dataesr/scientific-paragraphs-categorization huggingface dataset:
Endotoxin detection Protein endotoxin detection was performed using LAL Chromogenic Endotoxin Quantitation Kit (Thermofisher ref #88282) following the manufacturer instruction. Briefly, 10µg of SYN monomers, fibrils, ribbons and unbound Atto-550 were dissolved in 50µl of endotoxin free water provided in the kit and distributed in 96 well microplate. The LAL reagent was added next and the plate was incubated 10 min at 37°C in a thermomixer (Eppendorf, Germany). The chromogenic reagent was next added and the incubation further extended 6 min. The reaction was arrested with 25% acetic acid. Absorbance at 405nm was measured using a Flexstation microplate reader (FlexStation, Molecular Devices). Protein endotoxin units are presented in Extended Data Figure  1. rAAV-SYN vector endotoxin detection was performed using LAL bacterial endotoxin test (Endosafe®-PTSTM, Charles River) following the manufacturer instruction.
The samples were de-salted (with 5% acetonitrile, 0. 1% Trifluoroacetic acid (TFA)) and eluted from a C18 reversed-phase Zip-Tip (Millipore, Billerica, MA, USA) in 50% acetonitrile, 0. 1% TFA. Peptide samples were mixed in a ratio of 1:5 to 1:20 (v⁄v) with sinapinic acid (10 mg/mL) in 50% acetonitrile and 0. 1% TFA) and spotted (0. 5 µL) on a stainless steel MALDI target (Opti-TOF; Applied BioSystems). MALDI-TOF-TOF MS spectra were acquired with a MALDI-TOF⁄TOF 5800 mass spectrometer (Applied Biosystems) using linear mode acquisition. External calibration was performed using unmodified WT SYN. Acquisition and data analysis were performed using the Data Explorer software from Applied Biosystems. The nature of all SYN assemblies used was routinely assessed using a Jeol 1400 (Jeol Ltd. , Peabody, MA) Transmission Electron Microscope (TEM) after adsorption of the samples onto carbon-coated 200-mesh grids and negative staining with 1% uranyl acetate.
Acknowledgements The authors thank  Joris Van Asselbergs  and  Caroline van Heijningen  for their technical assistance and  Dr. Zeger Debyser  for revising the manuscript. We thank  Dr. Johan Hofkens  and  Charlotte David  for the use of the CLSM and  Dr Virginie Redeker  for assessing the number of atto dyes bound to SYN by mass spectrometry. The authors thank the  Leuven Viral Vector Core (LVVC)  for the rAAV vector construction, optimization and production. M. G. , R. P. , and A. M. are in debt with M. Wijnants and  D. Van Dyck  for their excellent technical assistance. Research was funded by the  FWO-Vlaanderen  ( G. 0768. 10,G. 0927. 14  and PhD fellowship to WP), the  IWT-Vlaanderen  ( IWT SBO/80020 Neuro-TARGET, SBO/110068 OPTOBRAIN  and  SBO/130065 MIRIAD ), the  FP7 RTD projects MEFOPA  ( HEALTH-2009-241791 ) and  INMiND  ( HEALTH-F2-2011-278850 ), the  KU Leuven  ( OT/08/052A ,  OT/14/120 ,  IMIR PF/10/017 ), the  Agence Nationale de la Recherche  ( ANR-09-MNPS-013-01  and  ANR-11-BSV8-021-01 ), the  Centre National de la Recherche Scientifique , a ' Coup d'Elan à la Recherche Française ' award from  Fondation Bettencourt Schueller , the  EC-FP7  ( Marie Curie Initial Training Network "NAMASEN ", grant n.
Background: In late 2012, a national pill crisis led French women to promptly change their behavior regarding contraception, with a significant increase in the use of first-generation and second-generation combined oral contraceptives to the detriment of third-generation and fourth-generation products (C3Gs and C4Gs). Objective: To assess the impact of the sharp changes in 2013 on the rate of women hospitalized for pulmonary embolism in France. Methods: All hospitalized pulmonary embolisms in women aged 15-49 years, excluding those occurring during delivery stay, were identified from the French national hospital discharge databases from 2010 to 2013. Hospitalization rates, overall and by age group, were calculated. We compared rates in 2013 with those in 2012, and with mean rates over the preceding 3-year period (2010)(2011)(2012).
Hospitalization data In France, all admissions to private and public hospitals are recorded in the French national hospital discharge databases (PMSI)  [17]. Those databases were queried from 2010 to 2013 to identify hospitalizations for PE (ICD-10 code I26) in women aged 15-49 years. Only patients for whom no hospitalization for PE had been reported in the last 12 months were included. Any PE occurring during delivery stay was excluded, because hospitalization data are not adequate for the identification of cases of PE occurring during pregnancy.
Quite similar but weakened results were observed when incidence rates in 2013 were compared with mean rates over the previous 3-year period, with a 7. 3% reduction and a difference of 227 cases of PE (95% CI À352 to À63; Table  2 ). The decrease, which was observed in all age groups, was only significant in the younger women aged 15-19 years (Table  2 ). These results suggest that the reduction in the number of hospitalizations for PE might have indeed begun in 2013. Hospitalization data from 2010 to 2013 were analyzed. This 4-year period was chosen to allow a reliable assessment of trends in the incidence of hospitalization for PE, with no possibility of a significant modification of existing practices regarding the diagnosis of PE and/or coding in databases. It should be mentioned that ascertainment of PE cases may appear to be questionable.
Nevertheless, a validation study performed in 25 French hospitals has demonstrated that the sensitivity of the ICD-10 diagnostic code for PE in the PMSI is 89%  [19]. In our study, the observed reduction of 10. 6% is based on all hospital admissions for PE, and not only on those occurring during the use of contraception. Indeed, because drug exposure is not reported in the PMSI, hospitalizations for PE were analyzed regardless of COC exposure. Investigation of the linkage between hospitalization diagnosis data and reimbursement data related to pharmacy purchases, although feasible, would have been useless, as third-generation and fourth-generation COCs have not been reimbursed since early in 2013. Therefore, even though the 10. 6% decrease supports the hypothesis of a role of the recent modification of contraceptive use on the reduction in venous thromboembolism morbidity, this result alone is not sufficient to allow firm conclusions to be drawn.
Statistical analysis In vivo gene expression results were analysed by a permutation test using the StaXact software (v5. 0-Cytel software) to obtain exact p-values. For the analysis of responses of MEC cells to the different bacterial agonists or to live bacteria, data were first compared using the Kruskal and Wallis test followed by exact permutation tests using StatXact. A p-value < 0. 05 was considered significant.
Microarray experiments had failed to detect a significant expression of IL-17 family genes in udder tissue after E. coli infection, presumably because of a low expression of these genes  [15]. In the present study, we thus used RT-qPCR to evaluate the expression of IL-17 family genes. No expression was detected for IL-17C and IL-17E (data not shown). On the contrary, expression of IL-17A and IL-17F was significantly increased in E. coli infected quarters, compared to non-infected quarters (Figures  1C  and D ): the mean fold-change for IL-17A was 72 in samples from cows infected by E. coli. Mean induction of IL-17F was 109-fold in the same samples (Figures  1C  and D ). Although induction of IL-17A gene was clearly observed in our tissue samples, IL-17A levels in milk samples from E. coli infected cows were below the detection limit of the ELISA assay used, that is below 200 pg/mL in milk.
Identification of two putative non-redundant tomato isopentenyltransferases To identify IPT encoding genes in tomato, Arabidopsis IPT1-9 coding sequences were used to screen the tomato genome database  [26]  (www. solgenomics. net). Among the selected expressed sequence tags (ESTs), two were apparently encoding full length proteins and could be amplified by PCR. For the first gene (GenBank accession JF423320), a 1122 bp coding sequence was cloned, including a 990 bp open reading frame (ORF) defining a 329 amino acid (aa) polypeptide of 37. 5 kDa (Figure  1A ). This gene was recently annotated as SlIPT3  [12]. For the second gene (GenBank accession JF433930), a 1073 bp coding sequence was amplified, exhibiting a 972 bp ORF predicted to encode a 323 a protein of 37. 1 kDa. This gene was classified as SlIPT4  [12].
Plates were then transferred to the growth chamber with a 16 h light (20°C)/8 h dark (18°C) photoperiod. For the analysis of salt stress tolerance, halfstrength MS medium containing 100 mM NaCl was used. The root length (from hypocotyl base to the root tip) of at least twenty vertically growing ten-days-old plants was measured. Differences in root length were tested for significance using a Mann-Whitney U test and data representing two biological replicates. Germination percentage was determined for eighteen seedlings after 24 h using a magnifying glass, when the radicle occurs. Survival percentage of eighteen seedlings was evaluated in thirteen-day-old plants. Total numbers of germinated and non-germinated seeds  (54)  were cross tabulated for each pair of groups and Fisher's exact test was then applied to the resulting 2x2 contingency tables.
Photosynthetic pigments and ion extraction, quantification and analysis The content of photosynthetic pigments (Chl a and Chl b, β-carotene, lutein, neoxanthin, violaxanthin, zeaxanthin and antheraxanthin) was determined in acetone extracts made from the lyophilized developing leaves of 4 weeks-old plants analyzed by a high-performance liquid chromatography (ECOM, Czech Republic). The analysis was made using a reversed phase column (Watrex Nucleosil 120 5 C18, 5 μm particle size, 125 × 4 mm, ECOM, Czech Republic). The solvent system comprised acetonitrile/methanol/water (80/12/10, v/v/v) followed by methanol/ethylacetate (95/5, v/v), the total analysis time was 25 min, and the linear gradient was run from 2 to 6 min (the flow rate was 1 cm 3 min -1 , the detection wavelength was 445 nm). Data were captured and calculated by PC-software Clarity (DataApex, Czech Republic).
Acknowledgements The authors thank  Dr Miroslav Kamínek  for critical reading of manuscript,  Dr Said Hafidh  and  Dr James Stones  for language editing and  Marie Korecká  for excellent technical support. We also thank  Abdelmounaim Errachid  for his help with confocal microscope, and  Dr Etienne G. Danchin  for his help with phylogenetic analyses. This work was supported by the  Czech Science Foundation  [ P506/11/0774 ]; the  Fonds National de la Recherche [FNRS ; convention n°1. 5117. 11];and the  Wallonie-Bruxelles International program  [ Rhéa 2011/35047  and  WBI/14-3 ].
2008a; Mcleod et al. 2008). However, disturbance regimes have proven a challenging dimension to include in MSP, often due to limitations in data availability and analytical capacity. The Great Barrier Reef (GBR) Marine Park is a global icon of marine ecosystem management. In 2004, the GBR Marine Park was rezoned to increase the proportion of the Marine Park protected within no-take areas  (Day 2002; Day et al. 2002 ). An expert focus group developed biophysical operating principles for the rezoning that suggested a minimum of 20% of the Marine Park be protected within no-take areas  (Fernandes et al. 2009). This minimum recommendation took disturbances such as cyclones, pollution events, climate change impacts, and other disturbances into consideration. 33% of the Marine Park was protected after application of an "insurance factor" (1.
2008; Beeden et al. 2015). COTS outbreaks can radically reduce live coral cover on healthy reefs within weeks  (Osborne et al. 2011). Bleaching, cyclones, and COTS outbreaks were identified as major contributors of the 50% decline in coral cover in the GBR from 1985 to 2012 described in  De'ath et al. (2012). Finally, low salinity caused by freshwater inundation can cause coral bleaching and increase susceptibility to diseases  (Kerswell & Jones 2003). We use spatial data on exposure to these four disturbances to map combined relative exposure and then: (1) conduct a post-hoc analysis of the extent to which the Marine Park zoning in 2004 accounted for exposure to disturbance, and (2) identify coral reef areas with lower relative exposure. The approach and results presented demonstrate the value of exposure mapping for adaptive, resilience-based management of coral reefs.
The total coral reef area was calcu-lated based on high-resolution vector spatial data of coral reef boundaries produced by the Great Barrier Reef Marine Park (GBRMPA). The area within no-take Marine National Park green zones was calculated for the entire Marine Park and for all four Marine Management Areas (MMAs): Far Northern, Cairns-Cooktown, Townsville-Whitsunday, Mackay-Capricorn (Figure  1 ). Total reef area (in km 2 ) within each of the 11 exposure classes was calculated, as was the reef area in each exposure class that is within no-take areas.
Secondly, we assumed the disturbances included in our analysis affect coral reefs equally; this is defensible from the perspective of normalizing disturbance frequencies because maximum frequencies of exposure are comparable for each disturbance (10-12 events over a 22-27 year period). However, the impacts caused by the disturbances will vary in space and time. Our processed datasets from our analysis enable more sophisticated approaches that could include assumptions of the degree of impact caused by each disturbance. Such modeling approaches (e. g. , belief networks) could include other aspects of vulnerability (i. e. , sensitivity and adaptive capacity) by setting initial and boundary conditions for benthic reef communities using available field data and interpolation  (Renken & Mumby 2009; Wooldridge & Done 2009; Anthony et al.
Acknowledgments Funding was provided for this research by the  GBRMPA  (via the  Climate Change Action Plan)  and an  ERC grant  to the lead and last authors. Foundational discussions included the authors and  P. McGinnity ,  J. Day ,  K. Anthony , and  R. Pressey. G. De 'ath assisted  E. Lawrey  with interpolating and interpreting the AIMS LTMP survey data on COTS outbreaks. Figures were developed in collaboration with D. Tracey. The contents in this manuscript are solely the opinions of the authors and do not constitute a statement of policy, decision, or position on behalf of NOAA or the  U. S. Government.
We mostly work on the object as part of a technical system. Our approach assumes that historical knowledge should not depend on physical representation (such as a 3D model) quality  [2]. Nevertheless, it can enhance the information system with the object geometrical features. This paper discusses the idea of making connexions between the physical object and a knowledge database. This connection allows identification of lacks of information, and cross navigation through the three variables mentioned above. In addition, semantic keyword navigation is possible. We study Nantes' (french city) harbour history through three different historical objects (see Fig. 1 ). This use case leads us to those considerations. Based on this use case of conservation and promotion of cultural and industrial heritage, we wanted to make connexions between the different pieces of information, gathering the knowledge capitalized regarding the parts of the use case.
II. Methodology: Multi-dimension knowledge modeling process 3D digitization has especially become more and more affordable and efficient. This leads to massive digitization projects and increasing amount of cultural heritage (CH) digital data  [3]. Every project in CH conservation and promotion we are involved into implies the creation of new historical knowledge under the digital form. Many of them have implicit links: geography, time, thematics. Therefore, we want to manage CH objects uniqueness by creating connexions in order to access information through different dimensions. This is what we call "mass customization for cultural heritage objects". We state here that every historical object can be represented by a combination of the three axis of Fig. 2  according to common practices in industrial archaeology  [4] ,  [5].
III. Use case presentation: heterogeneous data In addition to the 3 dimensions mentioned in section II, we also have to deal with heterogeneous historical materials  1. Three industrial archaeology studies compose our use case and illustrate this double issue. Yet, our proposition aims to be applied to any other cultural heritage study of this kind. a) "Nantes1900" project: a museum project focusing on industrial heritage through the case of a 100 years old scale model. This scale model is part of Nantes (France) history museum. In this project, we have a delimited spatial area which is the harbour of a city. We also have many heterogeneous historical documents related to hundreds of points of interest. The 3D model of the physical scale model comes from scanner digitization (Creaform HandyScan).
It is composed of 100 million points. In addition, we gathered a corpus of 1000 historical documents (postal cards, archives documents, paints, photographies, books, etc. ) and hundreds of notes written by historians. Based on this corpus, we created a knowledge database to handle these information. The global level of detail is related to the city scale approximately between 1899 and 1920. The database stores information about many thematics related to industrial activity: social ("labour conditions in the early 1900's", people biographies), economics (companies' chronicle), technology (shipyards, steam engines), architecture and urbanism (urban network), etc. b) "Halles Alstom": an industrial complex being restorated and based in the harbour of Nantes. This historical "object" is part of the scale model mentioned above.
Kinetic experiments were performed in the direction of glycogen synthesis as described previously. 14 Kinetic data for the inhibition of rabbit skeletal muscle glycogen phosphorylase were collected using different concentrations of α-D-glucose-1-phosphate (2-20 mM), constant concentrations of glycogen (1% w/v) and AMP (1 mM), and various concentrations of inhibitor. Inhibitor was dissolved in dimethyl sulfoxide (DMSO) and diluted in the assay buffer (50 mM triethanolammine, 1 mM EDTA and 1 mM dithiothreitol) so that the DMSO concentration in the assay should be lower than 1%. The enzymatic activities were presented in the form of double-reciprocal plots (Lineweaver-Burk) applying a nonlinear data analysis program. The means of standard errors for all calculated kinetic parameters averaged to less than 10%.
Acknowledgments Financial supports from  CNRS  ( PICS 2008-2010 n°4576 ), University Claude Bernard Lyon 1 and the  French Agence Nationale de la Recherche  (support of the  ANR  project  GPdia n°ANR-08-BLAN-0305 for both salary and expenses of DG ) are gratefully acknowledged. Dr F. Albrieux ,  C. Duchamp  and  N. Henriques  are gratefully acknowledged for mass spectrometry analyses. This study was supported by a grant from the  Hungarian Science Research Fund  ( OTKA CNK80709 ) and  TAMOP-4. 2. 2. A-11/1/KONV-2012-0025  to PG and TD. TD is a recipient of  Bolyai Fellowship  from the  Hungarian Academy of Sciences.
Data analysis -If a gene was expressed and modulated in both groups, its modulation profile was compared as a function of age by means of a two factors Anova test (p \ 0. 05). The genes that were markedly different according to age or interaction age/time were selected. -Some specific genes were significantly expressed and modulated in one age group but not in the other one. These genes were not included in the previous comparison. To select the core of them, we selected those whose modulation was the most relevant. For that purpose, we reduced the comparison to 6 and 30 h, because these two time points comprised the highest number of modulated genes in the young and aged group, respectively. A distance was calculated between the two age groups taking into consideration the differences found at 6 and 30 h.
We compare tropospheric column densities (vertically integrated concentrations) of NO 2 from three data sets for the metropolitan area of Paris during two extensive measurement campaigns (25 days in summer 2009 and 29 days in winter 2010) within the European research project MEGAPOLI. The selected data sets comprise a regional chemical transport model (CHIMERE) as well as two observational data sets: ground-based mobile Multi-AXis-Differential Optical Absorption Spectroscopy (car-MAX-DOAS) measurements and satellite measurements from the Ozone Monitoring Instrument (OMI). On most days, car-MAX-DOAS measurements were carried out along large circles (diameter ∼ 35 km) around Paris. The car-MAX-DOAS results are compared to coincident data from CHIMERE and OMI. All three data sets have their specific strengths and weaknesses, especially with respect to their spatiotemporal resolution and coverage as well as their uncertainties.
The paper is organised in the following way: in Sects. 2 and 3 we describe the data sets, their specific advantages and limitations and how to use them in a synergistic way. In Sects. 4 and 5 CHIMERE model data are compared to car-MAX-DOAS and OMI observations, respectively. Section 6 presents the comparison of coincident observations of all three data sets. A summary and outlook are provided in Sect. 7.
Data sets The car-MAX-DOAS observations in and around Paris were performed during two extensive measurement campaigns organised in the frame of the MEGAPOLI project  (Mahura and Baklanov, 2012 ; see also http://megapoli. dmi. dk/). In June and July 2009 car-MAX-DOAS measurements were performed on 25 days, and in January and February 2010 on 29 days. For almost all of these days model results from CHIMERE are available. OMI satellite observations are also available for most days, although many of these observations provide only limited information on the tropospheric NO 2 abundance due to the presence of clouds. The three data sets are described in the following sub-sections.
(2006). Meteorological data are produced with the PSU/NCAR Mesoscale Model (MM5;  Dudhia et al. , 1993). MM5 provides meteorological data for CHIMERE in an hourly time step. Observed wind speeds used for the comparisons are available at an hourly time step. In general, observed (and simulated) wind directions smoothly change form 1 hour to the next, at a rate of typically 10-20 • (see Fig. 2  in  Zhang et al. , 2013). However, especially during low wind speed periods, much larger jumps in observations are possible, which are then often not simulated. In these cases however, the average transport time between NO x emission sources and the measurements is of several hours, which averages out sudden jumps in wind direction. Boundary and initial conditions are taken from the LMDz-INCA2 and LMDz-AERO global models for gaseous and particulate species, respectively  (Hauglustaine et al.
Spatial coverage For most days the measurement strategy was to drive around Paris along large circles (with diameters of about 35 km, see Fig. 3 ), in order to estimate the total emissions from Paris  (Shaiganfar et al. , 2011 (Shaiganfar et al. , , 2015)). Such measurements were carried out once or twice per day. In addition, measurements along smaller circles, and other road segments were performed on individual days to gain more information on the horizontal NO 2 distribution in the Paris metropolitan area. The satellite provides daily global coverage. However, on many days gaps in the tropospheric NO 2 data are present, due to the presence of clouds or instrumental problems. CHIMERE simulations are performed over an area ranging from 0. 35  day between about 8:00 and 17:00 LT. CHIMERE data are available in hourly time steps.