dataesr/scientific-paragraphs-categorization huggingface dataset:
Immunohistochemistry Paraffin embedded liver samples were sectioned, dewaxed and hydrated. All procedures were done according to standard protocols with EnVision+ System HRP (Dako). Finally, samples were incubated with Vector Vip substrate (Vector) for purple color development. 10 random images per sample were taken with a 10x objective from a microscope AXIO Imager D1 (Carl Zeiss AG, Oberkochen, Germany). Quantification of staining intensity or area of each sample were calculated using the manual selection tool of FRIDA software (FRamework for Image Dataset Analysis) http://bui3. win. ad. jhu. edu/frida/. Stained area was measured using ImageJ64 software (NIH), images were transformed to RGB stacks, manually thresholded for selection of the stained área and measured with the measure tool to calculate the area percentage.
Protein Isolation & Western Blotting Extraction of total protein from cultured cells and livers was performed as described  [8]. 4 to 25µg of protein were electrophoresed on sodium dodecyl sulfatepolyacrylamide gels and transferred onto membranes. A description of the antibodies used is provided in Supplementary Table  VI. Band intensities were quantified using the ImageJ software and normalized to the β-Actin housekeeping. All experiments were performed at least 5 times.
RNA Isolation and Quantitative Real-Time PCR RNA was isolated with Trizol (Invitrogen), and its concentration and integrity were determined. PCRs were performed using iQ™ SYBR ® Green Supermix (Biorad) and the Bio-Rad iCycler thermocycler (Bio-Rad, Hercules, CA). The Ct values were extrapolated to a standard curve, and data was then normalized to the housekeeping expression (18S and GAPDH). The sequences of primers used are described in Supplementary Table  VII.
Cycloheximide Treatment Phb1-KO hepatocytes were transfected with Control or Nedd8 siRNA as described. Later, cycloheximide (CHX; 50 µg/mL) was added, and, at the indicated times, cells were lysed. Protein was analyzed by Western blotting using the indicated antibodies, quantified with Image J software, and presented as the percentage of remaining protein. Data are representative from three independent experiments.
Financial Support This work is supported by grants from  NIH   AT-1576  and  CA172086  (to S. C. L. ; J. M. M and M. L. M-C. ),ETORTEK-2011 (to M. L. M. -C),  Sanidad del Gobierno Vasco 2013  (to M. L. M. -C),  FIS PI11/01588  (to M. L. M. -C),  Asociación Española  contra el Cancer (T. C. D, and P. F-T),  SAF 2011-29851  and  Educación Gobierno Vasco  (to J. M. M. ),  FIS PI12/00402  and  Program Ramón y Cajal  (to N. B),  Sanidad Gobierno Vasco 2012  (to M. V. R. ),  Basque Goverment   IT-336-10 ,  Unidad de Formación e Investigación   UFI11/20 , and  University of Basque Country  (to P. A),  FIS PI 11/01830  (to J. B) Programma di ricerca Regione-Università 2007-2009 and  2010-2012 ,  Regione Emilia-Romagna  (to E. V. ). Ciberehd is funded by the  Instituto de Salud Carlos III.
This paper describes a system for off-line recognition of handwritten Arabic words. It uses simple and easily extractable features to construct feature vectors for words in the vocabulary. Some of these features are statistical, based on pixel distributions and local pixel configurations. Others are structural, based on the presence of ascenders, descenders and diacritic points. The system is evolved based on vertical and horizontal Hidden Markov Models and Dynamic Bayesian Network. Our strategy consists of looking for various architectures and selecting those which provide the best recognition performance. Experiments on handwritten Arabic words from IFN/ENIT database and ancient manuscripts strongly support the feasibility of the proposed system. The recognition rates achieve 91. 89% (IFN/ENIT) and 94.
BNs allow representing probability models in an efficient and intuitive way  [3] ,  [4]. A Dynamic Bayesian Network (DBN) is a BN which relates variables to each other over adjacent time steps. The temporal extension of BN towards DBN  [5] ,  [6] , have been recently applied to a range of different domains. In fact, DBNs have been used in speech recognition  [7]  as a flexible and efficient extension of HMMs. Another kind of application exploits the ability of DBNs to be trained to detect patterns. For that, the observed information used as an input for the DBN is made of pre-extracted features. It is possible to use low-level data such as image pixels, as shown for instance by the application of DBNs to character recognition  [8]. In  [17] , multiple models of BNs are applied to off-line recognition of Arabic handwritten Tunisian city names, extracted from IFN/ENIT database.
The ARCPL model is obtained by coupling both vertical and horizontal streams. ARCPL model was chosen to be used since it is superior to other coupled models, having achieved the highest recognition rate. In the same work, authors use independent models and types of coupled models for the recognition of real degraded old printed characters extracted from the British Library's collection of digitized Renaissance festival books. In  [9] , authors present four DBN models trained for classification of Latin handwritten digits. The structure of these models is partly inferred from the training data of each class of digit before performing parameter learning. The DBN models have their structure partly based on inter-slice links learned from data. Model 1 is a DBN made of evidence nodes only, with inter-slice links learned from the data (columns of pixels).
Model 2 has the same evidence nodes as in Model 1 , with one hidden node per slice, connected to every evidence nodes of the slice. Model 3 is a DBN observing columns and lines of pixels coupled through hidden nodes. Model 4 is same as Model 2 , completed with intra-slice links learned from the data (see Figure  8 ). Like work reported in  [8] , authors in  [10]  use independent models (auto-regressive horizontal and vertical HMMs). To evaluate the performance of their recognition system, experiments are conducted on the ADBase database. Currently, only a small set of 500 digits are used in experiments. Note that the system relies on the DBN classification and density features. The main drawback is the long training time required for some applications. To recognize Arabic handwritten words with DBN models, authors in  [11]  divide their work into three stages, namely pre-processing, feature extraction and classification.
Pre-processing includes baseline estimation and normalization as well as segmentation. Pixel features are then extracted from each of the normalized words based on a sliding window approach. More precisely, a feature vector for each word mirror image is performed by applying a horizontal sliding window having the same height of the word image. Words are finally recognized using HMM (a left to right Bakis topology) and DBNs (conceived as several coupled HMMs architectures: state coupled model, general coupled model and auto regressive coupled model). The DBN parameters are learned using the EM algorithm. The IFN/ENIT database is used for training and testing. We think that since DBN is working based on time slice, this is consistent with features extracted from sliding windows. In  [17] , multiple models of BNs are applied to recognition of Arabic handwritten city names.
7% Our system 21 words, 5279 samples DBN=81. 06%, VH-HMM=91. 89% Note that we proposed, as done by  [11]  a data fusion scheme which couples two data streams, image columns and image rows into a single DBN classifier. More precisely, we constructed a state coupled model by adding the directed edges between the hidden state nodes of both vertical and horizontal HMMs. But, it differs from the proposed one in  [11]  where only pixel features are used for word In fact, we proposed to use not only statistical features but also to combine them with structural ones. As it can be seen, the combined use of different types of features provides better results. From experiments, conducted using a subset from IFN/ENIT benchmark database, the recognition rates achieved by the proposed VH-HMM and DBN, in comparison to some related works, are among the best for the same task.
Statistical features are used to support structural features. For example, if one stem is detected at the beginning of the word, the number of black to white or white to black pixel transitions should be 2. -No word segmentation is required for feature extraction. This is especially crucial in case of cursive script recognition because it is not obvious that the handwritten Arabic word will be correctly segmented. We showed proposed models interest in off-line Arabic handwritten word recognition. First, experiments have been conducted using words extracted from ancient Arabic manuscripts, conserved in the national archives of Tunisia, to demonstrate how robust the proposed models are. Then, others experiments were conducted using a subset of the IFN/ENIT standard database. Experimental results and quantitative evaluations showed that a 2D-HMM outperforms DBN in terms of higher recognition rate and lower complexity.
These GPDs are of special interest as they are related to the total angular momentum carried by partons in the nucleon  [11]. A variety of GPD fits using all existing DVCS proton data has shown that the contributions of GPDs H f are dominant. They are constrained  [12, 13, 14, 15]  over the presently limited accessible x Bj range, by the very-low x Bj data of the HERA collider and by the high x Bj data of HERMES and JLab. There exist constraints on GPDs E f for valence quarks from fits to nucleon form factor data  [16] , HERMES transverse proton data  [17]  and JLab neutron data  [18]. A parameterisation of chiral-even GPDs  [9] , which is consistent with the HEMP data of HERMES  [19]  and COMPASS  [20] , was recently demonstrated to successfully describe almost all existing DVCS data  [21].
This is clear evidence for the consistency of the contemporary phenomenological GPD-based description of both DVCS and HEMP. There exist also chiral-odd -often called transverse -GPDs, from which in particular H f T and E f T were shown to be required  [22, 23]  for the description of exclusive π + electroproduction on a transversely polarised proton target  [24]. It was recently shown  [25]  that the data analysed in this letter are also sensitive to these GPDs. This Letter describes the measurement of exclusive ρ 0 muoproduction on transversely polarised protons with the COMPASS apparatus. Size and kinematic dependences of azimuthal modulations of the cross section with respect to beam and target polarisation are determined and discussed, in particular in terms of the above introduced chiral-odd GPDs.
Experimental set-up The COMPASS experiment is situated at the high-intensity M2 muon beam of the CERN SPS. A detailed description can be found in Ref. [27]. The µ + beam had a nominal momentum of 160 GeV/c with a spread of 5% and a longitudinal polarisation of P ≈ -0. 8. The data were taken at a mean intensity of 3. 5 • 10 8 µ/spill, for a spill length of about 10 s every 40 s. A measurement of the trajectory and the momentum of each incoming muon is performed upstream of the target. The beam traverses a solid-state ammonia target that provides transversely polarised protons. The target is situated within a large aperture magnet with a dipole holding field of 0. 5 T. The 2. 5 T solenoidal field is only used when polarising the target material. A mixture of liquid 3 He and 4 He is used to cool the target to 50 mK.
The dilution factor f , which is the cross-section-weighted fraction of polarisable material, is calculated for incoherent exclusive ρ 0 production using the measured material composition and the nuclear dependence of the cross section. It amounts typically to 0. 25  [20]. The spectrometer consists of two stages in order to reconstruct scattered muons and produced hadrons over wide momentum and angular ranges. Each stage has a dipole magnet with tracking detectors before and after the magnet, hadron and electromagnetic calorimeters and muon identification. Identification of charged tracks with a RICH detector in the first stage is not used in the present analysis. Inclusive and calorimetric triggers are used to activate data recording. Inclusive triggers select scattered muons using pairs of hodoscopes and muon absorbers whereas the calorimetric trigger relies on the energy deposit of hadrons in one of the calorimeters.
3  and 4 , respectively. Error bars show statistical uncertainties. The systematic uncertainties are represented by grey shaded bands. Average asymmetry values for all modulations are given in Fig. 5  and Table  2. For three of them, the experimental precision is as high as O (± 0. 01). All average asymmetry values are found to be of small magnitude, below 0. 1. Except A sin φ S UT , all other average asymmetry values are consistent with zero within experimental uncertainties. All results are available in the Durham data base. -0. 019 ± 0. 008 ± 0. 003 As already mentioned above, there exists presently only the model of Refs. [7, 8, 9]  to describe hard exclusive ρ 0 leptoproduction using GPDs. It is a phenomenological 'handbag' approach based on k ⊥ factorisation, which also includes twist-3 meson wave functions.
Co-expression analysis Results retrieved (Figure  6 ) from Atted-II database (Obayashi et al. , 2014) revealed that genes involved in GIPC biosynthesis, such as LAG ONE HOMOLOGUE (LOH) encoding a ceramide synthase  (Ternes et al. , 2011) , were co-expressed in several species with genes involved in the biosynthesis of RG-II such as ketodeoxyoctulosonic acid [involved in biosynthesis of 3-deoxy-D-manno-2-octulosonic acid (KDO)] and RGXT (RG-II xylosyltransferase; involved in side-chain A biosynthesis). Likewise, LOH genes are coexpressed with genes involved in the biosynthesis of RG-II's homogalacturonan backbone (GAUT1, GAUT7 and GAUT8, encoding three galacturonosyltransferases). Moreover, both RG-II and GIPC biosynthesis occur in the Golgi apparatus  (Mohnen, 2008) ; therefore, if the B-dependent dimerization of RG-II does require the intermediacy of a GIPC-B-RG-II complex, all necessary participants in the process would be present together in the endo-membrane/ exocytosis systemwhich is the major location of RG-II dimerization in vivo  (Chormova et al.
Different alternative approaches have thus been developed. Concerning the BC emissions, useful information may be gained from their evaluation relative to emissions of another compound for which uncertainty in emissions is expected to be smaller. For example,  Zhou et al. (2009)  derived BC emissions in two Chinese megacities from CO emissions and measured BC / CO ratios at sites 10-15 km downwind of the cities. However, given the large size of these megacities, the measurement representativeness for the city emissions remains an open question. Other methods specifically assess transport patterns of emissions to the receptor point. Xu et al. (2013)  developed a method based on in situ measurements and backward trajectory analyses to evaluate BC emissions over the North China Plain. A promising approach consists in using inverse modeling techniques, which were widely applied to NO x emissions using variational data assimilation  (Mendoza-Dominguez and Russell, 2000) , Bayesian Monte Carlo approaches  (Deguillaume et al.
, 2007; Konovalov et al. , 2008) , and Kalman filter approaches  (Napelenok et al. , 2008; Gilliland and Abbitt, 2001). NO 2 columns retrieved by satellites (e. g. , from GOME, SCIAMACHY, OMI, GOME-2) provide a valuable observational basis for many of these works because of their large data coverage. For BC, the only study using variational data assimilation we are aware of is that of  Hakami et al. (2005) , which aims at better constraining BC emissions over East Asia from in situ measurements. The aim of this paper is to evaluate emission inventories at the scale of a large city. In this context, it presents an original methodology based on airborne measurements in the city plume and chemistry-transport simulations. It is applied to BC and NO x emission inventories over the Paris megacity, using the CHIMERE model.
Measurement database In the framework of the EU FP7 MEGAPOLI project  (Baklanov et al. , 2010) , two 1-month intensive campaigns (July 2009 and January/February 2010) were organized in the greater Paris area to better characterize organic aerosol in a large megacity. The study presented here is based on observations obtained during the summer campaign. Petzold et al. (2013)  recently made some recommendations about the use of the term "BC" for black carbon, distinguishing various terminologies depending on the property used in the measurement technique: (i) the light absorbing coefficient σ ap , or equivalent BC (EBC) if the mass-specific absorption coefficient (MAC) is indicated, for instruments based on light absorption; (ii) refractory BC (rBC) for instruments based on refractory properties; and (iii) elemental carbon (EC) for instruments focusing on the chemical composition or the carbon content based on thermo-optical methods.
88, N = 533; see Sect. S1 in the Supplement, for details). NO x observations come from a chemiluminescence monitor (AC31M, Environment SA) equipped with molybdenum oxide converters. However, an efficient conversion of many other nitrogen-containing compounds (NO z = NO y -NO x ) by the molybdenum converter can lead to interferences in the NO x concentrations  (Dunlea et al. , 2007). This positive artifact varies from one location to the other, depending on the relative contribution of NO z compounds in the NO y family. Dunlea et al. (2007)  estimated a mean overestimation of +22 % in Mexico City. Among the chemical data available in the Paris plume, NO y and EBC airborne measurements aboard the French ATR-42 aircraft have been used (see  Freney et al. , 2014 , for a detailed description of the aircraft campaign).
BL height (BLH) estimations are available at the SIRTA (Site Instrumental de Recherche par Télédétection Atmosphérique) (48. 712 • N, 2. 208 • E) (suburban background site at about 20 km in southwest of Paris) and LHVP stations. At SIRTA, they are estimated from ALS450 Leosphere backscatter lidar data at a 5 min time resolution  (Haeffelin et al. , 2012). At LHVP, values are estimated from CL31 ceilometer data  (Haeffelin et al. , 2012). Traditional meteorological parameters (wind, temperature) are also measured at SIRTA, where, additionally, Leosphere wind cube lidar measurements are also available, providing wind measurements at a 10 min time resolution, each 20 m from 40 to 200 m above ground level (a. g. l. ).
Emission inventories Three European anthropogenic emission inventories are evaluated in this paper, all referring to year 2005: 1. The EMEP inventory  (Vestreng et al. , 2007) , with a longitude-latitude resolution of 0. 5 • × 0. 5   et al. (2012). The inventory is the year 2005 base case and also serves as a starting point for the inventory described next. In this paper it is referred to as the TNO inventory. 3. A third inventory based on the TNO inventory and with the same 1/8 • × 1/16 • longitude-latitude resolution but incorporating bottom-up emission data over four European metropolitan regions (Paris, London, Rhine-Ruhr and Po Valley). The city emission inventories were compiled by local authorities responsible for city emission inventories and air quality such as Airparif for Paris (Airparif, 2010).
It is described in more detail by  Denier van der Gon et al. (2011) , and has been previously used in  Zhang et al. (2013)  and  Timmermans et al. (2013). It will be referred to as the TNO-MP (MP for MEGAPOLI) inventory. The same EC / OC speciation table, primarily associated with the TNO inventory, is applied in all inventories. Sectordependent factors used to derive July emissions from annual ones are reported in Table  S2  in the Supplement. This table also shows the total sector-wise BC July emissions over the region for the three inventories. The resolution of both the TNO and TNO-MP inventory is considerably improved compared to the EMEP inventory. Despite its coarse spatial resolution, the comparison of this latter inventory with the two other refined ones remains relevant for several reasons: (i) before being applied to simulations, emissions are downscaled to the air quality model resolution, here to a 3 km horizontal resolution, using the 1 × 1 km resolved GLCF (Global Land Cover Facility) land use database  (Hansen et al.
Results and discussion In this section, we first evaluate meteorological input data (Sect. 4. 1). A first simple approach is then applied to evaluate BC emissions against NO x ones, based on ground-based measurements at the urban background LHVP site in Paris (approach no. 1, Sect. 4. 2). We then describe the procedure to evaluate BC emissions based on airborne measurements in the Paris plume, and present the corresponding results (approach no. 2, Sect. 4. 3). We finally discuss discrepancies between both methods (Sect. 4. 4). Statistical metrics are defined as follows: -Mean bias: MB = 1 n n i=1 (m i -o i ). (1) -Normalized mean bias: NMB = 1 n n i=1 (m i -o i ) o. (2) -Root-mean-square error: RMSE = 1 n n i=1 (m i -o i ) 2. (3) -Normalized root-mean-square error: NRMSE = 1 o 1 n n i=1 (m i -o i ) 2.
Acknowledgements. The research leading to these results received funding from the  European Union 's  Seventh Framework Programme FP/2007-2011  under grant agreement no. 212520. The authors also acknowledge the  ANR  through the  MEGAPOLI   PARIS  project and ADEME and LEFE through the  MEGAPOLI France  project for their financial support. This work is funded by a  PhD DIM (domaine d'intérêt majeur) grant  from the  Île-de-France region. We would like to thank the two anonymous referees for their valuable comments on this work. Edited by:  A. Baklanov.
Very active Source: Compiled by authors based on the regions' websites and secondary evidence. The product of these strategies is a database with a large N, which is not a perfectly exhaustive or representative collection of all participatory experiences but represents a quite diverse picture of what is the broader reality of participatory processes developed at the subregional level in these countries. With this type of results we try to go beyond the common research trends that tend to focus on "exemplary" institutions, focusing instead on the everyday and more mundane use of engagement techniques  (Cooper & Smith, 2012)  in the most common and less well-known cases. We cannot claim we have done a detailed mapping of any kind of bottom-up activity that shares these characteristics, but our institutionally recognized participatory processes represent a significant part of the participatory activity existing in (certain regions of) Italy and Spain dealing with public issues.
Perhaps this category is underrepresented due to the fact that some indirect collaboration of civil society actors in the promotion of the processes has not been visible during the interviews or the Internet data mining. 13 The smaller study made by the International Observatory on Participatory Democracy (IOPD) shows the same picture: the origin of 84% of European processes (27 of 32) lies in government and not civil society  (Font et al. , 2003). Local governments are not isolated promoters of deliberation in public administrations. In the two regions where this information is available (Andalusia and Apulia), around half of the local participatory experiences have been promoted with the contribution of other public administrations (usually provincial or regional). This multilevel involvement is also reflected in relation to the financing of participative processes.