binds the lipid A moiety of LPS  (Park et al. , 2009). The simulation data presented by Bond showed that MD-2 induces stronger binding of the agonist (LPS) by TLR4 and that the conformational changes predicted in MD-2 depend on the fatty acids of LPS. Sabina Chalabaev (Institut Pasteur, Paris, France) discussed the regulation of lipid A modification in biofilm-grown bacteria. Different growth conditions have been shown to lead to alterations in the composition of the bacterial cell envelope. For example, bacteria in biofilms are more resistant to antimicrobial agents and.
Sarah Rollauer (University of Oxford, Oxford, UK) described the 3-D structure of TatC from a themophillic bacterium Aquifex aeolicus, recently determined by X-ray crystallography  (Rollauer et al. , 2012). The TatC structure is a product of extensive groundwork employed to optimize the expression and solubilization of the protein using an elegant TatC-GFP fusion tool to facilitate the screening process. TatC has 6 transmembrane segments and a large surface area with a concave face oriented towards the cytoplasm. To assess its binding to other Tat components, cysteine cross-linking data provided information on putative interaction sites with TatA and TatB. The dynamic nature of these interactions, however, makes it difficult to provide a clear model of this complex in action or to understand how the translocation proceeds without compromising the membrane impermeability.
Kinect Calibration Since Microsoft Kinect can be set into a special mode where the raw IR images can be stored, it is possible to use standard stereo calibration procedure for obtaining the calibration parameters for the IR and the RGB view  (Bouguet, 2010)  (Fig. 2 ). IR view and the depth view are trivially associated with image offset (-4, -3). A single camera calibration is used to initialize IR and RGB camera parameters. Then calibration is followed by a stereo procedure which re-estimates all free parameters (K IR , K RGB , kc RGB ,T b ). The lens distortion parameters of the IR camera are forced to zero, because data has already been used to generate the raw disparity map. This means that the IR lens distortion is compensated by tweaking other parameters. The RGB camera lens distortion parameters kc RGB are estimated without any special concerns.
K * j were selected by picking RGB-D frames evenly from the recorded sequence. A keyframe database is illustrated in Figure  1. In Figure  5 , we show how the drift increases in a studio environment when using dense tracking. On the right-hand side, the drift problem is solved by tracking relative to keyframes 3. Note that in longterm use, even a small number of keyframes eventually outperforms the dense tracking due to drift. However, a small keyframe number produces drift jumps between the keyframes which can be visually disturb-.
To reuse one or several existing systems in order to develop a complex system is a common practice in software engineering. This approach can be justified by the fact that it is often difficult for a single Information System (IS) to accomplish all the requested tasks. So, one solution is to combine many different ISs and make them collaborate in order to realize these tasks. We proposed an approach named AspeCiS (An Aspect-oriented Approach to Develop a Cooperative Information System) to develop a Cooperative Information System from existing ISs by using their artifacts such as existing requirements, and design.
THE AWMM IMPLEMENTATION In order to validate the proposed weaving process, we have used the plug-in AMW in eclipse platform. The following code shows an extract of the AWMM in KM3 language. It contains two types of model weaving which are: WeavingCoreAspect and WeavingCoreAdditional. These weaving models are an extension of the WModel (lines (1),(  2  In this example, we use the WeavingCoreAspect to add two operations to M1, especially to the Student class. These operations are called Before the call of the Student. NewSubscription() operation, in order to add a second subscription. The first operation Verify Specialty. NbreOfHours(IdSpecialty) consists of the computation of the number of hours for the new subscription, the result of this operation is used by the second operation get SecondSpecialty() to verify the constraint imposed to authorize or not a second subscription.
RELATED WORKS Over the last past years, several approaches to weave models have been proposed,  [14] ,  [15] ,  [16] ,  [11] ,  [17] ,  [18]. The database metadata integration and evolution is considered, as one of the important domains, where the model weaving is widely applied. In this context the work presented in  [14]  proposes a generic metamodel management algebra which uses algebraic operators to manage mappings and models. In  [15] , authors introduce a UML extension to express mappings between models using diagrams, and they illustrate how the extension can be used in metamodeling. The extension is inspired by mathematical relations and it is based upon ideas presented in  [16]. This work defines transformation relationships between different components of a language definition, rendered as a metamodel.
The outline of this paper The outline of the paper is as follows. In Section 2 the basic model used in our simulations is presented. Section 3 is a general review of field-aligned coordinate systems. The new general fluxcoordinate independent (FCI) system is defined in Section 4. In Section 5 we describe the implementation of the FCI approach into a new code that we call FENICIA, discussed in Appendix A. In Section 6, the approach is validated and shown to be well-qualified. Finally, the results of this paper are summarized and discussed in Section 7.
Discretization of ∇ ∥ We developed a new code that we called FENICIA: Flux in-depENdent fIeld-aligned CoordInate Approach, in which we implemented the FCI approach described in Section 4. A sketchy description of this new code is given in Appendix A. The actual implementation of the parallel derivative depends on the scheme of choice. In the following, we consider second order centered finite differences, since they are used to solve the drift-wave test model  (2). Note that the use of finite differences is not a limitation. In particular, in the case of a kinetic model, the implementation of a semi-Lagrangian scheme for the parallel dynamics exploiting the same ideas is also possible. In FENICIA, one defines any field at nodes in the Cartesian (x, y, z) grid. Derivatives in the poloidal plane are computed in this reference frame by holding z constant.
This procedure is faster than the usual spline approach which requires the solution of a linear problem, and not less accurate. Accuracy also depends on the scale length of the function. For a function characterized by a wavenumber k and represented by N points in a given box, a simple scaling argument based on replicating the number of boxes shows that the actual error scales like (k/N) 4. We compared the maximum error given by the above interpolation scheme to the one given by linear interpolation, by a MATLAB cubic spline interpolation routine, by a 4th order Hermite interpolation with non-centered evaluation of derivatives and a 4th order Hermite interpolation with an exact value of the derivatives. The errors given by the different interpolation schemes are presented in Fig. 5. We show that the 4th order Hermite cubic interpolation with 4 points centered derivatives (solid red line with no marks) is as accurate as the 4th order MATLAB cubic spline interpolation.
Testing the ability of the code to simulate sound waves with a small toroidal resolution We now show that the code FENICIA is able to simulate driftwave propagation with high accuracy even when the mode number in the toroidal (z) direction exceeds the Nyquist cutoff N z /2. Tests were carried out for both Eq. (  28 ) and the full model of Eq. (  2 ). In the latter case, setting ρ * to zero allows one to obtain analytic solutions of the wave propagation, which turns out useful for testing purposes. For the density, we employ initial conditions of the form: N 0 = g 0 (r) × cos(mθ -nϕ), (40) with g 0 (r) = exp  - (r -r s ) 2 r 2 s m 2  ×  r r s  m ×  r -a r s -a  2 (41) where r s is the position of the rational surface such that q(r s ) = m/n. The equilibrium density profile is such that log(n 0 ) = - 1 2L n (r 2 -a 2 ), (42) in the full model  (2).
The method requires interpolation in the poloidal plane. To this end, Hermite cubic interpolation with direct computation of the derivatives at the control points is employed. Tests illustrate that this choice is as accurate as cubic splines but more efficient in terms of computational resources. Tests using the newly developed code FENICIA were carried out on the problem of spurious (numerical) diffusion of zonal fields, and on the problem of drift-wave propagation. The zonal field test shows that the numerical diffusion rate due to the new method is negligible with respect to the evolution rate of actual physics processes of interest. The wave propagation tests show that the error per unit time due to the computation of parallel derivatives with the new method is sub-dominant with respect to the error due to second order algorithms commonly used to treat the perpendicular dynamics, such as the Arakawa scheme.
Acknowledgments Fruitful discussions with  P. Tamain  and  A. Ratnani  are gratefully acknowledged. FH also acknowledges useful comments of G. W. Hammett ,  C. S. Chang  and  J. Candy  during the IPAM workshop on '' Computational Challenges in Magnetized Plasma '' at  UCLA (April 2012 ) and would like to thank most sincerely  Y. Sarazin ,  X. Garbet ,  Y. Peysson  and  X. Litaudon  for their help, support and insightful suggestions. This work, supported by the  European Communities  under the contract of Association between EURATOM and CEA, was carried out within the framework of the  European Fusion Development Agreement. The views and opinions expressed herein do not necessarily reflect those of the  European Commission. Part of this work was also supported by the  ANR  contract  E2T2.
NUCLEAR DATA PRODUCTION The nuclear data library JEFF3. 1. 1 contains most of the photon production data. Nevertheless, some data were missing (no photon production for all neutron interaction for Gd, Cd, Ag, In, which are nuclei of particular interest for JHR and PWR, no spectrum of the prompt gamma emitted by fission of 239, 241 Pu) or inconsistent ( 54,56,57,58 Fe, 62 Ni)  [3] , or based on quite old measurements (prompt fission gamma emission of 235 U). A new evaluation for radiative capture and inelastic scattering is proposed. These data are performed with the nuclear reaction code TALYS using a level density model and a strength function model to describe the transition probabilities. A nuclear structure library is also needed (RIPL2. 0 by default or the compilation of latest measurements performed at the Budapest facility EGAF and the ENSDF library).
For example, the 54 Fe analysis shows that the total gamma emission energy after a radiative capture is underestimated for more than 50%. At the end, 16 nuclei have been checked and new prompt gamma spectra from neutron radiative capture are proposed for the next beta version of JEFF (MF6-MT102 standards)  [4]. As it has been shown on figure  1 , the main contribution to the inner core gamma heating is coming from the fission reaction. It is also well known that even in the most recent nuclear data libraries (JEFF3. 1. 1, ENDF/B-VI. 8 and JENDL3. 3) gamma production data for the prompt gamma emitted in fission are lacking or based on quite old measurements. For the main fissile isotopes ( 235 U, 239 Pu), the prompt gamma spectra were measured in the early 70's and great discrepancies are observed between the obtained measurements.
Since that time, very little work has been devoted to the prompt gamma production from fission even if new measurements have been or will be done. Moreover, the fission process is highly complex to be described by theoretical models (spin 04001-p. 2 WONDER-2012 distribution and excitation energy) and even today, no qualified model is available for evaluation purpose. Nevertheless, a Monte Carlo code (FIFRELIN) dedicated to the simulation of the fission fragment de-excitation is being developed at CEA-Cadarache  [5]. A specific module based on the de-excitation gamma cascade simulation which needs a density level distribution model associated to a strength function, has been developed for the prompt fission gamma emission simulation  [6]. Preliminary results have been obtained for a one nucleus de-excitation ( 55 Mn radiative capture, deexcitation of 144 Ba) and 252 Cf spontaneous fission.
The integral experiment called PERLE has been performed in EOLE facility. It is a regular PWR type core, with 3. 7% enriched UO 2 pins surrounded by a 22 cm thick stainless steal reflector. Some TLD have been positioned inside the core and the reflector to measure the gamma KERMA. One of the purposes of PERLE program is to estimate the gamma heating in a heavy reflector for EPR TM. The stainless steal is a Fe, Ni, Cr alloy. The nuclear data library fails in giving accurate evaluation for photon production of Fe isotopes and 62 Ni (see chapter 2). The PERLE experiment will allow qualifying new data evaluations for these isotopes  [3]. Moreover, a recommended method for the total gamma heating one step calculation will be developed with The Monte Carlo simulation code TRIPOLI-4 © with the objective to evaluate directly the deposited energy within the whole geometry.
Conclusion During the last few years many programs have been supported especially for new generation reactor: EPR TM (GENIII + ) and MTR-JHR. One of the subjects of interest was the measurement of gamma heating for checking nuclear data evaluations which are obviously failing for some isotopes of very high importance (Fe, Hf, Al, Be). Different programs dedicated to improve the measurement methods (ADAPH + in MINERVE, CARMEN-1 in OSIRIS) and the nuclear data for photon production (PERLE and AMMON in EOLE) have been planed. All these works are linked and have to be developed using the progress of each others. They are still under study by the way of PhD works started since 2009 which are presented in this paper. The role of the Gamma Heating Working Group is to make exchange easier between students and to enlarge the public to others research group (CEA,DEN,DTN, Mc Master University from Canada, University of Marseille-Provence).
The multiphasic responses were partially recovered after wash-out. (B) Simulation of the neuron model with SK versus control experimental data (dashed lines). On/Off neurons (n = 6) were recorded for different stimulus durations (100 ms to 1 s, a single puff of the pheromone blend at 1 ng). The On duration depended linearly on stimulus duration: On duration = 0. 996(stimulus duration) +18 ms (Pearson correlation r 2 = 0. 97). The inhibitory phase was constant (p = 1, Kruskal-Wallis test): I duration = 3996106 ms. The neuron model (Text S1) was simulated with inputs mimicking a 1 ng pheromone blend stimulus (200, 500 or 1000 ms duration; 10 runs in each condition), resulting from fits of experimental data recorded in olfactory receptor neurons in vivo.
Electrophysiology (Recording and Data Analysis) Experiments were done on 5-day-old male moths A. ipsilon Hufnagel (Lepidoptera: Noctuidae). MGC neurons were recorded extracellularly by means of glass microelectrodes filled with Tucson ringer as described earlier  [41]. Moths were stimulated with a pheromone blend of three main components: cis-7dodecenyl acetate (Z7-12:OAc), cis-9tetradecenyl acetate (Z9-14:OAc) and cis-11-hexadecenyl acetate (Z11-16:OAc), in the ratio of 4:1:4. Stimulation of the antennae was controlled by a stimulation device (CS35, Syntech). The signal was amplified (IDAC 2000 amplifier, Syntech), band-pass filtered between 0. 3 and 5 kHz and sampled at 16 kHz. The activity of nearby neurons was recorded using the Autospike software (v3. 7, Syntech). Spike sorting was achieved with the R-package SpikeOMatic  [42].
All other data analyses and statistical tests were done in Matlab (The MathWorks, Inc. , Natick, MA, USA). Unless specified otherwise, data are presented as mean6s. d. The On response was identified   5B ). To allow realtime processing, the Off detection was not performed explicitly: we simply considered that the On was followed by the Off. (C) Search distance of 2step versus 1-step strategy (p,0. 01, Mann-Whitney test). doi:10. 1371/journal. pone. 0061220. g006 using the segmentation method described in Text S1. The spike timing jitter s (in ms) and the fraction of non-coincident spikes r were calculated with the stochastic event synchrony (SES) algorithm  [43]. Significance levels were determined by statistical comparisons with s* and r* obtained on shuffled trials (shuffling trials destroys within-trial temporal correlations while preserving interspike interval distribution).
Cyborg Experiments Tethered moths Agrotis ipsilon were mounted on a Khepera III robot (K-Team) and the EAG was recorded from a whole-insect preparation (Fig. 4A ). The insect was immobilized inside a styrofoam block allowing the head to protrude. For electrical contact, the last 2-3 segments of one antenna were cut-off. The recording electrode, a glass pipette filled with (in mM) 6. 4 KCl, 340 glucose, 10 Hepes, 12 MgCl 2 , 1 CaCl 2 , 12 NaCl, pH 6. 5, was maintained in contact using a micromanipulator (Narishige, UN-3C). A silver wire inserted into the neck served as the reference electrode. An EAG acquisition board was developed and embedded on the robot with appropriate processing. The EAG signal was transmitted via WIFI to a remote computer (dual Core laptop 1. 6 GHz running Linux) and used as input to the neuron model.
This work was funded by the  Agence Nationale de la Recherche , within the  French-British ANR-BBSRC  initiative (grant  BSYS-006  ''Pherosys''), by the state program Investissements d'avenir managed by  ANR  (grant  ANR-10-BINF-05  ''Pherotaxis''), and the  European Bio-ICT   convergence  project (grant  FP7-216916 ''Neurochem'' ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Such as automatic logistics system, automatic verification and seal technology, and a series of national laboratory had been built, which formed a systemic and complete precise management to the electric power meter. However, there were problems such as inadequacy of the status management to the on-site meter especially the gateway meters device, lack of efficient monitoring and management to the on-site electric stealing. Considering all the issues above, Electric Power Research Institute of Chongqing Power Electrical Corp. gets organized to develop a set of gateway electric power meters device status management system, which used Windows Server 2008 as its operational system platform, Oracle database management system and VS. NET system as its development tools, adopted n tiers system architecture and reusable component technique to realize automation, intelligent online monitoring and maintenance.
The trial operation tests of the system were performed in more than 20 220 kV substations in Chongqing, the result showed that the system combines with the front-end hardware to form an multifunctional and multi-purpose electric power metering analysis research platform, which had the function of electric power meters and test, data analysis and data collecting, chart drawing and so on of high capacity and can be extended for database support. This system adopts b/s architecture. The structure diagram of the system is as shown in Figure  1.
Architecture of the system The system adopts ASP. NET to realize b/s architecture, to operate on access scheme of the electric power system ORACLE database and the client resources, which is used for management on the status of metering device, the operation of the metering device and GPS information. In addition to such advantages that ASP. NET can run faster than the traditional ASP, has server controls, and is easier for writing code in adopting 'code-behind' method, the advantage of the ASP. NET is that it is available for the real-time update of application program, it is available for dynamic compilation files when necessary and can save the compilation result for reusing the subsequent requires. ASP. NET can also automatically detect errors (such as memory leaks, deadlock) and renew them to make certain of the availability of application program.