dataesr/scientific-paragraphs-categorization huggingface dataset:
This work was supported by grants from the  Agence Nationale de la Recherche  to  EC  ( ANR-10-JCJC-1303-03 ) and from the  Fondation pour la Recherche Médicale (FRM)  to CC ( DEQ2011-0421282 ). VSN is supported by a PhD grant from the  French Embassy in Vietnam , and TTHL is supported by a PhD grant from the  University of Sciences and Techniques of 1 Hanoi (USTH). LL is supported by a doctoral fellowship from the  French Ministry of Research. ED was supported by a  FRM post-doctoral fellowship  ( FRM-SPF20101221116 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
After 30min glucose deprivation in DMEM No Glc medium, a 1h-GLP-1 secretion test in response to DMEM without glucose, to DMEM with glucose (5. 5 mmol L -1 ) or in response to DMEM with glucose (5. 6 mmol L -1 ) plus phloretin (0. 5 mmol L -1 ) was performed at 37°C in DMEM plus 1% DPP4 inhibitor (Ile-Pro-Ile, Sigma Aldrich). Finally, medium was removed, centrifuged for 5min at 4°C at 13000 rpm and immediately frozen at -80°C. GLP-1 content in culture medium was measured as described below. The remaining tissue was washed in cold PBS and frozen at -80°C in NaOH 2N. Protein content was assessed according to BCA's method (Thermoscientific). Culture and immunostaining on human intestinal biopsies-Fresh human jejunum biopsies from normoglycemic subjects were obtained with informed consent as part of the A Biological Atlas of Severe Obesity (ABOS) study (ClinicalTrials.
gov; NCT01129297). Mucosa were dissociated from musculosa and cut into small pieces of 1 cm 2 before treatment for 16h with DMSO or GW4064 (5 μmol L -1 ) in RPMI medium + GlutaMAX ™ -1 (Cat. No. 61870-010, Life Technologies) containing glucose (11 mmol L -1 ), sodium pyruvate (1 mmol L -1 ) and supplemented with 10% Fetal Bovine Serum (FBS, Life Technologies) and penicillin/streptomycin (10000 U L -1 / 10 mg L -1 ) in a 37°C, 5% CO 2 controlled atmosphere. RNA extraction and qPCR analysis were performed as described below. For immunohistochemical analysis, human jejunal biopsies were O/N fixed with paraformaldehyde 4% (Sigma) before incubation with 20% sucrose during 20h and further inclusion in Jung Tissue Freezing Medium (Jung) and storage at -80 °C before processing. Twelve μm-thick slices were post-fixed in methanol/acetone 50/50 (v/v) during 10min at -20°C.
Microarray analysis-GLUTag cells were treated or not with GW4064 (5 μmol L -1 ) for 24h and 4 RNA samples of each treatment condition were hybridized on mouse GEP 8*60K arrays. Scanning clusters and data acquisition were carried out following the manufacturer's instructions (Agilent, One-color microarray Gene Expression Analysis). Data processing and analysis were performed using the Genespring Software. Biological Processes Analysis was performed using Gene Ontology Biological Processes on the Genomatix Software (Genomatix, Deutschland). Data are deposited at EBI under the E-MTAB-2199 number.
Supplementary Material Refer to Web version on PubMed Central for supplementary material. (a) Proglucagon qPCR on cDNA from GLUTag cells starved for 12h with lactate (10 mmol L -1 ) and then incubated for 24h in lactate (10 mmol L -1 ), glucose (5. 6 mmol L -1 ) or 2deoxyglucose (5. 6 mmol L -1 ) media containing DMSO, GW4064 (5 μmol L -1 ) or CDCA (100 μmol L -1 ) (n=3; performed 3 times). Data are represented as mean +/-SD. Two-Way ANOVA analysis followed by Bonferronni's posthoc test. ***P≤0. 001: effect of GW4064 and CDCA on proglucagon mRNA levels in each medium conditions. § § § P≤0. 001: effect of glucose on proglucagon mRNA levels in DMSO, GW4064 and CDCA conditions. (b) Chrebp qPCR on cDNA from FACS-sorted proglucagon-negative and proglucagon-positive cells from the ileum (ileum L-; ileum L+) and colon (colon L-; colon L+) of GLU-VENUS mice (lower panel; n=3) and ChREBP protein expression from cytoplasm and nucleus extract from GLUTag cells (upper panel; performed 3 times).
Acknowledgments We wish to thank  Meryem Tardivel  and  Anne-Sophie Drucbert  of  BiCeL-IFR114 Facility  for access to systems and technical advice. Bart Staels is a member of the  Institut Universitaire de France. Grant support: MST was supported by a grant from the  French Ministry for Education and Research. VS was supported by grant from the  "Fondation pour la Recherche" (FRM). This work was supported by grants from  Région Nord-Pas de Calais, INSERM, A. N. R. (FXREn) ,  Université Lille 2, Université Lille Nord de France  and  European Genomic Institute for Diabetes (EGID ,  ANR-10-LABX-46 ). YS was supported by grant from the  Lille Métropole Communauté Urbaine (LMCU). FMG, FR and CAB are funded by the  Wellcome Trust  ( WT088357/Z/09/Z ,  WT084210/Z/07/Z  and the  WT PhD programme in Metabolic and Cardiovascular Disease ).
Plant material The two apple core collections used in this study had been previously constituted by choosing the individuals that maximized the genetic diversity based on a set of 24 microsatellite markers in the INRA Angers germplasm collection of dessert and cider apple cultivars. Shortly, the core collections were built by retaining individuals from larger sets of apple accessions (737 and 188 for dessert and cider apples, respectively) using the 'Maximum Length Subtree' option of the DARwin software  (Perrier et al. 2003; Perrier and Jacquemoud-Collet 2006). The two core collections included 48 dessert and 48 cider apple cultivars, respectively (Supporting information). Reflecting the content of the INRA germplasm collection, both core collections mainly include old (generated before the 1950's) French apple cultivars, some of them being clones of cultivars grown in other European countries under different names.
SNP filtering SNPs were filtered using the Genotyping Module (version 1. 8. 4) of the Illumina â GenomeStudio software (Illumina Inc. , San Diego, CA, USA). A visual inspection of each SNP was performed, and SNPs exhibiting a good genotypic clustering in distinct spots were kept. Paralogous SNPs were removed by performing BLAST onto the apple genome and removing probes having two equally good best hits onto the reference genome. This step was necessary for avoiding potential paralogy, due to the whole-genome duplication having occurred in the apple evolutionary history  (Velasco et al. 2010). There were a few missing data in the dataset obtained from GenomeStudio, we therefore used fast-PHASE 1. 2  (Scheet and Stephens 2006)  with the default parameters, and we indicated whether an individual belonged to the cider subgroup or to the dessert one to impute the missing data and to phase the SNPs belonging to a given linkage group (LG).
Estimation of linkage disequilibrium The levels of linkage disequilibrium were estimated using the r 2 parameter between all pairwise comparisons using the Haploview 4. 2 software  (Barrett et al. 2005 ) and a minor allele frequency (MAF) cutoff of 0. 01. A first analysis was run without taking into account the structure and kinship in the collections; the levels of linkage disequilibrium were then corrected for population structure (see below) and kinship using the R package LDcorSV  (Mangin et al. 2012). The kinship matrix, reflecting the degree of genetic covariance among individuals, was calculated with the Cocoa 1. 1 software  (Maenhout et al. 2009).
Analysis of population structure The ADMIXTURE 1. 23 software  (Alexander et al. 2009 ) was used to investigate the genetic population structure in the dataset. The number of genetic clusters K was assessed using values ranging from 1 to 10, and we chose the number of clusters for which the cross-validation error was the lowest. The cross-validation procedure masks one-fifth of the genotypes (five runs altogether) and calculates estimates for these genotypes. Each genotype is then predicted, and the software calculates a prediction error across all masked genotypes. The Q matrix, that is, the posterior probabilities for each individual to belong to a given cluster, outputted by ADMIXTURE 1. 23 was used for the genotype-phenotype association analysis.
Identification of candidate genes The online apple genome browser hosted on http:// www. rosaceae. org/, containing the gene model predictions made on the apple genome sequence, was used to investigate the putative functions of genes present in the genomic regions detected in the tests above. The Blast2Go 3. 0 software  (Conesa et al. 2005)  was used to perform BLASTX on these sequences with a maximum Blast ExpectValue of 10 À3. After gene ontology (GO) functional annotation, the KEGG tools were used to visualize the corresponding metabolic pathways. A BLASTN was run, and its results were used as inputs in Blast2GO 3. 0 to retrieve GO annotations for the entire gene set of the apple genome. The regions of interest were then tested for enrichment of particular gene functions.
SNP genotyping After visually screening the 7867 SNPs of the IRSC apple 8K SNP array v1 on GenomeStudio, a set of 4234 polymorphic SNPs evenly spread across the apple genome was obtained; after removing potential paralogous SNPs, the number of markers was reduced down to 3704. The number of markers per linkage group was approximately proportional to their length. The average distance between two adjacent SNPs was 140 kb, with the maximum distance separating markers ranging from 1. 26 Mb on LG17 to 4. 25 Mb on LG15. The distribution of the SNP minor allele frequencies (MAF) was quite uniform across the different possible MAF values (Fig. 1 ) whether considering the cider or the dessert cultivars. Overall, few data were missing in the dataset, with 2981 markers having no missing data at all and the maximum percentage of missing data being 5.
Estimation of linkage disequilibrium The nonlinear regression model used to analyze the decay of linkage disequilibrium (LD) with the physical distance showed that the squared allele correlation parameter r 2 decayed below 0. 2 within 100 kb (Fig. 2 ). When analyzed separately, the cider and the dessert core collections showed very similar behaviors. The results obtained on the whole dataset when taking into account kinship or/and population structure were very similar too. We therefore assumed that loci distant from more than 100 kb were not in LD and considered windows of 100 kb on both sides of outlier SNPs for finding candidate genes possibly evolving under divergent selection.
Differentiation between cider and dessert apples -Analysis of population structure Pairwise F ST between cider and dessert apples ranged from 0 to 0. 24, with a mean value of 0. 014, confirming the weak differentiation between the two core collections. ADMIX-TURE analyses revealed a minimum value of the cross-validation error for K = 2. Only a quarter of the individuals actually showed a clear assignment (membership probability >0. 9) to any cluster, supporting the lack of further structure in the dataset. The Q matrix for K = 2 (Fig. 3 ) confirms the lack of strong differentiation according to the cider/dessert classification, even using genome-wide markers.
6 PCR products were cloned into pCR2. 1 TOPO vector (Invitrogen, Carlsbad, CA), and DNA sequencing was performed using Big-Dye terminators (Applied Biosystems) on a 16-capillaries electrophoresis system 3130 XL (Applied Biosystems). Sequences were analyzed using FinchTV software and aligned on Multalin (http://multalin. toulouse. inra. fr/multalin/).
They could be associated with devices such as Nose to Text software (Brechbuhler, Switzerland) or Voice Chromatogram Interface (Atas/GL Sciences, The Netherland,  [29] ) that merge vocal information into numerical data through a voice recognition system. However, these last appliances do not prevent perturbations associated with speaking. Besides, descriptors are often freely chosen by judges and for a same odor event, a consensus is complicated to obtain between judges. This lack of consensus is due to the difficulty for humans' brain to link the olfactory and the semantic memories and thus, to clearly associate a word to an odor. It explains why odor identification frequently leads to a fail  [30]. To come through this problem, judges can be constrained to choose a term among a suitable short list  [31].
Conversely, the pan-fried onions are characterized by more odorant zones detected associated with higher intensities and notably by an enhanced perception of some Maillard compounds. The aromatic profile of sautéed onion is qualitatively close to that of sué onion but is associated with more important intensities. Particularly, the presence of pyrazines could contribute to the specific aroma of the sautéed onions. This knowledge can be notably capitalized by food industry to create or enhance culinary notes in food products. The assessment of olfactometric profiles obtained for onions prepared by three different modes of cooking and the comprehension of such fine nuances in aroma could not have been performed without the precision and the accuracy of data recorded by the laboratorydeveloped software coupled with the statistical processing of intensity scores.
Effluent from the end of the GC column was split 1:3 between the MS, the FID, and the olfactometric port (250 °C, air/H2 flow 450/40 mL•min -1 ). Peak areas were integrated using MSD Chemstation software (Agilent Technologies). Mass spectra were recorded in electron impact mode (70 eV) between a mass range of 33 to 300 m/z at a scan rate of 2. 7 scan•s -1.
Olfactometric conditions GC effluent was carried to the sniffing port using a deactivated and uncoated fused silica capillary column, heated to 200 °C. The GC sniffing port is equipped with a nose glass funnel where assessor puts his nose. The olfactometric port was supplied with humidified air to prevent dehydration of the nasal mucosa. Olfactometric data were recorded in real time with laboratory-designed software that records the following parameters synchronously the GC-MS analysis: times of perception of an odor, intensity, and associated descriptor. Descriptors were generated from literature on aroma compounds found in raw and cooked onions  [8, 13, 61, 62]  and from previous sniffing sessions performed by two expert judges on each of the three onion preparations. They were presented on a dedicated wheel aroma especially designed for the study of cooked onions samples (Fig.
Odorant compound identification Odorant compounds were identified by comparison of their mass spectra with those of a reference database (Wiley 6. 0 and internal laboratory database). Linear retention indices (LRI) of detected compounds were calculated by means of n-alkane injections (C6 to C32) and compared with those of standards injected in the same conditions and with those found in the literature. Descriptors given for each detected compound were also compared with those found in the literature.
Acknowledgements This research was part of global program "Mise au point d'ingrédients végétaux multifonctionnels innovants" financially supported by the  Unique Interministerial Fund  and the  French public investment bank  ( FOI-AAP10 ). This program was also labeled by Valorial. The authors acknowledge  Eric Vouland  for his active participation in setting up the project,  Rob Evans  for the follow-up of the study,  Claude Inisan  and  Sébastien Langlais  for their proofreading of the manuscript, and  Ehsane Khadraoui  and  Cécile Pussat  for their contribution in the lab pre-tests. The authors also want to thank the judges for their involvement in olfactometry analyses.
Sampling and maintenance of gammarids Male and female Gammarus fossarum were collected with a hand-held net (2-2. 5mm) at La Tour du Pin, upstream of the Bourbre River (France)  [19, 31]. The station has good water quality according the data records of the RNB (French Watershed Biomonitoring Network). After sampling, the gammarids were brought to the laboratory, where they were kept in 30-L tanks under constant aeration at 14±0. 5°C using a 10/14-hr light/dark photoperiod. The tanks were continuously supplied with drilled groundwater mixed with softwater (obtained by reverse osmosis) to adjust to the sampling site conductivity of 600 μS/cm. Throughout the 15 days of the acclimatization period, gammarids were fed ad libitum with alder leaves (Alnus glutinosa) collected from a pristine site and previously conditioned for at least 6 (±1) days in groundwater.
Method of calculation Semi empirical calculations have been performed using Hyperchem program version 8. 0. 6 for windows  16  running on a Windows seven with a core i5 vPro. The initial geometry optimization of the studied molecules were performed with the molecular mechanics (MM+) force field  17, 18  , where the lowest energy conformations are obtained. Further, Geometry optimization was done by performing the semi-empirical molecular orbital theory at the level parametric method (AM1)  19  , within restricted Hartree-Fock (RHF) level  20. The Polak-Ribier algorithm was used for the optimization  21. The convergence is set to 0. 01 kcal/mol.
Correlation A study was conducted using IBM SPSS Statistics v 21 to find a correlation between the maximal reaction rate (V max ) and the HOMO energy. The results were given in Table  5  and Fig. 7. Correlation quantifies the extent of the relationship two quantitative variables, here V max and E HOMO. When high values of V max are associated with high values of E HOMO a positive correlation exists. However, a negative correlation obtained, when high values of V max are associated with low values of E HOMO. A strong correlation is observed between the maximal reaction rate (V max ) and HOMO energy, so the correlation is significant (r = -0. 794; P = 0. 019), here the correlation is negative. These results show a good linear correlation between the maximal reaction rate and HOMO energy. This correlation proves the existence of a relationship between the catalytic activity, which is presented by V max , and HOMO energy, so we can estimate V max by calculating of the HOMO energy for this kind of ligands.
d. × 150 mm, 3 μM particle size). Peptides were loaded onto a LC-Packings pre-column (Acclaim PepMap 100 C18, 5 μM particle size, 100 A, 300 μM i. d × 5 mm) in 0. 1 % formic acid for 5 min at a flow rate of 20 μL/ min to desalt samples. A gradient employed of 5-55 % B in 60 min was used to elute peptides (Solvent A = 0. 1 % formic acid in water and solvent B = 5 % acetonitrile with 0. 1 % formic acid in water). Data were processed using Bioworks Browser (version 3. 3. 1 SP1, ThermoFisher), and searched using MASCOT (Matrix Science Ltd) using a fixed modification of carbamidomethyl and a variable modification of oxidation (M). The databases used were NCBInr 060629 Rattus or Homo sapiens with a Peptide Mass Tolerance of ±1 Da and a Fragment Mass Tolerance of ±0. 8 Da.
As an alternative approach, we sought to estimate the size of the inhibitory protein, which would then facilitate a bioinformatic search. For this purpose, fractions obtained following CM and High Q separation were spiked with two proteins of known molecular weight [immunoglobulin G (IgG), 150 kDa, and lysozyme, 14 kDa] before they were further separated on S100 Sephadex size-exclusion columns. The addition IgG and lysozyme to protein fractions did not change the distribution of the inhibitory activity. Based on the localization of the inhibitory activity relative to the reference proteins, the size of the predicted protein was calculated to be approximately 51 kDa (Fig. 2a , Supplementary Fig. 2 ). Taking into account that post-translational modifications may alter the size of the protein core, we conducted PubMed Protein Database searches for signalling proteins expressed in the CNS that fall within a size range of 30-55 kDa (search terms: "030000:055000 [Molecular Weight] and membrane and signalling and ligand and brain").
Agents are assumed to be able to communicate via reliable materials, in order to achieve some plan called coordinated plan. The paper contribution. We propose to model plan in a more attractive way using the standard algebraic language based on LOTOS, seeing plans as the execution of concurrent processes  [3]. In fact, LOTOS specifications supplies modular concepts useful to describe some plan over several agents. Moreover, LOTOS-basic specifications are translated in daTA relative time rates (daTA-RT). daTA-RT compactly represents the possibly infinite behaviors of the coordinated plans, this model is concerned by the timing constraints defined over the MAS plans, taking into account relative time rates that distinguish the speeds of the agents in coordination. In this paper, we show how to build a (finite) region graph structure from a daTA-RT specification, for decidability assessment and proof.
e. agents) by message passing, in addition to classical features of concurrent processes. In our case the basic LOTOS is sufficient for what we intend to present. Paper outlines. In Section 2, the specification of coordinated MAS plans is presented, based on LOTOS concepts, the relative time rates are explained and our running example is built. In Section 3, the daTA model is recalled, its extension to relative time is defined and an informal meaner of generating daTA structure from LOTOS expression is shown. The main contribution of this paper is proposed in Section 4, where the semantic of daTA is presented and formally defined. In all the paper the same example is used to clarify concepts and applications. The end section concerns conclusion and some immediate perspectives.
From Basic LOTOS with Action Durations to daTA with Relative Time Rates In this section, we informally present the manner of generating in an operational way a daTA-RT starting from a Basic LOTOS specification with action durations. The approach is very close with the one of  [4]  for the generation of MLTS (Maximality based labeled transition system). In our context it's viewed as an unfolding operation of the behavior expression to state transition structure. Take again the behavior of the system described in the example of transport which is expressed as the parallel composition of two subsystems with synchronization on the action meet. where no action was launched yet. From this configuration, action can be allowed. A clock , is assigned to this occurrence of , it will be initialized to zero.
Newly identified SNPs that were significantly associated with DMARD-free sustained remission in the Leiden EAC cohort were selected for evaluation in the ESPOIR cohort. Within the Leiden EAC cohort, the HLA-DRB1 alleles were genotyped using two-digit typing which was complemented by four-digit typing of the DRB1*04 alleles and by specific probes to detect the presence of the SE   [23]. Genotyping data on rs1896368, rs1896367, and rs1528873 in DKK-1 and on rs1485305 in OPG were retrieved using Illumina's Golden Gate platform with an overall error rate <2. 5 % and success rates >95 %  [19, 22]. rs26232 in C5Orf30 was genotyped using LightSnp (Roche) with an overall error rate <1 % and success rates >99 %  [20]. Genotyping data on rs2104286 in IL2RA, rs11908352 in MMP-9, and rs451066 at chromosome 14 were retrieved using Illumina's Immunochip with an overall error rate <1 % and success rates >98 %.
For the genetic variants, the cutoff for statistical significance was set at p <5. 56 × 10 -3 (0. 05/9 tests) using the Bonferroni correction for multiple testing. For the test on the serum level, p <0. 05 was considered significant. In the ESPOIR cohort, a similar Cox proportional hazard regression analysis adjusted for age and gender was performed. ESPOIR RA patients were diagnosed in a relatively short interval and no adjustments were made for initial treatment strategies. Results of the two cohorts were combined in an inverse variance weighted meta-analysis. Analyses were performed using IBM SPSS version 20 (Armonk, NY, USA) and STATA version 12 (College Station, TX, USA).