dataesr/scientific-paragraphs-categorization huggingface dataset:
We mixed 3 ml of a 256 diluted cDNA (or 1 ng/ml) with FastStart DNA MasterPLUS SYBR green I mix with 500 nM of each primer, and the reaction mix was loaded on the capillaries and submitted to 40 cycles of PCR (95uC/15 s; 60uC/10 s; 72uC/20 s for the Lightcycler and 50uC 2 min; 95uC/20 s; [95uC/1 s-60uC/25 s]640 for the ABI instrument), followed by a fusion cycle in order to analyze the melting curve of the PCR products. Negative control without the reverse transcriptase was introduced to verify the absence of genomic DNA contaminants. Primers (see Table  S2 ) were defined within exons (for mRNA-s) or in one intron and one exon (for pre-mRNA-s) using the PrimerSelect program of the Lasergene software (DNAStar). BLAST searches were performed to confirm    S1 ), justifying their gene specificity and the absence of multilocus matching at the primer site.
Fluorescence intensity of individual cells was quantified from digital images of single focal planes with the NIH ImageJ software. We calculated a fluorescence index: I = 1 00(S-B)/B, which gives the fluorescence percentage above background (S (Signal) is fluorescence intensity and B (Background) is average intensity of the region adjacent to the positive cell). Index values were then averaged for the four PDF-positive s-LNv cells of 12-20 brain hemispheres for each time point. Table  S1  Mean values of quantitative RT-PCR results with associated s. e. m. Relative values of mRNA abundance measured by quantitative RT-PCR (see Material and Methods) are indicated for samples on per 0 or tim 0 background collected at CT2 and CT14. Mean levels are normalized to the highest value in the control genotype (per 0 w;tim-gal4 or w;tim 0 tim-gal4;) set to 100.
Acknowledgments We thank  F. R. Jackson  for his generous gift of unpublished  UAS-FLAG-CkIIß flies and I. Edery ,  P. E. Hardin ,  J. Jia ,  R. Karess ,  M. Rosbash ,  R. Stanewsky , and the  Drosophila Genomics Resource Center (Bloomington, U. S. A. )  for fly stocks, antibodies, and other materials. Fly stocks were also provided by the  Bloomington Drosophila stock center (United States) , the  Vienna Drosophila RNAi Center (Austria) , and the  National Institute of Genetics fly stock center (Mishima, Japan). We are grateful to  A. Plessis ,  J. Menet , and especially  A. Lamouroux  for help with S2 cells, as well as  Eric Jacquet  for expert advice on quantitative RT-PCR. We also thank  E. Che  ´lot and  M. Krecsmarik  for help with microscopy,  C. Vias  for dissections,  M. Boudinot  for the FaasX software, and the members of the  Rouyer lab  for critical reading of the manuscript.
This work was funded by  Agence Nationale de la Recherche ''DrosoClock'', ''ClockGene'' and ''FunGenDroso'', ''Equipe FRM '' program of  Fondation pour la Recherche Medicale , and European Union 6th  Framework Programme ''EUCLOCK' '. AS was partly supported by  Association pour la Recherche sur le Cancer  and FR is supported by  Institut National de la Santeet des Etudes et Recherches Me  ´dicales. TR was funded by the  DFG SFB1047  grant from  Deutsche Forschungsgemeinschaft. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgments The authors would like to thank  Frans Van-Gool  for his renewed support for our investigations into drug efficacy evaluation. They would also like to thank  Chandrawathani Panchadcharam  for her input and personal communications. We wish to express our sincere gratitude to the  Thailand International Cooperation Agency (TICA)  for the financial and diplomatic support given to the research project " Mammal Trypanosomes in Thailand. " This research was also funded by  Kasetsart University Research and Development Institution (Kor-Sor-Dor. 65. 51 ),  Kasetsart University. Dr. Zhao-Rong Lun 's laboratory was supported by the Grants (nos. 31071955 ,  31272305 ) from the  National Natural Science Foundation of China. The authors are very grateful to  Isis Olivier  for the efficient revising of our English paper.
Bacterial infection also results in the production of high levels of reactive oxygen species (RoS) in the gut lumen, which induces cell damage and ec apoptosis. upd3, and to a lower extent, upd2 produced in apoptotic ecs induce both iSc proliferation and eB differentiation, in order to regenerate gut epithelium. The cells in which JAK-STAT signaling is required to stimulate iSc proliferation and the role of eGF-R signaling in this process remain to be firmly established. The position of the peritrophic and basal membranes (pm and bm respectively) is indicated on the left. Recherche (ANR-11 BSV2 00801), ARC (Association pour la Recherche sur le Cancer), FRM (Fondation pour la Recherche Médicale: DEQ 20090515429), and a MRT fellowship for IM.
Because the expression of the VRN-A1 gene is known to increase following vernalization  [23] , our data suggested a positive correlation between DNA methylation and gene transcription. To identify whether the DNA methylation shift observed following vernalization was correlated to the expression of the VNR-A1 gene, we performed qRT-PCR for both vernalized and nonvernalized conditions, using the same leaf powder used for DNA methylation analyses. qPCR results indicate a 10 Ct change between vernalized and non vernalized plants, pointing to a 1000 fold increase of VRN-A1 leaf mRNA levels following vernalization (Figure  5 ). This expression increase is associated with the DNA methylation shift observed, with VRN-A1 being expressed when the gene shows higher gene body methylation.
DNA methylation profile analysis of fragments 6. 8 k(a) and 7. 6 k revealed that all cytosines show a methylation profile typical of non vernalized plants (Figure  3 ), therefore providing evidence that the increase in DNA methylation induced by vernalization is reset in the next generation. The sequence of winter allele of VRN-A1 harbor TE fragments not found in VRN-B1 and VRN-D1 copies TE annotation within the VRN-A1 winter genotype sequence using the most recently updated wheat transposable element database  [44]  revealed the presence of several TE fragments, most of which are located within the second half of intron 1 (Figure  2 ). Interestingly, the region covered by these TEs is the region showing the highest methylation level, harboring methylated Cs from CG context, but also from CHG and CHH contexts.
The recent expression comparison of VRN-A1 expression in nearisogenic lines of wheat carrying different alleles of the gene clarified that the promoter insertion allele has a larger effect on gene expression than the intron deletion  [26]. Altogether, this suggests that histone-based regulation of gene transcription occurring at the promoter is likely explaining most of the expression phenotype observed for VRN-A1. But this does not rule out the possibility of redundant switches in which intron 1 could participate in the regulation of the gene, with a lesser extent. Oliver et al. [26]  also report that the Langdon allele (Genbank accession AY747598), while still inducible by cold, has a 10 fold higher basal expression level than the wild type Triple Dirk allele (Genbank accession AY747600).
Interestingly, alignment comparison of these two allele sequences reveals that deletion in the Langdon allele extends from nucleotide 1082 to nucleotide 8253 on the wild type Triple Dirk allele, thus including fragments 6. 8 k and 7. 6 k (data not shown). Hence, while not critical for the low-temperature response, the hypermethylated region observed could play a role in the regulation of the VRN-A1 gene. But what role? Recently, methylation at CHHs in the close vicinity of genes was shown to positively correlate with gene expression in maize, suggesting that this methylation mark may be interlinked with gene expression  [42]. In Arabidopsis, DNA methylation at CG and CHG sites in the large IBM1 intron was shown to positively correlate with accumulation of the long transcriptional form of the gene, thus suggesting that intronic DNA methylation at CG and CHG sites may be required for proper IBM1-L transcript elongation  [71].
Bisulfite analysis using direct sequencing of the converted amplified products Sodium bisulfite treatment of genomic DNA was performed using the "EZ DNA Methylation-Gold" kit (Zymo Research), following manufacturer's protocol. Around 350 ng of DNA were used as input for bisulfite treatment, and 2 μl of the 10 μl eluted solutions were used for each PCR reaction. Bisulfite PCR primers were designed for the plus strand, using the Methyl Primer Express v. 1. 0 software (Applied Biosystems). Primer design was based on the TripleDirkC sequence (Genbank accession AY747600) and is detailed in Additional file 1. Primer pairs amplifying the 9 analyzed fragments are listed in Table  1. For fragments 6. 8 k and 7. 6 k, which overlap with repetitive sequences, search for possible cross-amplification was performed by aligning sequences of these amplicons to available wheat shotgun sequences, using BLASTN searches (http://wheat-urgi.
PCR reactions were performed in 30 μl with 1X Go Taq buffer, 1. 5 mM MgCl 2 , 0. 25 mM dNTP, 1X Q-solution (QIAGEN), 0. 5 μM of forward and reverse primers, 2 μl of GoTaq polymerase (Promega) and 10 ng digested DNA using the following PCR program: initial denaturation step (94°C, 4 min) followed by 10 touch-down cycles (denaturation: 94°C, 1 min; annealing: 68°C-60°C, 1 min, 1°C decrease after each cycle; elongation: 72°C, 1. 30 min) followed by 18 to 30 cycles (94°C, 45 sec; 60°C, 45 sec; 72°C, 1 min), and a final elongation step (72°C, 5 min). Five microliters of each PCR product were loaded on a 2% agarose gel and amplicon quantity was estimated using the ImageJ software  [83]. Details on primer design and number of PCR cycles are described in Additional file 1. Gene expression analysis using qRT-PCR 30 μg of total RNA were treated with DNase (Ambion) then reverse transcribed using random hexamers (Invitrogen), 100 units of SuperScript II (Invitrogen) and 40 units of recombinant RNasin Ribonuclease Inhibitor (Promega) in a final volume of 20 μL.
TE annotation in the VRN-A1 winter genotype sequences To check for possible presence of transposable elements within the VRN-A1 winter allele, we ran a Repeatmasker analysis  [85]  with default parameters, using the VRN-A1 sequence of the winter wheat TripleDirkC cultivar (corresponding to Genbank accession AY747600) as query and a wheat transposable elements database obtained from 18 Mb of the 3B chromosome sequence  [44]  as database. For each case of homology, percent identity between the TripleDirkC VRN-A1 sequence and the sequences from the database were also extracted. Note that TripleDirkC and the two studied genotypes (G1 and G2) share the same VRN-A1 haplotype. The same analysis was also performed on VRN-B1 (Genbank accession AY747604) and VRN-D1 (Genbank accession AY747606) genes from Triple DirkC, to check whether the TE described in VRN-A1 were shared in the other two VRN1 homeologous copies.
Acknowledgements The authors thank  S. Jouanne  and  N. Galic  for help in plant material growth,  C. Remoué  for DNA and RNA extractions and cDNA production,  M. -P. Jacquemot  for help in qRT-PCR setting and analyses,  J. M. Casacuberta  for technical tips on bisulfite analyses,  F. Choulet  for providing exemplar wheat TE database,  E. Paux  for providing DNA to test for primer specificity, and  S. Castelletti  for help in comparative gene sequence analyses. We are also grateful to  V. Colot ,  K. Dawe ,  J. Gent  and  H. Vaucheret  for helpful discussions on the results, to  S. Maury  and  M. Mirouze  for critical reading of a first version of the manuscript and valuable suggestions to improve it, and to two anonymous reviewers for their valuable comments on the original manuscript. This study has received funding from the  European Community 's  Seventh Framework Programme  ( FP7/ 2007-2013 ) under the Grant Agreement n245058-Solibam (Strategies for Organic and Low-input Integrated Breeding and Management).
Acknowledgements The authors acknowledge:  Xunta de Galicia  (Project no. 10PXIB206258PR ),  MICINN-Spain  ( MAT2011-25501 ) and  Universidad Nacional del Sur  ( PGI 24/ZQ07 ),  Concejo Nacional de Investigaciones Cientícas y Técnicas de la República Argentina (CONICET ,  PIP-11220100100072 ).
Electrophoresis of PCR products was performed on an ABI 3730XL sequencer as follows: 2 mL of PCR product for each individual was diluted (3 mL PCR product +50 mL H 2 O), combined with 8 mL of GeneScan500 Size Standard (10 mL GS500 (2250Liz) +900 mL Formamide), denatured at 95uC for 3 minutes and then injected into the sequencer. The microsatellite profiles were analysed in GeneMapperH software version 4. 1. File format conversions were all performed using PGDspider 2. 0. 1. 9 [41]. FSTAT 2. 9. 3. 2  [42]  was used for calculations of allelic richness (AR) and frequencies and for the computation of mean observed and expected heterozygosities (Ho and He, respectively) over all loci for each cohort. To calculate private allele richness (PAR), we used the rarefaction procedure in HP-RARE  [43] , which compensates for the increase in likelihood of sampling rare alleles as sample size increases.
Temporal Genetic Structure The genetic differentiation between pooled genetic data from 'even'  (2000, 2002, 2004, 2006 and 2008)  and 'odd'  (1999, 2001, 2003, 2005 and 2007)  cohorts was low and non significant (Fst = 0. 2%), suggesting that the bimodal pattern of adult emergence did not influence the temporal genetic structure of the population. The temporal genetic structure of the Mont Ventoux population was also analyzed using pairwise Fst between cohorts. The matrix of pairwise Fst obtained with the correction for the presence of null alleles is given in Table  3. Fst values were significant in 40% of cases (14 out of 36 estimations) but were generally relatively low (1. 3-2. 9%). The 2004 and the 1999 cohorts were the most frequently significantly differentiated from other cohorts, while the 2005 one was never found to be significantly differentiated (Table  3 ).
6%) and the significant departures from Hardy-Weinberg equilibrium in each cluster led us to postulate first that we could have dealt with two subpopulations that do not coexist. Our dataset did not allow us to test formally this hypothesis as we could not retrace the precise sampling location of each individual in the field, i. e. , clarifying whether all individuals of a given cluster were sampled on trees clearly distinct from those on which all individuals of the other cluster were sampled. Seed-specialized wasps have been shown to select trees in response to diverse visual and olfactory cues  [24]. However, the potential for intra-population variation in the responses to these cues and whether there could be significant segregation in the use of space between individuals has never been investigated.
Acknowledgments We are grateful to  Geraldine Roux-Morabito ,  Carole Kerdelhue ,  Thomas Guillemaud  and  Eric Lombaert  for insightful discussions on earlier drafts of this manuscript. We acknowledge  Henri Picot  for his help with cedar cone collections and seed extractions, and  Marion Sondo ,  Anne Roig  and  Matthieu Lingrand  for their help with DNA extractions and microsatellite genotyping.
ACKNOWLEDGMENTS We thank  Nadine Mézière ,  Yolande Jaguelin  ( INRA, Saint-Gilles, France ),  Jean-Marc Hallouis ,  Fréderic Mercerand ,  Isabelle Jottreau ,  Sabine Crochet ,  Thierry Bordeau ,  Estelle Cailleau-Audouin , and  Cécile Berri  ( INRA, Nouzilly, France ) for their collaboration in this experiment.
ACKNOWLEDGMENTS Based in New Zealand but of the world,  Dr Rod Bonfiglioli  was a talented and widely respected plant virologist. His passing in May 2009 in New Zealand sadly coincided with the start of his long anticipated GLRaV-3 control project. It will remain an enduring legacy to a man unlikely to be forgotten by his many friends and colleagues. Rodrigo P. P. Almeida ,  Kent M. Daane ,  G. K. Blaisdell , and  Monica L. Cooper  acknowledge funding from the  American Vineyard Foundation ,  Viticulture Consortium West ,  Oregon Wine Board ,  California Fruit Tree ,  Nut Tree  and  Grapevine IAB ,  California Department of Food and Agriculture , and  United States Department of Agriculture (SCRI). Monica L. Cooper  gratefully acknowledges the support of Napa wine grape growers and their staff.
The reduced forms of the proteins could not be detected (data not shown), probably due to aggregation or precipitation. Oxidized proteins were detected in a large majority of cases when fused to partners with redox activity (between 70 to 100% for thioredoxin and its mutants, 92% for DsbA and 100% for DsbC, see Figure  7 ). This percentage is lower when fusions have only a solubilizing role (60% for ZZ, 70% for MBP, 58% for GST). To access the oxidation state of DRPs larger than 6500 Da, we also analyzed selected DRPs in fusion with their solubilizing partner with an LTQ-Orbitrap mass spectrometer. As DsbC was by far the best fusion partner among those investigated, the exact masses of 25 DsbC-DRP fusions were determined. These analyses demonstrated that out of these 25 samples, 17 fusion proteins had molecular masses in agreement with the expected masses considering fully oxidized cystine residues, with a mass difference between the observed and expected masses of less than 0.
Characterization by mass spectrometry Detection of oxidized DRPs used MALDI-TOF and LTQ-Orbitrap. The purified fusion protein samples were digested by TEV protease at 4°C. Samples were loaded onto C18 reverse phase ZipTips, desalted and eluted by 70% acetonitrile/ H 2 O /0. 1% TFA before spotting on a MALDI plate with 4-CHCA matrix at 10 mg/mL. MALDI-TOF analyses were performed on a MALDI-TOF/TOF™ 4800 Analyzer from AB-SCIEX (Foster City, CA). The isotopic pattern measured was compared with the theoretical one determined from the amino acid sequences using DataExplorer software (Version 4. 9, Applied Biosystems). High resolution/high mass accuracy measurements were performed on an LTQ-Orbitrap instrument (Thermo, San Jose, CA) by UHPLC-MS essentially as described previously  [67]. Briefly, DRP samples were loaded and separated on a C18 Hypersil GOLD column (2.
1 mm x 150 mm, 175 Å, 1. 9 μm, ThermoScientific) at a flow rate of 300 μL/min with a linear gradient of 0 to 80% B in 10 min (with solvent A: H 2 O containing 0. 1% formic acid and solvent B: acetonitrile containing 0. 1% formic acid). MS acquisition was performed in the positive ion mode from m/z 500 to 2000 using a resolution set at 30000 (at m/z 400). The resulting mass spectra were deconvoluted using ProMass software (ThermoScientific).
Funding This work was supported by the  ANR PFTV , the  GIS IBiSA , the  ANR FRISBI  ( 10-INSB-05-01 ) and by  INSTRUCT (ESFRI). Dr Natalie Saez  was supported by the  VENOMICS  project , European project  grant  N°278346  ( FP7 HEALTH 2011-2015 ).
, 2007; Blokhuis et al. , 2010). The present study focuses on broiler chicken production, and all the data used here were collected within the Welfare Quality project (Arnould and  Butterworth, 2010). The animal-based measures (ABM) used to quantify welfare aspects stem from current broiler chicken welfare issues  (Bessei, 2006; De Jong et al. , 2012a). The ABM selected herein included contact dermatitis (measured using scores of foot-pad dermatitis, FPD, and hock burn, HB), lameness (measured as gait score), human-animal relationship and fear responses (measured using the avoidance distance test, ADT, touch test, TT, and novel object test, NOT), and the bird's emotional state (measured by qualitative behavior assessment, QBA). We do not regard this set of ABM as complete, but as a useful system that will evolve with time.
Subjects and Data Collection In a cross-sectional type study, 89 traditional intensive, indoor-reared, broiler chicken flocks were inspected between  2007 and 2009. Of these, 16, 19, 36, and 18  flocks were located in France, the United Kingdom, the Netherlands, and Italy, respectively. Most farms were visited during spring and summer, participation was voluntary, and for each farm one flock was inspected on a single occasion in the week before slaughter. Twelve assessors collected the data, 2 in France and the United Kingdom, and 4 in the Netherlands and Italy, respectively. All assessors were trained within the Welfare Quality project. Data were collected by means of a farmer questionnaire and an on-farm inspection protocol: the variables recorded are shown in Tables  1  and 2. The ABM were measured in situ using a test order of, first, QBA, and second, NOT/TT/ADT carried out as a set of tests at 3 different locations.
After a 30-min pause, FPD/HB/ gait scores were recorded, also as a set (of tests) at 10 different locations within the house to ensure that a cross-sectional sample of the flock was assessed. The same birds were scored for FPD and HB, while a new group of birds was penned for gait scoring. Testing or scoring the same bird twice was avoided by systematically moving through the house during the assessment. Data on age, BW, and mortality were obtained from the farmers' records. If necessary, BW on the day of visit was calculated using interpolation from the known weight records. The FPD, HB and gait score were measured as categorical variables at bird level, but they were analyzed as continuous variables at flock level, presented as the sum of birds (in percentage of the flock) with scores regarded to represent compromised welfare.
ACKNOWLEDGMENTS We sincerely thank all the farmers who allowed us to assess their flocks. We are also grateful to  Jan Hultgren ,  Swedish University of Agricultural Sciences, Department of Animal Environment and Health, Uppsala, Sweden , and  Bryan Jones ,  Animal Behaviour  and Welfare Consultant ( Edinburgh, Scotland, UK ), for valuable comments on an earlier version of the manuscript. We further wish to acknowledge the 3 anonymous reviewers for their work, and  Svenska Djurskyddsföreningen (Swedish Animal Welfare Society) ,  Stockholm, Sweden , for financial support for the dissemination of this study's results. Our study was partly financed by the  Swedish University of Agricultural Sciences, Uppsala , and the  European Commission  ( Welfare Quality  project, contract No. FOOD- CT-2004-506508 ).
, 1979;  Padilha et al. , 1996). In the last 10 years, molecular microbiology techniques have led to substantial progress in the knowledge of the microbial diversity of digestive ecosystems. Bacterial community cloning revealed the uniqueness of the rabbit caecal microbiota and showed that most of the sequences correspond to new uncultivated bacterial species not found in the databases (90%  Abecia et al. , 2005 , 80% Monteils et al. , 2008). The overwhelming majority of the sequences were listed in the Firmicutes phylum (over 90% of sequences), whereas the Bacteroidetes represented only 4%. This corresponded to 10. 8 log 10 and 9. 7 log 10 copies of 16S rDNA/g of caecal contents, respectively  (Combes et al. , 2011)  (Figure  1 ). More recently, deep 16S rDNA pyrosequencing, which could be considered as a second generation 16S rDNA fingerprinting (Lamendella et al.
ACKNOWLEDGEMENTS Access to fossil collections was accorded by many colleagues:  Herbert Lutz  and  Thomas Engel at the Naturhistorisches Museum, Mainz ,  Oliver Sandrock  and  Eric Milson  at the  Hessisches Landesmuseum, Darmstadt. We have been helped by curators in London ( Andy Currant ,  Pip Brewer ,  Emma Bernard ),  München (Gertrud Rössner) ,  Stuttgart  ( Reinhard Ziegler ),  Vienna  ( Ursula Göhlich ),  Graz  ( Martin Gross ),  Madrid  ( Jorge Morales ,  Patricia Perez ),  Lyon  ( Abel Prieur ,  Emmanuel Robert ,  Didier Berthet ),  Toulouse  ( Francis Duranton ), Basel.