dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular networks of LC-MS/MS data were created using the GNPS data analysis workflow (https://gnps. ucsd. edu/ProteoSAFe/status. jsp?task=42443130e8a5451dbad8963736b803d7). The default parameters were used for molecular networks except for the following: a precursor mass tolerance of 0. 1 Da and a MS/MS fragment ion tolerance of 0. 1 Da to create consensus spectra. Molecular networks were visualized using CYTOSCAPE 3. 3. 0 [27]  (electronic supplementary material, figure  S5 ). The MS/MS spectra were searched against GNPS's spectral libraries and others including Massbank, ReSpect, HMDB and NIST14. Detected features were considered a match to known spectra when they had a cosine score above 0. 7, at least six matched peaks and less than 20 ppm of relative error.
(h) Statistics For all experiments, the area under the curve of 'PAF C16' (m/z 524. 371) and 'Lyso-PAF C16' (m/z 482. 361) was calculated manually using the DATA ANALYSIS software (Bruker Corporation, MA, USA). The abundances of PAF and Lyso-PAF were normalized to a standard (amitriptyline) abundance per sample as well as the individual mass per sample. Samples from the time-course experiment were normalized to the dry mass of the lipid extract. Pairwise comparisons for the UVR and field interaction experiments were made on raw data using a t-test for normally distributed data and the non-parametric Mann -Whitney U-test for non-normally distributed data. Datasets with more than two groups were analysed with analysis of variance (ANOVA) following a log transformation in order to achieve normality (e.
The samples were associated to the corresponding 3D coordinates using the OPTIMUS workflow to create a csv file. The 3D model and the corresponding MS/MS data were visualized using 'ili toolbox (https://github. com/MolecularCartography/ili). Graphing and statistical analyses were performed using GRAPHPAD PRISM 6 (GraphPad Software, San Diego, CA). The midline represents the median. The 3D model and csv file were uploaded as part of the MSV000080662 submission to GNPS. ( j) Bioinformatic identification of enzyme homologues involved in platelet-activating factor mode of action Human protein sequences of the PAF receptor (GI: 298581) and protein kinase C (GI: 4506067) were used with tBLASTn to query a coral transcript database generated from transcripts sequenced and described earlier  [10].
Acknowledgements. The authors thank the husbandry team of the  Birch Aquarium at Scripps , with a special thanks to  Sean Bruce ,  Ryan Schaeffer  and  Fernando Nostratpour. The authors also thank  Susan Kram  for laboratory assistance and  Javier Jara  for assistance in the field in Panama. The authors offer a special thanks to the  Smithsonian Tropical Research Institute in Bocas del Toro, Panama  for the use of their facilities.
An important finding is that we established an epigenetic signature associated with H2Bac in the hippocampus of cognitively deficient tauopathic mice. Very few studies investigated histone acetylation in pathological context at the genome-wide level. Our recent studies showed selective decreased H3K27ac at neuronal identity genes regulated by a super-enhancer, in the striatum of Huntington's disease mice  (Achour et al, 2015; Le Gras et al, 2017). In the hippocampus of the CK-p25 AD mouse model, H3K27ac levels were decreased at promoter/enhancers of genes associated with synapse and learning functions and preferentially bound by CBP  (Gjoneska et al, 2015). Our data show for the first time a significant alteration of H2Bac levels in mice bearing AD Tau hallmarks. As H3K27ac levels between THY-Tau22 and WT mice were unchanged, we suggest that H2Bac loss may be an early mark of a disease state in the hippocampus.
Statistics For behavioral data, we have used a sample size to more than 10. Exclusion/inclusion criteria: Outliers were defined as results differing from the mean by 3 SD. Stressed mice were defined upon ethical criteria: stayed immobile in the cage or showed aggressive behavior. A floating behavior in the Morris water maze was defined as a floating during more than 30s/assay of 60s. These mice were excluded from the experiment and usually represented on average 1 per experiment. One-or two-way ANOVA was used for data analysis with repeated measures when appropriate. Escape latencies recorded during acquisition were analyzed using ANOVA, followed by Newman-Keuls multiple-comparisons test when appropriate. For the probe tests, the time spent in the target quadrant was compared with the chance level (15 s for a test duration of 60 s in four quadrants) using a one-sample Student's t-test.
Real-time qRT-PCR analyses Samples with OD 260/280 and OD 260/230 ratio close to 2. 0 were considered for cDNA synthesis. 0. 5-1 lg of total RNA was reverse-transcribed (iScript cDNA synthesis kit; Bio-Rad). Bio-Rad iCycler System (CFX) was used to perform qPCR using SsoAdvanced SYBR Green SuperMix (Bio-Rad). A specific standard curve was performed in parallel for each gene, and technical duplicates were performed. The conditions for qRT-PCR were 3 min at 94°C, followed by 40 cycles of 45 s at 60°C and 10 s at 94°C. Data were analyzed by gene regression using iCycler software and normalized to housekeeping genes (RNA polymerase II, 36B4) levels.
Statistics for biochemical studies For these studies, we have tried to always have n values > 5. For Western blot studies comparing WT to THY-Tau22 mice, inclusion was verified by performing an immunostaining against a pathological form of Tau protein (Tau5, Tau-Ph404). All samples were used until exhaustion which explains some variability in the number of Western blot samples (n = 5-7). For RT-qPCR validation experiments, all samples (n = 5) were included. All statistical analysis involving three groups (WT, THY-Tau22 CSP, and THY-Tau22 CSP-TTK21) were performed using ANOVA followed by uncorrected Fisher's for multiple-comparisons tests. For comparison between two groups, Student's t-test was performed. Data were expressed as the mean + SEM. The significant level was set at P < 0. 05.
Dendritic spines labeling and counting after Golgi staining Mice that had underwent a 4-day training in the MWM were killed 4 days later. The Rapid Golgi stain kit (FD Neurotechnologies, Inc. ) was used according to the manufacturer's instructions. Freshly dissected brains were immersed in solution A and B for 2 weeks at room temperature and were then transferred to solution C for another 24 h at 4°C. 150-lm-thick coronal sections containing the rostro-caudal axis of hippocampal region CA1 were made using a Vibratome (VT1000M; Leica). Images were acquired using a brightfield microscope equipped with automated motorized stage and MorphoStrider software (Explora Nova, La Rochelle, France). 63× magnification images were taken from secondary and tertiary dendrites from CA1 pyramidal neurons. For each genotype, condition and treatment 8-10 dendritic segments per animal were analyzed.
Statistics Dendritic spines counting scores were from about 25 (Golgi staining) and 70 (GFP lenti) dendritic segments which were from material of 15-30 neurons and two to three animals/condition. Data are presented as mean AE SEM. For GFP staining, Kolmogorov-Smirnov test was performed on each data set to test the distribution normality. Statistical analyses were run with Prism software (GraphPad 5. 0). Dendritic spine analyses were compared across groups by means of one-way ANOVA followed by post hoc analyses that were performed using Holm-Sidak multiple-comparisons tests. For Golgi staining, dendritic spines were compared across different groups by using a two-way ANOVA followed by Newman-Keuls multiplecomparisons tests.
Extracellular field excitatory postsynaptic potential (fEPSPs) were recorded from the apical dendritic layer of the CA1 area, using a glass micropipette filled with 2 M NaCl. fEPSPs were evoked by the electric stimulation of Schaffer collaterals⁄commissural pathway at 0. 1 Hz with a bipolar tungsten stimulating electrode placed in the stratum radiatum (100 ls duration). The averaged slope of three fEPSPs was measured using pclamp software (Axon Instruments) for 20 min before conditioning stimulation. Long-term depression (LTD) was induced by applying a low-frequency stimulation at 2 Hz (1,200 pulses for 10 min). The sequence was repeated three times, with an interburst interval of 10 s. Testing with a single pulse was resumed for 60 min to determine the level of LTD. Any change in synaptic strength was expressed relative to the control level (100%).
Statistics Average values of the fEPSP slope were calculated for the last 10 min and expressed as a percentage of the baseline response (% baseline) AE SEM. In order to take into account the correlations inherent to repeated measures in electrophysiological recordings, P-values were calculated using multivariate analyses of variance followed by post hoc unpaired Student's t-tests using StatView software. In all cases, differences were considered significant when P ≤ 0. 05.
Acknowledgements The authors thank  Dr. Matthieu Gerard  ( CEA Saclay, Gif-sur-Yvette, France ) for his helpful comments on an early version of the manuscript. The authors are grateful to  O Bildstein ,  O Egesi ,  G Edomwonyi , and  C Strittmatter  ( UMR 7364 ) for their assistance in animal care. We also thank  Drs Nathalie Mandairon  and  Marion Richard  ( CRNL, Lyon, France ) for their counseling on lentiviruses, and  Gisèle Froment ,  Didier Nègre , and  Caroline Costa  from the lentivector production facility/ SFR BioSciences de Lyon  ( UMS3444/US8 ). Sequencing was performed by the  GenomEast Platform , a member of the " France Génomique "  consortium  ( ANR-10-INBS-0009 ). TKK is a recipient of the  Sir JC Bose national fellowship (Department of Science and Technology, Govt. of India ).
SC was supported by  IFCPAR/CEFIPRA  (No. 4803-3 ). RC was a recipient of a doctoral fellowship from the  French government. AS-A was supported by the  ANR  ( ANR-12-MALZ-0002-01 ). LB and DB are supported by programs d'investissements d'avenir  LabEx (excellence laboratory)  and the  DISTALZ (Development of Innovative Strategies for a Transdisciplinary approach to ALZheimer's disease) ,  France Alzheimer ,  FHU VasCog research network (Lille, France ),  Fondation pour la Recherche Médicale, LECMA/Alzheimer Forschung Initiative ,  Fondation Plan Alzheimer ,  Inserm ,  CNRS ,  Université Lille 2, Lille Métropole Communauté Urbaine, Région Nord/Pas-de-Calais ,  FEDER ,  DN2M , and  FUI MEDIALZ. This work was supported by the  CNRS , the  University of Strasbourg ,  ANR  ( ANR-12-MALZ-0002-01  to ALB),  France Alzheimer  (to ALB), the  Department of Biotechnology, the Government of India  (Grant /DBT/CSH/GIA/1752  to TKK), the  Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) , and the  Indo-French Centre for the Promotion of Advanced Research (IFCPAR/CEFIPRA  (No.
Molecular dynamics simulations. Ab initio molecular dynamics simulations predict that the diffusion mechanism of Na x CoO 2 in the high temperature disordered phase is highly sensitive to Na-Na correlations, and differs from the di-vacancy mechanism of Li x CoO 2 30 , due to the stabilisation of multi-vacancy clusters comprising vacancies on 2d sites and ions promoted to 2b sites  31. Figure  1(c)  shows typical diffusion pathways. We performed first-principles density-functional calculations and MD simulations incorporating the observed Na-Na correlations using the CASTEP code  32. It is particularly instructive to examine the calculations in the partially disordered stripe phase at T ~ 350 K, since the relatively small departures from a simple superstructure make it a good prototype in which to understand self-diffusion in Na x CoO 2.
There is excellent agreement with the data at all temperatures, suggesting that 2d to 2b hops are the dominant diffusional process in both dynamic phases. The fit to the QENS data at T = 300 K gives a mean residence time, τ QENS = 490(60) ps. The diffusion coefficient for a random walk in 1D along the stripe, D RW = d 1D 2 /(2τ 1D ) = d QENS 2 /4τ QENS = 1. 4 (2) × 10 -7 cm 2 s -1 , see Supplementary Figure  S7. This corresponds to an upper limit. The temperature dependence of the diffusion coefficients from the QENS data are shown in the Arrhenius plot in Fig. 5(d). Different activation energies are determined in the partially disordered stripe phase and the fully disordered phase. At elevated temperatures in the disordered phase our experimentally determined activation energy, E A ~ 85(5) meV, is in good agreement with the value of about 100 meV obtained from previous MD simulations  31.
Methods Experiment. Crystals of Na 0. 8 CoO 2 were grown using an optical floating-zone furnace at Royal Holloway. Sub-millimetre single crystals were cleaved from the boule, and the structure was determined using x-rays at the Mo K-edge using an in-house Agilent Xcalibur X-ray diffractometer. The sample was placed in a stream of nitrogen gas from a Cryojet temperature controller, and at each temperature, large volumes of reciprocal space were surveyed with a CCD detector. Diffraction measurements at T ~ 100 and 300 K produced superlattice reflections that corresponded to the fully ordered and partially disordered tri-vacancy stripe phases  25  , respectively. The low-temperature superstructure was obtained via a model-independent reverse Monte Carlo fit to the superlattice reflections. An elegant alternative model based on di-vacancy clusters and with different periodicity  37  can be ruled out by the data for this composition.
For the much larger powder sample the better counting statistics allowed the Q-dependence of the QENS to be determined. QENS measurements of the powder sample were carried out for 12 hours at T ~ 200, 300, 350, 400, 450, 500, 550, and 600 K. At T ~ 200 K the QENS is resolution-limited in energy transfer by reference to measurements from a vanadium standard. At all other temperatures quasi-elastic energy broadening was detected. The data were reduced using the Mantid software suite (version 3. 5. 0)  41. The detectors were grouped into pairs and energy bins of 4 μeV were chosen to reduce statistical noise. A combination of the static resolution function from the T ~ 200 K data, and a convolution of the resolution function and a Lorentzian function, was used to fit the scans in energy transfer at each Q.
Fits of the Chudley-Elliot model  34  to the Q-dependence of the Lorentzian FWHM gave the diffusion rate at each temperature. The variation in diffusion rate with temperature provides the activation energy and diffusion constant. Theory. The density functional theory (DFT) simulations used the plane-wave pseudopotential approach and spin polarised Perdew-Burke-Ernzerhof 42 generalized gradient approximation as implemented by the CASTEP code  43. Vanderbilt-type ultrasoft pseudopotentials were generated within CASTEP. For Na and Co the C7 CASTEP library was employed, whereas a custom-made slightly softer pseudopotential with a core radius of 1. 5 Å was used for O. The plane-wave cut off was set to 500 eV based on convergence tests using a primitive cell of NaCoO 2. The metallic nature of the conduction bands was described using Gaussian broadening of width 0.
The x-ray datasets generated during and analysed during the current study are available from the corresponding author on reasonable request. The MD simulations and CIF files are available via Royal Holloway's Figshare repository from doi:10. 17637/rh. 5692846 (MD simulations), doi:10. 17637/rh. 5692942 (fully ordered stripe phase), doi:10. 17637/rh. 5692963 (partially ordered stripe phase) and doi:10. 17637/rh. 5693002 (disordered phase). All raw neutron data and the associated metadata obtained as a result of access to ISIS, reside in the public domain, with ISIS acting as the custodian. The QENS data can be accessed from doi:10. 5286/ISIS. E. 24090568 (single crystal) and doi:10. 5286/ISIS. E. 49912250 (powder).
Acknowledgements We thank  M. S. Pandiyan  and  D. F. Bowman  for their help, and  D. J. P. Morris ,  D. A. Tennant ,  A. T. Boothroyd ,  J. R. Stewart  and  R. I. Bewley  for helpful discussions. EPSRC supported this research via grant  EP/J011150/1 , and through use of the UK national supercomputing facility  ARCHER  under grant  EP/K013750/2. Neutron experiments were supported by  STFC  and other calculations used STFC's e-Science facility. T. J. W. acknowledges financial support from the  South East Physics Network  and the  ISIS Facility.
Introduction The AirGreen 2 project is an Innovation Action funded by the Clean Sky 2 Joint Undertaking under the European Union's Horizon 2020 research and innovation programme, under Grant Agreement n. CS2-REG-GAM-2014-2015-01. One of the main scopes of the project is the "econolomic" manufacturing of the Outer Wing Box (OWB) of a Regional Turboprop Aircraft. The Liquid Resin Infusion (LRI) and Out of Autoclave (OoA) manufacturing process is the focus of the activity, starting from some validations already reached at laboratory level in the previous project AirGreen of Clean Sky (CS1),  [1]. Hand-Layup (HLU) and Automated Fiber Placement (AFP) dry preforming processes are applied, by improving weight and cost reduction, lower energy consumption, high productivity and minimal (manual) reworking time, less intensive labour, minimal scrap and lower buy/fly ratio.
NOVOTECH has validated and verified the great potential of the liquid resin infusion process based on preforms laydown with the AFP technology  [2]. SICAMB, involved in the HLU process, has also optimized the infusion process through a commercial software (ESI-PAM/RTM, [3]) varying the models with different inlet/outlet configurations to verify the best solution to obtain the full infusion with the shortest process time. Besides, the vulnerability to thermal loads and to lightning has been tested by IMAST, ONERA, CIRA and SAMTECH experimentally and numerically. Technical considerations useful for the next manufacturing of large parts and components, are assessed.
LRI optimisation and HLU technique The LRI technique has been optimised by the development of dedicated mechanical/fluid dynamic models, simulating the liquid resin flow through stiffened wing panels preform and assisting equipment and tools design. PAM RTM software has been used for this scope; it integrates thermo-chemistry and viscosity models as appropriate. The activity is aimed at identifying possible causes of the slow down or non-uniform distribution of resin flow that may cause dry spots, poor saturation of the preform and partially filled composite parts. The LRI model is based on Darcy's law that governs the flow of a liquid resin through porous media. PAM RTM has supported the evaluation of different impregnation strategies and the identification of optimum key process parameters: the location of distribution media, inlet and outlet pipes and impregnation temperature.
35 mm tow head (maximum bandwidth of 50. 8 mm). The compaction is performed by a suitable roller that guarantees a force of 500 N. The contact surface of the roller is approximately 55 mm × 15 mm. Therefore the average contact pressure applied is around 0. 6 MPa and it is limited by the stiffness of the robot. The programming of the panels is performed using the Coriolis CADFiber software. The small scale demo has been useful to set the AFP preforming process and infusion strategies (injection lines, bagging scheme, etc. ). With regard to the infusion process, a composite curing oven coupled with an advanced online monitoring system developed from BriskHeat Corporation for the control of the manufacturing process parameters (temperatures, vacuum level) has been used. Similar systems have been developed in the past  [5].
As example, Figure  12  shows the results for the engine fire scenario. SAMTECH, by using Samcef software [11], has developed FE models for thermal simulations with degradation due to the temperature, and models used for thermo-mechanical simulations. As example, Figure  13  shows the results of the simulation of the Short Beam Shear Test (thermo-mechanical model). A good correlation was observed between Samcef results and experimental ones, under or over the matrix glass temperature, for the slopes, the maximum loads and the delamination locations, Figure  13(a). At mechanical glass temperature, the behaviour over maximum load as well as the fact that a permanent deformation occurs were correctly simulated, Figure  13(b). The results illustrated in this work are essential for the next steps of AirGreen 2 project.
Acknowledgments The research leading to these results has received funding from  Clean Sky 2 Joint Undertaking  under the European Union's  Horizon H2020 research and innovation programme , under grant agreement n. CS2-REG-GAM-2014-2015-01. The Authors thank the colleagues that have worked and contributed to the activities shown in this work:  V. Iannone  (NOVOTECH),  R. Zazza ,  B. Auriemma  and  S. D'Onofrio  (SICAMB),  M. Ferraiuolo ,  R. Scigliano  and  U. Mercurio  ( CIRA ),  S. Inserra (MAST) ,  L. Chemartin ,  G. Leplat  and  C. Zaepffel  ( ONERA ),  A. C. Goupil  (SAMTECH),  V. Ascione  ( LEONARDO Aircraft ).
Similar analyses were also performed to obtain scaled SLP change ( SLP scaled ), zonal wind change and energy budget change in the atmospheric column. Several observational and reanalysis datasets were also employed in this part of our study. For precipitation, Global Precipitation Climatology Center (GPCC) monthly precipitation data  (Schneider et al. , 2011) , provided by NOAA/OAR/ESRL from their website (https://www. esrl. noaa. gov/psd/data/gridded/data. gpcc. html#detail, last access: 12 June 2018), are employed. It is a high-quality gridded dataset that is mainly derived from terrestrial stations. For SLP, we use HadSLP2 data  (Allan and Ansell, 2006) , which are created by combining marine observations from ICOADS data  (Worley et al. , 2005)  and land (terrestrial and island) observations (available at https: //www.
esrl. noaa. gov/psd/data/gridded/data. hadslp2. html, last access: 12 June 2018). We also use NCEP/NCAR reanalysis data  (Kalnay et al. , 1996) , downloaded from https://www. esrl. noaa. gov/psd/data/gridded/data. ncep. reanalysis. derived. surface. html (last access: 12 June 2018), for the comparisons of zonal wind. All these datasets have undergone rigorous quality control and have been widely used in the climate community, including the IPCC 2013 assessment report  (Hartmann et al. , 2013). The trends of the observed and reanalysis data were estimated by a simple linear regression applied to the same period of the datasets. The combination of WMGHGs, BC and SO 4 exerted a strong drying trend in the Mediterranean (Fig. 6a ). The drying trends shown here are statistically significant and consistent with the observations (Fig.
Acknowledgements. We thank the two reviewers for their insightful comments. We also acknowledge the  NASA   High-End Computing Program  through the  NASA Center for Climate Simulation at Goddard Space Flight Center  for computational resources to run the  GISS-E2R  model and support from  NASA GISS. PDRMIP is partly funded through the  Norwegian Research Council  project  NAPEX  (project number  229778 ). Oliviér Boucher acknowledges HPC resources from CCRT under the gencmip6 allocation provided by  GENCI  ( Grand Equipement National de Calcul Intensif). Piers M. Forster  and  Thomas Richardson  were supported by  NERC  grants  NE/K007483/1  and  NE/N006038/1. Øivind Hodnebrog  was partly funded through the  Norwegian Research Council  project  HYPRE  (project no. 243942 ). Apostolos Voulgarakis  and  Matthew Kasoar  are supported by  NERC  under grant  NE/K500872/1.