dataesr/scientific-paragraphs-categorization huggingface dataset:
Implementation RepeatsDB was designed with a multi-tier architecture, using separate modules for data management, data processing and presentation functions. To simplify development and maintenance, all tiers handle the common JSON (JavaScript Object Notation) format, thereby eliminating the need for data conversion. The MongoDB database engine is used for data storage and Node. js as middleware between data and presentation. RepeatsDB exposes its resources through RESTful web services, by using the Restify library for Node. js. The Angular. js framework and Bootstrap library were selected to provide the overall look-and-feel. Angular. js to Bootstrap integration is available through the angular-ui project. A customized version of the BioJS (44) sequence component is used as sequence visualizer.
USING REPEATSDB The user interface presents an intuitive tree-based browsing mechanism, where the root of the tree is the full database, second-level nodes repeat classes and third-level nodes subclasses. When clicking on a node, the user is presented with the list of RepeatsDB entries corresponding to the selected category. Each row of the list shows basic information about the entry, like its entry ID, title and organism. All annotated chains corresponding to an entry are displayed in a single page. The user interface presents a structure and sequence visualization widget (Figure  1 ). The user may choose to visualize the structure in four static images, or by using the 3D visualizer. If the entry features detailed annotations, the repeat regions, units and/or insertions are displayed using a combination of colours.
The sequence visualization widget displays the sequence and secondary structure corresponding to the structure. It displays the same colour as the structure visualization widget, associating repeat annotations in the structure and sequence views. Additional information at the structure and chain levels is also provided. The RepeatsDB search toolbar, available on top of every page, allows to search for entries either by database IDs or UniProt text query. The database ID search allows comma-separated PDB or UniProt IDs. The UniProt text search query uses the full UniProt search engine, see online documentation. RESTful web services are directly accessible through HTTP URLs. All data available on RepeatsDB are also available for programmatic access. Please refer to the 'Help' section of the website for details on using the RepeatsDB web services.
Statistics Analysis of the full PDB dataset yielded 10 745 repeats predicted by RAPHAEL, of which 2797 were finally classified into the RepeatsDB schema. Table  1  shows the distribution between classes and subclasses. The bulk of the annotations (90%) consist of entries belonging to classes III and IV. No effort was made to balance the distribution of entries between classes in this initial release. As coverage increases in the future, we expect the balance to approximate the real distribution more closely, although it may be necessary to fine-tune RAPHAEL. Of the classified entries, 321 representatives of the entire dataset were annotated in detail with information about the start and end of repeat regions, repeat units and/or insertions (Table  1 ). It is interesting to note the different distribution of insertions between classes.
CONCLUSIONS AND FUTURE WORK RepeatsDB's goal is to provide the community with a resource for high-quality tandem repeat protein structure annotations. The user can either interactively analyse his proteins of interest via the user interface, or create and download datasets for offline use. Far from being a static classification process, the annotation effort for the initial RepeatsDB dataset alone already motivated the extension of the original classification schema  (14). Some of the curated structures, while clearly representing structural repeats, did not belong to any of the pre-defined subclasses. To allow them to be classified, subclasses IV. 5 (a/b prism) and IV. 6 (a-barrel) were added to the initial schema  (14). Class V also underwent a re-classification according to the secondary structure content of the single domain repeats ('beads') to allow a broader classification range beyond individual repeat families, as the list of possible beads-on-a-string folds may be considerably larger than currently appreciated.
The 'other' subclass was also added to allow collection of repeats that do not fit into the current classification scheme. RepeatsDB provides the community with a previously unavailable opportunity to easily create datasets of tandem repeat proteins. The detailed annotation subset further presents a unique opportunity to better understand the nature of tandem repeat proteins. Beyond its initial release, RepeatsDB is a continuous effort to expand, revise and improve tandem protein repeat annotations. Predictions for new PDB structures are simple and fully automated, allowing regular database updates every 3 months. Manual curation of new entries for inclusion is also ongoing, aiming at regular and steady updates. Options to involve the community into the annotation process through crowdsourcing tools are currently being analysed.
ACKNOWLEDGEMENTS The authors are grateful to  Diego Ferreiro  for insightful discussions and to  Manfred Sippl  for his software tools. FUNDING FIRB Futuro in Ricerca [RBFR08ZSXY] and  AIRC  [MFAG 12740] (to S. T. ); AIRC research fellow (to G. M. ) and CONICET PhD student (to R. G. P. );  Ministry of Education and Science of the Russian Federation , project  8831  (to A. V. K. ) (in part). Funding for open access charge: FIRB Futuro in Ricerca [RBFR08ZSXY].
We describe further development of a previous laboratory prototype pulsed cavity ring-down spectroscopy (CRDS) sensor into a field-deployable system for hightime-resolution, continuous, and automated measurement of gaseous elemental mercury (GEM) concentrations in ambient air. We employed an external, isotopically enriched Hg cell for automated locking and stabilization of the laser wavelength on the GEM peak absorption during measurements. Further, we describe implementation of differential absorption measurements via a piezoelectric tuning element for pulse-by-pulse tuning of the laser wavelength onto and off of the GEM absorption line. This allowed us to continuously correct (at 25 Hz) for system baseline extinction losses unrelated to GEM absorption. Extensive measurement and calibration data obtained with the system were based on spike addition in both GEM-free air and ambient air.
Challenges and interferences that occurred during measurements (particularly in ambient air) are discussed including temperature and ozone (O 3 ) concentration fluctuations, and steps taken to reduce these. CRDS data were highly linear (r 2 ≥ 0. 98) with data from a commercial Tekran 2537 Hg analyzer across a wide range of GEM concentrations (0 to 127 ng m -3 ) in Hg-free and ambient air. Measurements during periods of stable background GEM concentrations provided a conservative instrument sensitivity estimate of 0. 35 ng m -3 for the CRDS system when time averaged for 5 min. This sensitivity, along with concentration patterns observed in ambient air (with the CRDS system and verified with the Tekran analyzer), showed that the sensor was capable of characterizing GEM fluctuations in ambient air.
3. 2); automation of data acquisition and real-time signal processing at 50 Hz (Sect. 3. 3); and configuration of the system for field deployment (Sect. 3. 4). We then show extensive measurements and GEM spike additions in both Hg-free and ambient air in the urban airshed of Reno, Nevada, compare results to data obtained with a Tekran 2537 sensor, and discuss interferences for CRDS measurements in ambient air (Sect. 4). 2 Pulsed cavity ring-down spectroscopy and other methods to measure GEM.
23;  Spuler et al. , 2000). The peak of the 200 Hg absorption corresponded well to the peak of the ambient pressure GEM absorption (i. e. , the peak that should be present in the measurement cavity when operated under ambient air conditions). Therefore, we used this 200 Hg low-pressure cell to precisely position and control the laser wavelength during measurements. Maintaining the laser wavelength on the peak absorption of the 200 Hg cell was automated with a custom LabVIEW control program. A set of commands was implemented to continuously correct for slight drifts in laser wavelength (which are inherently caused by mechanical instabilities due to temperature and other changes). The program minimized the PD Hg /PD Ref ratio by changing the laser wavelength in small increments (0. 0002 nm) using a grating tuning element: if moving in one direction caused a decrease in PD Hg /PD ref ratios (i.
3 nm to its second harmonic of 253. 65 nm. After the differential measurement setup was finalized, we noticed that the frequency conversion efficiency of online and offline measurements changed through time, which caused large drifts in differential extinction measurements as online and offline measurements were affected differently by these drifts. As a result, we had to implement a mechanism to continuously adjust the FCU position in order to maintain equal wavelength conversion efficiencies for both wavelengths of the differential measurements. We implemented a function in our LabVIEW control program to adjust the FCU position to reduce the difference in signal power to less than about 2 % of the signal voltage between the online and offline signals measured by the PD Ref.
Signal acquisition, automated signal processing, and calculation of GEM concentrations In our system, energy from laser pulses in the cavity leaks out through the back mirror of the cavity where signals are captured by a photomultiplier tube (PMT; Model H6780; Hamamatsu, Japan). A CompuScope data acquisition card (Com-puScope 12100, GaGe, Lockport, Illinois, USA) is used to digitize the analog signal, which is then processed in real time by our custom LabVIEW CRDS program (Fig. 2a ). The exponential ring-down of each laser pulse (at 50 Hz pulse repetition rate) is quantified by 200 measurement points recorded with an acquisition rate of 1 MS s -1. Each acquisition is initiated by the laser Q-switch trigger signal synchronizing signal acquisition with laser pulses. Since the first few data points of each ring-down signal showed non-exponential decay patterns, possibly caused by an incomplete match between transverse beam and cavity modes, we eliminated the first 15 points of each ring-down.
3. 2). Unexpectedly, we found that the presence of O 3 concentrations still caused significant interference during measurements as evident in inverse relationships between O 3 concentrations and differential extinction (Fig. 5c ). Possible reasons for this interference are that high (> 10 ppb) O 3 concentrations that cause strong extinction losses (∼ 2000 Mm -1 ) Fig. 7. Ambient air measurement for 1. 5 h and comparisons of GEM measured by the CRDS system and a Tekran 2537B Hg analyzer (in ng m 3 ) with 1-2 ng m -3 GEM spike additions. ) and a commercially available GEM sensor (GEM concentrations in ng m -3 ) that operates with a 2. 5 min time resolution. The graph shows the whole dataset of measurements made in ambient air with spikes at various concentrations of GEM using a GEM permeation source.
In Fig. 8 , we show a longer term dataset of GEM concentration measurements with occasional GEM spike additions performed during 10 days of measurements. This dataset shows larger differences between CRDS measurements and corresponding Tekran GEM measurements compared to results of spike additions shown in Figs. 3  and 6. Statistical analysis showed that differences between the CRDS and Tekran measurements for a total of 73 h of measurements were within 0. 1 ng m -3 for 12 % of the data, within 0. 2 ng m -3 for 23 % of the data, within 0. 5 ng m -3 for 43 % of the data, and within 1. 0 ng m -3 for 63 % of the data. The increased variability observed during multiple days of observations is attributed to instability of the CRDS sensor through time. To confirm this, we analyzed the data using Allan variance, a method that summarizes variability in temporal data as a function of the time integration period  (Werle et al.
Acknowledgements. We would like to thank  Nicholas Nussbaum  for software development,  Rick Purcell  for technical assistance and engineering,  Luke Arnone  for technical help,  Roger Kreidberg  for editorial assistance,  Mike Crumb  for technical laser assistance, and the facilities crew at the  Desert Research Institute  for assistance with the mobile trailer setup. This system development and study were supported by a  US National Science Foundation Major Instrumentation (NSF MRI)  grant (Award Number:  0923485 ) and an  NSF  grant from the  Division of Atmospheric and Geospace Sciences  (Award Number:  1101924 ). Edited by:  P. Werle.
The reflected intensity is measured by an amplified Si-photodiode (New Focus 2001) placed after the beam splitter. This "back signal" is a superposition of the transmitted light from the second, opposing fiber tip and the reflection from the tip and, if applicable, the trapped particle. Fiber tips are mounted on two sets of xyz translation stages : piezoelectric translation stages (PI P620) with sub-nanometer resolution and 50 µm range, and inertial piezoelectric translation stages (Mechonics MS 30) with ≈ 30 nm step size and up to 2. 5 cm range. Transverse transmission intensity maps are recorded by scanning one fiber tip in a plane perpendicular to the tip axes. The entire set-up is controlled by homemade software in the LabView environment. A homemade microscope with a ×50 objective (Mitutoyo) coupled to a CMOS camera (Thorlabs) is used for visualizing the trapped particles.
Commercial 1 µm polystyrene spheres (Corpuscular) are used for trapping in aqueous suspension with 0. 125 mg/mL concentration. Light power at the end of the fiber tips is measured by means of a power meter. Transmission measurements between two identical fiber tips indicate that the fiber-to-fiber transmission is about 3 times more efficient in water than in air. Thus, for the trapping measurements a correction factor of 1. 73 is applied to the measured intensity. All values given in this paper are measured and corrected intensities at the end of one single fiber tip. An automatic particle tracking software is developed in the open source Scilab environment in order to exploit trapping videos with more than 3 × 10 5 frames. The program detects the center of the particle surface in each frame.
Acknowledgments Funding for this project was provided by the  French National Research Agency  in the framework of the  FiPlaNT  project ( ANR-12-BS10-002 ). Authors thank  Jean-Francois Motte  for the elaboration of the applied fiber tips. Helpful discussions with  G. Colas des Francs ,  G. Dantelle , and  T. Gacoin  are gratefully acknowledged.
Electrophysiological recordings Multi-unit activity (MUA) was recorded using a commercial amplifier (MEA-1060-inv-BC; MCS, Reutlingen, Germany) with frequency limits of 150-3,000 Hz and a gain of X1,024. Data were digitized using a data acquisition board (PD2-MF-64-3M/12H; UEI, Walpole, MA). Each channel was sampled at a frequency of 16 k samples/s. Data processing was performed using a Simulink-(The Mathworks, Natick, MA, USA) based xPC target application (see ref. [16]  for details). We added 6 mM bicuculline-methiodide to the bathing solution, and given that the dissociation constant is around 5 mM  [17]  this was assumed to block most of the inhibitory transmission. We used a total of seven recordings, each one corresponding to a different culture: one 2h-recording, four 1hrecordings, two 1/2h-recordings.
Acknowledgments We are greatly indebted to  Shimon Marom  and  Netta Haroush , from  Technion  at the  Israel Institute of Technology , who provided us with the experimental data. We would also like to thank  Dan Goodman  and  Romain Brette  for having developped the efficient and user-friendly Brian simulator [25], as also for their excellent support,  Mikail Rubinov  for sharing his implementation of the Kolmogorov-Smirnov statistical test for power-law distributions with us,  Tom Morse  and ModelDB [49] for distributing our code, and finally  Michael Kolkman  (http://helice. nl)for his excellent language polishing work.
This work was funded by the  European Union   Seventh Framework Program  ( FP7/2007-2013 ) under grant agreements no. 269459  (Coronet). GD was also supported by the  ERC  Advanced Grant: DYSTRUCTURE (n. 295129), by the  Spanish Research  Project  SAF2010-16085 , and by the  CONSOLIDER-INGENIO  2010 Program  CSD2007-00012. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Studies dealing with the use of physical joint in multibody dynamic simulation are of growing interest. In multibody simulation, real cylindrical or spherical joint have been used  [11, 12]. A recent work proposes a model of planar deep groove ball bearing that can be used in planar multibody system  [13]. The purpose of this study is to introduce a non-planar dynamic model of non-lubricated ball bearing with clearance which can be used in dynamic simulation of M. G. B. This model is directly integrable in multibody dynamic simulations. Its utilization is not limited to simplified shaft architecture as could be specialized codes for bearing simulation  [14]. Also, specialized codes for gearboxes simulation are often limited to quasi-static analysis. Some of them, as RomaxDESIGNER c , propose a coupling with an external multibody dynamic software.
6) makes HAT-P-26 b a less favorable target for follow-up studies. GJ 3470 b therefore presents an ideal opportunity to investigate the internal structure, atmospheric composition, and possible formation pathways of low-density Neptune-size planets (e. g. ,  Rogers et al. 2011). All transit photometry available so far for GJ 3470 has been collected from the ground. While these time-series confirm the transiting nature of GJ 3470 b, they do not precisely constrain the transit parameters, resulting in poorly determined planetary properties. We present in this paper the analysis of two transits of GJ 3470 b obtained with the Spitzer Space Telescope at 4. 5 µm in the frame of our DDT program  (Demory et al. 2012b ), submitted shortly after GJ 3470 b's discovery. These data yield a significant refinement of the system parameters.
Spitzer IRAC 4. 5-µm photometry We observed two consecutive transits of GJ 3470 b at 4. 5 µm using Spitzer's InfraRed Array Camera (IRAC;  Fazio et al. 2004 ). Observations took place on 11 June 2012 and 15 June 2012 UTC as part of our DDT program PID 80261. For each transit we obtained 780 sets of 64 subarray frames each, with an exposure time of 0. 40 s per frame. Each Astronomical Observation Request (AOR) lasted 6. 5 hours, including 30 minutes overhead for the Pointing Calibration and Reference Sensor peak-up sequence. This step allowed GJ 3470 to be precisely slewed on the position of maximum sensitivity on the 4. 5µm channel subarray field-of-view  (Ingalls et al. 2012; Demory et al. 2012a). All data were processed by the Spitzer pipeline version S19. 1. 0, which produced the basic calibrated data necessary for our reductions.
We first convert fluxes from the Spitzer units of specific intensity (MJy/sr) to photon counts, and transform the data timestamps from BJD UTC to BJD TDB following  Eastman et al. (2010). We then perform aperture photometry on each subarray image using the APER routine from the IDL Astronomy User's Library 15. We compute the stellar fluxes in aperture radii ranging between 1. 8 and 4. 0 pixels, the best results being obtained with an aperture radius of 3 pixels. We use background annuli extending from 11 to 15. 5 pixels from the Point Response Function center. For each block of 64 subarray images, we discard the discrepant values for the measurements of flux, background, and x-y centroid positions using a 10-σ median clipping for the four parameters. We then average the resulting values, the photometric errors being taken as the uncertainties on the average flux measurements.
WIYN Speckle Observations We supplemented our GJ 3470 b Spitzer photometry with speckle observations to explore the possibility of blended companions at close angular separations from GJ 3470. Speckle observations of GJ 3470 were obtained at the WIYN 3. 5-m telescope on 2 December 2012. The camera used was the Differential Speckle Survey Instrument, which is described by  Horch et al. (2009). It is a dual-channel instrument that records images in two colors simultaneously. In the case of this observation, the filters used had center wavelengths of 692 nm and 880 nm, with filter widths of 40 and 50 nm, respectively. A speckle sequence of 3000 50-ms frames was taken on the target, followed by 1000 frames taken on a bright point source (HR 3163) located near in the sky to GJ 3470. These latter data are used as an estimate of the speckle transfer function for deconvolution in the reduction process.
The final model and phase-folded Spitzer light curves are displayed in Figure  3. We find for GJ 3470 b a radius of R p = 4. 83 +0. 22 -0. 21 R ⊕ , which is 13% larger than previously reported in the literature. This increase is driven mainly by the larger stellar radius from Sect. 4. Combining the planetary radius with the mass M p = 13. 9 +1. 5 -1. 4 M ⊕ that relies on the radial-velocity data set yields a very low planetary density of ρ p = 0. 72 +0. 13  -0. 12 g cm -3 , which is 33% smaller than the estimate in the discovery paper. These planetary parameters are also listed in Table  2. Finally, we performed a new fit for the purpose of as-sessing the robustness of the orbital period determination for GJ 3470 b, which in our solution is constrained both by the two Spitzer transits and the radial velocities.
Support for this work was provided by  NASA  through an award issued by  JPL/Caltech. The  WIYN Observatory  is a joint facility of the  University of Wisconsin-Madison, Indiana University, Yale University , and the  National Optical Astronomy Observatory. Support for LAR was provided by  NASA  through  Hubble Fellowship grant   HF-51313. 01-Aawarded by the  Space Telescope Science Institute , which is operated by the  Association of Universities for Research in Astronomy, Inc. , for  NASA , under contract  NAS 5-26555. This work was supported by the  European Research Council/European Community  under the  FP7 through Starting Grant  agreement number  239953  and by  Fundação para a Ciência e a Tecnologia (FCT)  in the form of grants  PTDC/CTE-AST/098528/2008  and  PTDC/CTE-AST/120251/2010.
The financial support from the  "Programme National de Planétologie" (PNP)  of  CNRS/INSU, France , is gratefully acknowledged. GT acknowledges partial support for this work through  NSF  grant  AST-1007992. VN would also like to acknowledge the support from the  FCT  in the form of the fellowship  SFRH/BD/60688/2009. MG is Research Associate at the  Belgian Fonds National de la Recherche Scientifique (FNRS). Facilities: Spitzer, Magellan, WIYN.
This paper presents the formal definition of a domain-specific language, named Pantagruel, following the methodology proposed by David Schmidt for language development. This language is dedicated to programming applications that orchestrate networked entities. It targets developers that are professionals in such domains as building management and assisted living, and want to leverage networked entities to support daily tasks. Pantagruel has a number of features that address the requirements of the domain of entity orchestration. Furthermore, Pantagruel provides high-level constructs that make it accessible to developers that do not necessarily have programming skills. It has been used to develop a number of applications by non-programmers. We show how the user-oriented programming concepts of Pantagruel are expressed in the denotational semantics of Pantagruel.