dataesr/scientific-paragraphs-categorization huggingface dataset:
Peptides ions were analyzed using Thermo Xcalibur (version 2. 0. 7) using the following data dependant steps: (1) full MS scan with a 300 to 1400 m/z range in the Orbitrap with a resolution of 15,000; (2) fragmentation by CID in the linear trap with a normalized energy at 35%. Step 2 was repeated for the three most intense ions with a minimum intensity of 500. Dynamic exclusion was set to 30 seconds. Raw files were converted to the mzxml format using msconvert (3. 0. 9576 http://proteowizard. sourceforge. net/tools. shtml). Database search was performed using X!tandem JACKHAMMER  (Craig and Beavis, 2004). Tolerance was set to 10 ppm for precursor ions and 0. 5 Th for fragment ions. Cys-carboxyamidomethylation was set to static modification. Methionine oxydation, Nter acetylation of proteins, glutamine Nter deamidation and glutamic acid Nter water loss were set to variable modifications.
Three databases were used: the Spodoptera frugiperda  (Smith)  EST database (http://www. ncbi. nlm. nih. gov/nucest version 2015, translated in the six reading frames and filtered to a minimum of 80 amino acids; 392,538 entries); the Zea mays database (from maizegdb, version v5a; 136,770 entries) and a standard contaminant database (55 entries). Identified peptides were filtered using X!tandemPipeline v3. 3. 4  (Langella et al. , 2016)  with the following criteria: peptide E-value less than 0. 03, minimum 2 peptides per protein, protein E-value less than 10 -4. Unassigned spectra were subjected to de novo identification using denovopipeline v1. 5. 1 (http://pappso. inra. fr/bioinfo/denovopipeline/), that allows the selection of unassigned spectra of good quality and their submission to pepnovo (v2010117, Frank 2005).
Spectrum quality score was set to 0. 2 and pepnovo score to 70. De novo sequences were then aligned to the same databases as for X!Tandem search using Fasts. v36. 06  (Mackey et al. , 2002). Proteins with a homology score less than 10 -4 were validated. The biological and analytical reproducibility were addressed by a quantitative western blot (see next section). Identified EST sequences obtained from digested peptides were submitted to a BLAST procedure (BLASTX, NCBI). The resulting protein was characterized by the name, the source and the molecular weight and a E-value/log E-value coverage. In order to calculate the coverage per cent of a peptide, the EST sequence was translated into a protein sequence using the Expasy Translate tool (http:// www. expasy. org/tools/dna. html).
5 ). In Drosophila, tricholine citrate ensures a good electrical contact and inhibits the water cell  (Wieczorek and Wolff, 1989). Taste responses were recorded for 2 s and were performed under a microscope (Z16 Apo, Leica France). Electrodes Translation; sampling rate = 10 kHz, 16 bits), stored on computer, and analysed using dbWave  (Marion-Poll, 1996). Spikes were detected and analysed using software interactive procedures of dbWave. We evaluated the action potential frequency by counting all spikes occurring during the first second of recording. The responses to the following stimulants were recorded extracellularly and compared using 30 mM tricholine citrate (all compound tested were suspended into this solution to inhibit the gustatory neuron to water) as control: -oral secretion of C.
Statistical analysis The Marascuilo's procedure was used to separate the percentages of wasps that exhibited positive responses (i. e. antennation + stinging attempts)  (Marascuilo, 1966). For bioassays with known proteins, the percentage of positive response was calculated from a group of 5 wasps replicated 6 times (i. e. n=6). A non-parametric Kruskal-Wallis test was applied with type of proteins as factor. ANOVA was not used because none of the data were normally distributed and had homoscedastic variance. Following Kruskal-Wallis test, a pairwise Wilcoxon's rank sum test was conducted with false discovery rate (FDR) correction for multiple testing. Comparisons among sensilla chaetica responses towards oral secretions of Chilo partellus and different proteins were conducted using one-way analysis of variance (ANOVA) with the Tukey's contrast test for multiple comparisons between means.
Database search allowed the identification of two distinct maize proteins with 5 and 2 peptide sequences, respectively, while de novo sequencing allowed the identification of 22 peptides that matched to accession gi|295290041|gb|FP379314. 1|FP379314| of the S. frugiperda database of mid gut cDNA sequences (Supplementary Table  1 ). The protein sequence blasted significantly with α-amylase superfamilies (Fig. 2 ). The confirmation of α-amylase assignation of the electrophoretic band no 4 was done by western blot analysis (Fig. 3 ). The anti-α-amylase of D. melanogaster linked mostly with the band no 4 (≈ 50 kDa) of the oral secretion of C. partellus and with that extracted from the gel. The activity elicited by different α-amylases from different origin, including α-amylase of D. melanogaster, confirmed the involvement of this enzyme in C.
Acknowledgements The authors whish to thank the  University of Nairobi  and icipe capacity building for hosting the PhD student. Thanks are given to  Julius Obonyo  and  Peter Malusi  for rearing the host insects and the parasitoids; and to  Peter Ahuya  and  Kevin Sambai  for their technical assistance in collecting the oral secretions and some behavioural assays, all from icipe. Thanks are also given to  Fritz Schulthess  for his review of the manuscript.
The 22E films were more rough and not entirely uniform even at 3000 and 4000 RPM. The measured surface roughness is included as error in Tab. 1. In the remaining part of this study, we used the thinnest and most uniform PAAD samples produced at 4000 RPM. For these samples, the profilometer estimates of the layer thickness were independently verified by the ellipsometry measurements. Figure  3  shows the result of the complex refractive index measurements of the PAAD 22D films in the spectral range from 300 to 1400 nm determined by ellipsometry. The ellipsometry data in the spectral region between 800 -1400 nm were fitted using a Cauchy model  [32]  in order to evaluate the thicknesses of the thin films. The complex refractive index n + ik of the PAAD films were evaluated using Lorentz oscillator  [33]  and B-spline  [32]  models, which have been widely applied for the calculation of refractive indices.
, 2016; Salese, Di Achille, Neesemann, Ori, & Hauber, 2016; Wilson, Howard, Moore, & Grant, 2016) , recent findings stated MFF is partly Hesperian-aged  (Kerber & Head, 2010; Tanaka et al. , 2014; Zimbelman & Scheidt, 2012). With the main aim, firstly, to provide a detailed cartographic base and, secondly, to bind the geographic distribution, the stratigraphic relations and ultimately the evolution of the sedimentary deposits of the Aeolis Dorsa region, we produced a geological map (Main Map) at the 1:430,000 scale, using multiple datasets including altimetry and visible images at various spatial resolutions (e. g. from 50 m pixel -1 to 25 cm pixel -1 ). Our mapping partly matches the  Kite et al. (2015)  division, butin order to reflect Journal of Map's spirit here we present a Main Map that shows the geological framework of Aeolis Dorsa attempting a 'two-scales analysis approach', e.
Datasets Visible imagery at different scale was used to reconstruct the stratigraphy of the studied region. High Resolution Stereoscopic Camera (HRSC) images (12. 5-25 m pixel -1 )  (Jaumann et al. , 2007; Neukum & Jaumann, 2004)  were used for morphological interpretations at a regional scale. The Context (CTX) camera (6 m pixel -1 )  (Malin et al. , 2007)  and the High Resolution Imaging Science Experiment (HiRISE) camera (25 cm pixel -1 )  (McEwen et al. , 2007)  provided detailed images which were useful to reconstruct stratigraphic relationships. Visible images were used in association with altimetry data at different scales, such as the Mars Orbiter Laser Altimeter (MOLA) dataset  (Smith et al. , 1999)  at ∼463 m pixel -1 , digital elevation models (DEMs) constructed from HRSC stereo images at ∼50-150 m pixel -1 , and CTX and HiRISE DEMs with the minimum gridding of 6 and 1 m pixel -1 , respectively.
Software CTX and HiRISE DEMs were processed to produce stereo pairs using the NASA Ames Stereo Pipeline  (Broxton & Edwards, 2008; Moratto, Broxton, Beyer, Lundy, & Husmann, 2010) ; CTX stereo pair images were then radiometrically corrected and projected using the USGS software ISIS (Integrated Software for Imagers and Spectrometers). All data were integrated into the Arc-GIS platform (v. 10. 2. 2) and co-registered in the geographic coordinate system for Mars with a sinusoidal map projection (central meridian 155,0).
Stripe loss during ontogeny occurs multiple times in Amphiprion The observation that A. frenatus juveniles have more stripes than adults prompted us to further document the evolution of ontogenetic trajectories of color pattern in clownfishes. For this, we compiled ontogenetic information on 26 Amphiprion species with a multi-tiered approach utilizing the primary literature, online databases, and field observations made by various experts (Additional file 1: Table  S1 ). We observed that a minimum of nine species show extra stripes during the juvenile phase when compared to adult. This is illustrated on Fig. 5  for four species: A. frenatus, A. melanopus, A. rubrocinctus, and A. ephippium. This contrasts with other cases (e. g. , A. nigripes or A. sandaracinos; Fig. 5e, f  ) for which the number of stripes is invariant over ontogeny.
Phylogeny, ancestral state reconstruction, and stochastic mapping We used stochastic character mapping  [54]  to infer possible histories of the stripe pattern and stripe pattern ontogenesis. The stochastic mapping and the ancestral state reconstruction was produced using the function make. simmap in the package phytools (version 0. 5. 38; [55] ) for R  [56]. We then sampled 10,000 character histories allowing the incorporation of the uncertainty associated with the timing of the transitions between morphological states. For the parameterization of make. simmap, we used the estimated ancestral state and the best model for the transition matrix from our empirical data. To assess the best model for the transition matrix, we fitted a model with equal rate of transition between states and a model with all rates different using the function ace in the R-package ape  [57].
Model of striped pattern evolution To test whether the evolution of striped patterns is not random in clownfishes, we compared transition rates between stripe morphs using the "multiple state speciation extinction" (MuSSE) method. MuSSE is an extension of the BiSSE maximum likelihood-based test, which is described in  [28, 29]. To test our hypotheses, we used the R-package diversitree  [29]  to compare the fit of four different models: (i) a model in which all transition rates vary independently, (ii) a model with an equal rate transition matrix (e. g. , q 14 = q 41 ), (iii) a model in which the loss or the acquisition of two stripes by evolutionary color shift is not allowed (i. e. , q 31 = q 41 = q 42 = q 13 = q 14 = q 24 = 0), and (iv) a model combining the constrains of model (ii) and model (iii).
Ecological and morphological data Our morphological analysis includes body elongation, body size, and dorsal fin morphologies. Maximum body size was retrieved from Fishbase  [59]. Body elongation and dorsal fin morphology quantifications were determined using pictures of Amphiprion sp. individuals found in Fishbase  [59]  or nicely provided by J. E. Randall (http://pbs. bishopmuseum. org/images/JER/) and J. Williams. Others were studied in the marine vertebrate collections of S. Planes (CRIOBE) and Museum of Natural National History (MNHN). This analysis includes 22 species over the 30 described species (Additional file 1: Table  S1 ). The species A. chagosensis, A. latezonatus, A. leucokranos, A. mccullochi, A. pacificus, and A. sebae are not studied here because of the lack of individuals for quantifications.
To quantify body elongation, we used the ratio between body height and the standard length. In order to describe the ingression between the anterior and the posterior lobe of the dorsal fin, we calculated two indexes based on the length of the third dorsal spine (l1), the length of the most posterior spine (l2), the length of the longest soft ray (lr), and the length of the dorsal fin (L). Anterior and posterior lobe morphology indexes correspond to (l1-l2)/L and (lr-l2)/L, respectively (Fig. 6e ). Ecological data (i. e. , number of host sea anemones) were retrieved from FishBase  [59]  and the primary literature  [33, 60].
Relationships between striped patterns and fish morphology Body size and body elongation describe the overall fish shape, and it has been shown to be linked with swimming performance and with adaption towards different macro-habitats  [35, 36]. Dorsal fins are associated with stability and thrust  [61] , and their shape may thus provide information on the swimming behavior of clownfishes. We predicted that the striped pattern of clownfishes is related to ecological and behavioral differences, and thus, phylogenetic generalized least-squares (PGLS) regressions using a Brownian motion model were used to test for correlated evolutionary relationships between the number of stripes and the forms of fish body and dorsal fin. PGLS analyses were performed in the R-package geiger (version 2. 0. 6; [62] ).
Funding Our clownfish husbandry has been supported by the CNRS (interdisciplinarity actions) as well as EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-02. BF was funded by the "Fonds National de la Recherche Scientifique of Belgium" (F. R. S-FNRS) and the Belgian Science Policy Office (Belspo).
Acknowledgements We thank  V. Logeux ,  N. Trouillard , and  P. Romans  for fish husbandry and  G. R. Allen ,  J. E. Randall ,  J. Williams ,  S. Planes , and the  Museum of Natural History of Paris (MNHN)  for sharing pictures or clownfish collections. We also thank  N. Salamin ,  M. Besson , and  T. Lorin  for the critical discussions concerning the manuscript.
Microscopy DIC micrographs were taken with a Zeiss AxioImager. M1 equipped with 40X and 100X objectives. For measurements of hyphal length, cells were fixed with 70% ethanol, then pelleted and resuspended in 2% H 2 SO 4 to reduce cell clumping. Lengths were measured with the Axiovision software measuring function. The person performing the measurements was blinded to the identity of the cultures. Statistical analysis of cell size distributions (t-test, regression analysis) was performed using Microsoft Excel's analysis package. For visualization of Pan1-GFP, cells were fixed by addition of formaldehyde to 2% and incubating 10 min at 30 • C in a roller. The cells were then washed twice with phosphate-buffered saline (PBS), separated by repeated aspiration through a 29G needle and resuspended in Vectashield mounting medium.
Stress-based multiaxial fatigue life prediction method A fatigue post-treatment tool based on the Dang Van criterion  [11]  is implemented by using a Python script in order to analyse the fatigue behaviour of the spot welded steel sheet specimens. A multiaxial fatigue criterion has been used since the stress states are multiaxial in stress concentration zones (Fig. 12 ). The Dang Van criterion in  its first version (1973) is the first fatigue criterion introduced in the French industry (PSA Group). In this criterion, Dang Van postulates that crack initiation may occur in the most unfavourable oriented grains, which was subjected to a plastic deformation even if the bulk stress is elastic. This criterion is constructed on a microscopic approach to fatigue behaviour and the research for a critical shearing plane.
Comprehensive stress-strain material property characterisation was then undertaken, extending to the isothermal cyclic tests necessary to calibrate the mixed isotropic-kinematic material hardening models required for accurate weld residual stress prediction. Parallel residual stress measurement and simulation round robins were performed by a large number of participants from around the world. Residual stresses were measured using neutron and high energy synchrotron diffraction, surface X-ray diffraction, surface and deep hole drilling, the contour method, and ultrasonics. Neutron diffraction measurements were made at eight different instruments. The diffraction measurements database alone is large enough to generate reliable mean profiles, to identify clear outliers, and to establish that there is no statistically significant difference in the residual stress field in the specimens used for the non-destructive measurements.
TG4 materials characterisation The AISI 316L(N) plate used for NeT TG4 has very similar physical and mechanical properties to the plate used for NeT TG1. The materials testing performed to support TG4 thus concentrated on the monotonic tensile and isothermal cyclic behaviour for both the parent AISI 316L (N) plate and the AISI 316L TIG weld metal. All other materials data were obtained from the database assembled for NeT TG1. A detailed materials compendium was compiled, comprising approximately 180 Mb of test data. Clearly space does not permit its inclusion in this paper.
Monotonic tensile properties Only room temperature tensile tests were performed on the TG4 AISI 316L(N) material. These revealed behaviour very similar to the NeT TG1 material, so TG1 data obtained at temperatures up to 750 °C were also supplied to participants in NeT TG4. These detailed test data were supplemented by simplified proof stress vs. temperature data derived for TG1 that extended up to the melting point of 1400 °C. The simplified data are presented in Table  8  and Fig. 11 , while the full test data are listed in Table  10. Tests have been performed on ER316L TIG weld metal made using welding wire of the same specification used for TG4, although not the same batch. Several different processing histories were used to produce weld metal suitable for testing, namely: • Material extracted from a multi-pass weld pad, and tested in the as- welded condition • Material extracted from a multi-pass weld pad, and tested after so- lution heat treatment • Material extracted from two-pass welds laid into grooves (the minimum number of passes that produced sufficient weld crosssectional area to manufacture test specimens), and tested in the aswelded condition • Material extracted from the same two-pass welds, and tested after solution heat treatment The processing history has a marked effect upon the tensile properties of weld metal, discussed in detail in another paper in this special issue  [44].
Isothermal cyclic test data AISI 316L cyclically hardens strongly, and its mechanical behaviour during welding is best described using mixed isotropic-kinematic material hardening models  [36, 39, 40, 48, 49]. Isothermal cyclic test data are required to fit the parameters in mixed hardening models. Cyclic testing was performed on both the parent plate material and on solution-treated two-pass TIG weld metal. The test parameters (strain rate and strain range), were chosen to be relevant to the expected response during welding, using the recommendations in the weld modelling guidelines incorporated into the R6 structural integrity assessment procedure  [8]. These in turn were based upon a large internal research programme conducted by EDF Energy, one of the TG4 participants  [50]. The full test matrix is given in Table  10 , and extended up to 700 °C, above which AISI 316L ceases to cyclically harden.
Residual stress measurements round robin The measurement round robin commenced in 2009. To date, the reported measurements include high energy synchrotron X-ray diffraction measurements made on two specimens at the European Synchrotron Radiation Facility in Grenoble  [40, 51, 52] , neutron diffraction measurements performed at eight different facilities (including several re-measurements), deep hole drilling and incremental deep hole drilling measurements on two specimens, transverse and longitudinal   contour method measurements on a number of specimens, and ultrasonic measurements. This is believed to be the largest measurements database ever developed on a welded benchmark specimen. The diffraction measurements database (listed in Table  11 ) is large enough to generate reliable mean profiles, to identify clear outliers, and to establish that there is no statistically significant difference in the residual stress field in the two specimens used for most of the non-destructive measurements.
The full field synchrotron X-ray diffraction measurements made at ESRF  [40, 51, 52]  used a spiral slit technique to make measurements at 861 individual locations within a TG4 specimen, and recovered the entire residual stress field in the TG4 specimen, see Fig. 13  and Fig. 14. The value of the diffraction measurements database lies in its size and in the care with which it was constructed. Here we consider only sample results on a through wall line at the centre of the TG4 specimen, identified as line BD, see Fig. 15. Measured stresses in all three stress directions obtained using diffraction techniques are plotted in Fig. 16 , which shows: • Individual measured data, with the uncertainties declared by the participating laboratory (usually, but not always, the fitting error for the raw diffraction peaks).
The laboratories are anonymised, but the measured specimen is identified, and the instrument used may be found from Table  11. • The best-estimate measured profile, calculated using techniques originally developed in Ref. [26]. • An uncertainty of ± one standard deviation on the best estimate. The best-estimate calculations employed a simplified approach that has been shown to achieve similar outcomes to a full Bayesian "duff data" analysis  [26, 53, 54]. The arithmetic mean at each measurement location was evaluated, followed by the deviation of each individual datum from the mean. Outliers were then eliminated if they deviated by more than ± 70 MPa from the mean. The final mean was then recalculated using non-censored data. Uncertainties were evaluated after first adjusting each measurement dataset for systematic uncertainty by subtracting the average of its residuals from the individual data.
The standard deviation at each position was then evaluated using residuals after correction for systematic uncertainty. The calculated uncertainties in the final best estimates are of order ± 20-40 MPa, and are largest near free surfaces and in "pass 1" weld metal (weld metal with three thermo-mechanical load cycles). The final best-estimate profiles have very small normal stresses, which is as expected and an encouraging outcome. While this low level of final uncertainty is very encouraging, it is based upon analysis of a large dataset, and it is evident from Fig. 16  that the uncertainty in individual measurements is higher. The measurements may be classified as "consensus + outliers". The first set of measurements made at ENGIN-X were withdrawn. Separate records were kept of the stress-free reference specimens used for each measurement.
Limited measurements were made at NPI, but not delivered to the TG4 project. There were two clear outlier datasetsthe SALSA measurements, which have unrealistic normal stresses, and an initial set of measurements at ENGIN-X, which were "clearly outliers" and were withdrawn. However, it is noteworthy both that some of the "consensus" measurements fall outside the best-estimate uncertainty band, and that the true uncertainty of any single set of measurements is usually greater than the fitting uncertainty normally quoted. Structural Integrity Assessment procedures such as R6  [8]  recommend that residual stresses are measured using both diffraction and strain-relief methods, since they tend to have different characteristic errors. Good agreement between such independent techniques is deemed to be strong evidence of reliable measurements.