dataesr/scientific-paragraphs-categorization huggingface dataset:
Radouani and Anselmetti  [3]  proposed methods for identifying geometric surfaces based on a solver without the hypothesis of small displacements. Weber et al. [4]  introduced a unified linear approximation technique for use in evaluating the forms of straightness, flatness, circularity and cylindricity. Nonlinear equation for each form is linearized using Taylor expansion, then solved as a linear program using software written in C++ language. Huang  [5]  developed a method to show that straightness and flatness errors can be obtained without the construction of the whole convex hull. Samuel and Shunmugam  [6]  presented techniques for evaluating circularity and sphericity errors from CMM data. They evaluated the form errors directly from CMM data by employing circle/sphere as assessment features and using normal deviations.
In addition, a comparison is made between the flatness results estimated by the three association criteria (minimum zone (MZ), least squares and minimum volume). A recommendation on the measuring points number and the criterion to be used will be given. 2 Criteria for fitting a perfect mathematical surface to a cloud of points Minimum zone is the standard criterion that is used for evaluating the form defect of a surface; it is also known as the Chebyshev criterion. Indeed, for the same distribution of sampled points, this criterion leads to the smallest value, as compared to the other fitting criteria. Nevertheless, this is not the criterion used by default by the software that suggests at least two others: the LS criterion; the outer or inner matter shell criterion. With the least squares method, a uniform distribution of points over the entire surface is required  [9].
The LS criterion leads to a surface fitted in the "middle" of the sampled points, which means that the points are on the outer side of the matter with respect to the adjusted surface and the others are inside. Some software suggests the option of shifting this adjusted surface to the outermost point, but this action does not change the measured form defect. The outer or inner matter shell criterion is essentially proposed for palpated circles and cylinders. In this case, it is a matter of maximizing or minimizing the diameter of the circle or the cylinder under the condition that the adjusted surface is on the outside or inside of the matter. This criterion is normalized in order to take the centre of a circle, the axis of a cylinder, or the centre of a sphere as reference. Regarding the plane, some software packages propose fitting algorithms capable of giving planes adjusted on the external side of matter with respect to the points, so that these planes can again be used as a reference, because as everyone knows, the MZ criterion may lead to fittings that are not representative of the actual surface, as it was illustrated by Pairel  [11]  on a "ski-shaped" surface, as shown in Figure  1.
Practical aspects The Z-coordinate of the nodes on the various surfaces was divided by 10 in order to have a plausible form defect with regard to their size (76 Â 76 mm 2 ). Then, it was decided to remove one node out of two in order to obtain the definitions 8 Â 8, 4 Â 4, 2 Â 2 and finally 1 Â 1. The coordinates of these nodes were formatted and saved in text files that are understandable by the GEOVERIF software, which was used to calculate the planes adjusted on each definition of each distorted plane, and according to each criterion, this gives 7 Â 5 Â 3 = 105 adjustments.
Results Biochemical characterization of PfCCT catalytic domain construct. In order to provide structural insights into the mechanism of action of PfCCT, we set out to crystallize the constitutively active C-terminal catalytic domain of PfCCT. Several constructs were tested and our attempts were successful only in case of PfCCT (581-775) that corresponds to the exact region visible in the crystal structure of RnCCT (PDB: 3HL4)  20  (Fig. 1a ). While this construct proved to be highly crystallogenic, activity assays revealed its reduced catalytic rate together with an increased K M for CTP as compared to the longer construct PfCCT (528-795) used in our previous studies  16  (Table  1  and Supplementary Fig. S1 ). We further assessed the functionality of PfCCT (581-775) by characterizing its substrate and product binding ability.
Structure of the free PfCCT C-terminal catalytic domain. The structure of PfCCT (581-775) was determined at 2. 2 Å resolution by molecular replacement using RnCCT structure  20  (PDB: 3HL4) as a search model (Table  3 ). The enzyme forms a globular dimer with an α/β Rossmann fold that is well conserved in CCTs and other members of the cytidylyltransferase enzyme family (Fig. 1b ). Here, the homodimer state likely mimics the full-length PfCCT conformation with two almost identical catalytic sites. The dimerization interface of PfCCT is mediated by inter-molecular contacts between several structural elements of each chain. Residues of helix αC of one chain are in contact with residues of loop L3′, helix αA' and helix αE' of the other chain (Fig. 1c, d ). In addition, residues of helix αE contact residues of helix αE' and loop L2′.
The differences observed for CDPCho binding to PfCCT or to the RnCCT-mimicking construct may be interpreted by a slightly more constrained CDPCho interaction in the wild-type PfCCT enzyme. This is also supported by the reduced flexibility of the nucleotide binding pocket in the CDPCho-PfCCT structure in comparison to the CDPCho-RnCCT structure (PDB: 3HL4), as suggested by B-factor values.
Discussion Prior to our study, only two high resolution structures of CCT catalytic domain and six structures of members of the Rossmann-folded cytidylyltransferase enzyme family were available from the Protein Data Bank. These include ECT (CTP:phosphoethanolamine cytidylyltransferase) and GCT (CTP:glycerol-3-phosphate cytidylyltransferase) catalytic domain structures that together with CCT share the conserved fold architecture as well as some key active site residues comprising the RTEG(I/V)ST(S/T) and HxGH signature sequences. All these enzymes are specialized in the cytidylyl transfer reaction with a hallmark of exploiting basic residues for substrate coordination and catalysis  31, [33] [34] [35]. The herein presented structural data complemented with biochemical characterization provide an unprecedented step-by-step view of the enzymatic cycle of PfCCT.
Meanwhile, K663 moves to coordinate the P α group in addition to the P β group of CDPCho that originated from ChoP, allowing the phenolic OH of Y714 to coordinate P β moiety (Fig. 5 ). K663 may also be involved in the formation of a productive ES 1 S 2 ternary complex and in the catalytic step. Its position and function during the transition state remains to be resolved. It may either coordinate nucleophile phosphate of ChoP or provide a bridge between the two phosphate moieties directly involved in catalysis, a conformation apparent in CDPCho liganded PfCCT and RnCCT structures and reminiscent of the position of K46 in GCT  34. So far no CCT structure complexed to CTP is available. Structural insights of related GCT:CTP  36  and ECT:CTP (PDB: 4XSV) complexes reveal that the serine and threonine residues corresponding to T761 and T762 of PfCCT participate in the coordination of CTP phosphate moieties.
For CTP and CDPCho titrations of PfCCT (528-795) K663A, and CTP titrations of T761A and T762A variants of PfCCT (528-795) , mean and SD from two independent experiments are provided, whereas for CDPCho titrations of PfCCT (581-775) and PfCCT (528-795) mean and SD from three independent experiments are provided. For PfCCT (528-795) (Y626F/Q636A), errors of model fit to data of a single ligand binding experiment are given. 2D 1 H NMR Spectroscopy. NMR experiments for the assignments of the flexible part of PfCCT (581-775) were recorded at 283 K on a Bruker 700 MHz NMR spectrometer equipped with a cryogenic 5 mm Z-gradient probe head. The aqueous samples were containing 0. 5 mM unlabeled PfCCT (581-775) in 20 mM Tris/HCl pH 7. 5, 150 mM NaCl and 2 mM EtSH in 10% D 2 O as an internal lock. Two-dimensional 1 H-1 H TOCSY (isotropic mixing: 60 ms) and 1 H-1 H NOESY (mixing time: 200 ms) were performed for the assignments of the backbone and aliphatic side chain 1 H resonances.
Water suppression was achieved with the WATERGATE sequence  42  in both experiments. NMR spectra were processed using GIFA software  43. Crystallization and diffraction data collection. 10 mg/ml of PfCCT (581-775) with 20 mM of CDPCho (final protein concentration 8 mg/ml) in the lysis buffer were screened by commercially available Classics screen (NeXtal, Qiagen) by sitting drop method. 200 nl sitting drops were set up using a 1:1 ratio between protein and precipitant in 96-well Greiner crystallization plates using a Cartesian dispensing robot  44. After one month crystals of protein-CDPCho complex appeared in 0. 2 M NaF, 0. 1 M HEPES pH 7. 5, 20% PEG 3350 at 20 °C. The ligand-free PfCCT crystals were grown by the hanging-drop vapor-diffusion method at 4 °C by mixing 1 µl of protein solution at concentration of 10 mg/ml and 1 µl reservoir solution (0.
Crystals appeared after one week and were left to grow for an additional three weeks. Crystals were mounted and soaked in oil as cryosolvent, then frozen in liquid nitrogen. Diffraction data were collected at beamlines ID29, ID23-1 and ID23-2 of the European Synchrotron Radiation Facilities in Grenoble, France. These crystals belong to space group I 222 with the asymmetric unit containing one monomer in the case of the free, CMP-bound, ChoP-bound and Cho-bound forms, and six monomers in the case of the CDPCho-bound form. Structure determination and refinement. The indexing and integration of obtained data sets were carried out using XDS (Pilatus)  45, 46. The scaling, merging and calculating of structural factor amplitudes were executed using programs TRUNCATE  47  and SCALA  48  from CCP4 software  49.
Crystal structures were constructed by molecular replacement using Phaser  50  with RnCCT (PDB: 3HL4) and free PfCCT (PDB: 4ZCT) as search models, followed by model building in Coot  51. The structure refinements were done using REFMAC 5. 8. 0073  52, 53  and PHENIX 1. 9. 1692  54. Molecular graphics representations were created using PyMol  55. All the ligand structures were created using PRODRG server  56. Crystal diffraction data and final refinement statistics were summarized in Table  3. Accession codes. Atomic coordinates and structure factors for the reported crystal structures have been deposited in the PDB under ID codes 4ZCT, 4ZCP, 4ZCQ, 4ZCR and 4ZCS for the free, CMP-, Cho-, ChoP-and CDPCho-bound PfCCT, respectively.
Acknowledgements This work was supported by the  French Agence Nationale de la Recherche  ( ANR-09-BLAN-0397 ) and by the  National Research, Development and Innovation Office  ( K109486 ,  K119493 ), the  Hungarian Academy of Sciences Medinprot program  and  ICGEB CRP/HUN14-01. The authors thank the support of collaboration visits by the  French-Hungarian Bilateral S&T Cooperation  ( TÉT_14_FR-1-2015-0024 ). This work was also supported by the  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INBS-05. EG was funded by the  European Commission   FP7 Marie-Curie Initial Training Network "ParaMet " [grant number  290080 ]. Financial support from  ÚNKP-16-2  to FHa is gratefully acknowledged. The authors also acknowledge the  European Synchrotron Radiation Facilities (Grenoble, France)  for provision of synchrotron radiation facilities and we are grateful to staff scientists for assistance in using the beamlines ID29, ID23-1 and ID23-2.
Here we propose a 1D full-deconvolution, regularized, non-parametric inverse problem algorithm that enforces smoothness and uses constraints of causality and positivity to estimate the Water Residence Time curve. Compared to Bayesian non-parametric deconvolution approaches, it has a fast runtime per test case; compared to the popular and fast cross-correlation method, it produces a more precise Water Residence Time curve even in the case of noisy measurements. The algorithm needs only one regularization parameter to balance between smoothness of the Water Residence Time and accuracy of the reconstruction. We propose an approach on how to automatically find a suitable value of the regularization parameter from the input data only. Tests on real data illustrate the potential of this method to analyze hydrological datasets.
In fact, rainfall datasets have long range memory properties and therefore we simulate the input rainfall for synthetic tests as a multifractal signal  Tessier et al. (1996). One important difference from other non-parametric deconvolution methods is that we enforce causality explicitly through projection. We also discuss the importance of this aspect to avoid a sub-optimal solution when using a Fourier Domain based convolution  McCormick (1969). In  Neuman et al. (1982) ;  Dietrich & Chapman (1993) ;  Delbart et al. (2014)  the causality constraint was not mentioned. In  Skaggs et al. (1998) ;  Cirpka et al. (2007) ;  Payn et al. (2008) ;  Gooseff et al. (2011) , causality is taken into account through a carefully constructed Toeplitz matrix for the convolution operation. We propose a new algorithm to estimate the residence time with the following properties: • passive: only input rainfall and output aquifer levels are required; • flexible: in the sense that it handles even unexpected solutions (double peaks or unexpected shapes of the residence time).
Implementation Details We provide a distribution package in Matlab for our algorithm and the download link can be found at the end of this article. Although in the previous sections the model and the solution are written in matrix form, the Matlab implementation of the convolution for our AM algorithm is done through dot product multiplication in the Fourier Domain with appropriate zero padding, meaning that no Toeplitz matrix is explicitly defined here for the convolution. It is also possible to carefully implement a causal convolution by designing a proper Toeplitz matrix. However, the convolution in the Fourier Domain appears to be more efficient in general. This implementation also allows for the estimation of a k residence time longer than the inputs x and y, although this would be under-determined.
The AM algorithm is consistently faster than the  Cirpka et al. (2007)   The tests on real data are conducted on data sets made available from the "Base de Donnes des Observatoires en Hydrologie" c  Irstea, Irstea (2017). The data is gathered in the Ile de France region, in France. The measurements are from two neighboring sites, one at a higher altitude for rainfall measurements and the second at a lower altitude for aquifer measurements, taken at every 1 hour intervals, between January 1 st , 2016 until January 1 st , 2017. For the real data, the estimates are based on the λ corrCoe f f strategy with λ s chosen around the optimal values found with the synthetic data set, between 10 8 to 10 2. In Figure  12  and in Figure  13 Figure  13 : Same as in Figure  12. In all cases, the estimated curves honor the given positivity and causality constraints.
We find small but significant changes in the residence time curve for different data sets of the same channel, as also identified in other datasets  Delbart et al. (2014). This may be due to the seasonal variability of the inputs (rainfall) and its effects on the hydrological process. This aspect would be of interest to study into more detail for specific sites to better understand it. Another observation to be made is the fact that if non-linearities of the system are present (in transit or at the aquifer level), our approach may also lead to over simplification. Nonetheless the question arises if a hydrological channel could be considered as a linear and stationary system by parts (smaller time series) and therefore allow the use of our method for estimating partial residence time curves which can then be put together in a more complex mapping of the channel.
Conclusion We propose a new approach to estimate a smooth residence time taking into account positivity and causality constraints and having a fast runtime. We highlight why these constraints must be used all along the algorithmic process to reach the expected solution in the case of non-parametric 1D deconvolution for the AM algorithm presented here. The estimation of the residence time k est was done using a fast Alternating Minimization algorithm with two steps: (1) 1D deconvolution and (2) estimation of the aquifer initial level. All tests have been done on a personal laptop, with CPU Intel(R) Core(TM) i7-6600U CPU @ 2. 6GHz 2. 81 GHz, 16. 0 GB RAM, 64-bit OS, x-64-based processor, using Matlab R. We validated the approach on synthetic tests and proposed several strategies to automatically estimate a hyper-parameter, λ , that controls the smoothness of the residence time curve.
Acknowledgments We thank the  Base de Donnes des Observatoires en Hydrologie  for providing the data acquired in the field. c Irstea, BDOH ORACLE c , July 24, 2017. We thank  Prof. Olaf A. Cirpka  at  the department for Hydrogeology, Universtät Tübingen, Germany , for kindly providing the algorithm referenced in Cirpka et al. (2007). We thank  Amine Hadjyoucef  and  Christian Kuschel  for carefully proof-reading this text and offering us their comments about unclarities and English phrasing. We also want to thank the editor and the reviewers for their constructive questions and observations throughout the reviewing process. This work is supported by the  Center for Data Science , funded by the  IDEX Paris-Saclay ,  ANR-11-IDEX-0003-02. We acknowledge support from the  "Institut National des Sciences de l'Univers" (INSU) , the  "Centre National de la Recherche Scientifique" (CNRS)  and  "Centre National d'Etude Spatiale" (CNES)  and through the  "Programme National de Plantologie " and  MEX/PFS Program.
We consider the prospects of probing features in the primordial power spectrum with future Cosmic Microwave Background (CMB) polarization measurements. In the scope of the inflationary scenario, such features in the spectrum can be produced by local nonsmooth pieces in an inflaton potential (smooth and quasi-flat in general) which in turn may originate from fast phase transitions during inflation in other quantum fields interacting with the inflaton. They can fit some outliers in the CMB temperature power spectrum which are unaddressed within the standard inflationary ΛCDM model. We consider Wiggly Whipped Inflation (WWI) as a theoretical framework leading to improvements in the fit to the Planck 2015 temperature and polarization data in comparison with the standard inflationary models, although not at a statistically significant level.
The Wiggly Whipped Inflation (WWI) has provided a framework for classes of model with primordial features which improves the fit to the Planck 2015 data with respect to the power law model  [8, 9]. These features can be localized on certain scales or they can represent wiggles over a wide range of cosmological scales. Within the WWI framework, we consider inflationary phase transitions where the scalar field rolls from a steeper potential into a nearly flat potential through a discontinuity in the potential or in its derivative. We obtained five types of features that provide a ∆χ 2 ∼ 12 -14 improvement, compared to the power law, in the fit to the Planck data, with the addition of 2-4 extra parameters depending on the model. These features help improve the fit to the Planck 2015 temperature and polarization anisotropies separately and in combination.
Several reconstruction of the PPS from the CMB have demonstrated  [18]  the hints of suppression of power and oscillations at large and intermediate scales  ( 40)  and sharper oscillations that continues to small scales. As mentioned before, given the uncertainties in the CMB data associated at different scales, while these features are not statistically significant, they are interesting because of following three reasons: firstly, some of these features are consistently present since WMAP observations  [19] [20] [21] [22] ; secondly, Planck temperature and polarization observations jointly support these features; and finally, within a single framework of inflation, WWI, these three classes of features can be generated at the required cosmological scales  [9]. The main goal of this paper is to investigate what a future concept for space mission dedicated to CMB polarization can tell about the existence of features as generated by a temporary violation of the slow-roll condition during inflation.
Also this parametrization does not allow unphysical reionization histories. We consider a monotonic increase in neutral hydrogen fraction with redshift and we provide the constraints with Planck 2015 data and the forecast for CORE capabilities. We also discuss the degeneracy between the reionization history and a particular shape of large scale power spectra supported by Planck data. The paper is organized as follows: in section 2 we review the WWI potential. We first summarize the features that are supported by Planck 2015 data  [9] , we introduce a minor change in the WWI parametrization with respect to previous treatments. In section 3 we provide all the necessary details for the analysis and present the results. In the reionization dedicated part 4, we discuss the different parametrizations, both the commonly used model and the one utilized in this paper.
We use publicly available CAMB and COSMOMC for our analysis. The codes are modified in order to incorporate the WWI through BINGO and the new reionization history. In standard Tanh reionization scenario, we use the baryon density (Ω b h 2 ), cold dark matter density (Ω CDM h 2 ), the ratio of the sound horizon to the angular diameter distance at decoupling (θ) and the optical depth (τ ) as free parameters. Note that the standard nearly instantaneous reionization history is described by one parameter τ. These four parameters will be common to all the analyses in this paper. When using real data from Planck 2015 release we will allow also the foreground and nuisance parameters to vary according to the Planck likelihood set up. Extra parameters corresponding to inflationary models and reionization used in this paper will be mentioned in the subsequent sections.
CORE specifications We now describe the methodology we use to forecast the capabilities of a concept for a future CMB space mission as CORE to constrain the primordial origin of the features. As fiducial cosmologies, we choose the WWI best-fits of the Planck 2015 temperature and polarization data  [9]. We perform the CORE forecasts as described in  [26, 27]. We use an inverse Wishart likelihood with an effective noise sensitivity and angular resolution obtained from an inverse noise weighted combination of the central frequency CORE channels whose specifications are: We assume that systematic effects are subdominant and that foreground contaminations are kept under control by the lower 6 (down to 60 GHz) and higher 7 (up to 600 GHz) frequency channels  [24, 25]. In addition to temperature and polarization anisotropies, we consider the CMB lensing potential power spectrum C PP , which an experiment like CORE will be able to reconstruct up to the scales where linear theory is reliable.
Forecasts for primordial features The results for the WWI models with Planck 2015 data, although in a slightly different form, were presented in  [9]. In the following results we use the best fits of  [9]  as fiducial values for the CORE simulated data. Though in this paper we use a slightly modified form with respect to  [9] , note that since the latter is nested in the more general form used here the local best fits will not change; a simple change of variable translates the old best fit parameters to the modified parametrization. 1. Background and inflationary parameter constraints WWI projected for CORE. For WWI potential we present the constraints on the parameters when CORE data is simulated using the four local best fits to the Planck data. For WWI potential also we provide the constraints expected from CORE.