dataesr/scientific-paragraphs-categorization huggingface dataset:
2013)  was also included in the dataset. The 131 amino acid sequences were aligned using MAFFT version 7 (http:// mafft. cbrc. jp/alignment/server/) (Katoh and Toh 2010)  and a neighbor-joining tree was built using the BioNJ algorithm as implemented in SeaView v. 4  (Gouy et al. 2010). Node support was assessed using a bootstrap procedure based on 1000 replicates. The figure was created using the iTOL web server  (Letunic and Bork 2007).
Rapid Amplification of cDNA Ends (RACE) PCR of CpTRPA5 To extend CpTRPA5 by RACE-PCR in 5 0 and in 3 0 direction, 5 0 and 3 0 cDNAs were created from 1. 0 mg antennal RNA using First Choice RLM-RACE kit (Ambion, Life technologies, Grand Island, NY USA) and SMARTer kit (Clontech). Amplifications were conducted according to the recommended protocols. Primers were designed by hand using existing contig data as reference. Thermodynamic features were checked by OligoEvaluator (Sygma Genosys, http://www. oligoevaluator. com), and putative oligodimerization was checked by OligoAnalyzer 3. 1 (Integrated DNA Technologies, http://eu. idtdna. com/calc/analyzer). Primer melting temperatures were estimated using the salt-adjusted algorithm on the OligoCalc website (ww. basic. northwestern. edu/ biotools/OligoCalc.
Quantification was conducted using a Nanodrop 3300 Fluorospectrometer (Thermo Scientific) with the PicoGreenV R dsDNA reagent kit (Molecular Probes, Life Technologies). Samples were sequenced (Sanger sequencer, 3730xl Applied Biosystems, Life Technologies) using gene specific primers. Alignment of amplicon sequences from RACE-PCR amplifications was performed using Multalin (http://multalin. toulouse. inra. fr/multalin/) (Corpet 1988). The 5 0 and 3 0 sequenced regions were assembled with existing contig data to generate a partial CDS-template of 1677 bp. Despite being partial, this sequence was checked using the online tool ORF Finder (http://www. ncbi. nlm. nih. gov/gorf/orfig. cgi).
Querying Genome and Transcriptome Assemblies In order to identify the full-length CDS of the CpTRPA5 TRP, we used Blast  (Altschul et al. 1990 ) on preliminary assemblies of a whole shotgun sequenced genome and an Illumina sequenced transcriptome (which are still under analysis and will be published elsewhere). We blasted the assemblies using the 1677 bp CpTRPA5 TRP from RACE-PCR as query in tblastn searches. Scaffolds that passed a threshold of e-30 were mapped against the query and manually assembled by hand using BioEdit v7. 2. 5  (Hall 1999 ) into a single scaffold that contained the putative full length CDS. The five genome scaffolds and the four transcripts that matched our RACE-PCR template are available for download and inspection at https://www. researchgate. net (DOI: 10. 13140/RG.
Reverse Transcription (RT)-PCR To investigate transcripts of CpTRPA5 and its splice forms, RT-PCR was performed on cDNA samples prepared from antenna, thorax, abdomen, leg and wing total RNAs. Amplifications were performed using the GoTaq Green Master Mix (Promega), splice form-specific forward primers designed based on Sanger sequencing data of pDONR221 clones (Table  2 ) and the reverse primer Rv_CpTRPA5, previously used to amplify the final assembled CDS (Table  1 ). Except for CpTRPA5_M17 and CpTRPA5_M418 cases, all forward primers were designed to overlap splicing sites, the position of which were identified by sequencing pDONR221-clones and comparing these to the sequence of the final assembled CDS. For the final assembled CDS form, parallel amplifications were conducted using the Fw_CpTRPA5 and Rv_CpTRPA5 primers (Table  1 ).
g. B. mori XM_004926128. 2; 3764 bp) was more than three times longer than our CpTRPA5 TRP contig (1012 bp), which also lacked of start and stop codons in frame, we judged the latter to be incomplete at both 5 0 and 3 0 ends. In an attempt to extend the sequence to full length, we performed 5 0 and 3 0 -RACE-PCR. A partial coding sequence (CDS) of 1677 bp was generated by merging a 703 bp 5 0 -RACE-PCR product and a 432 bp 3 0 -RACE-PCR product with the 1012 bp contig, with an expected stop codon but without any candidate start codon. This was used as a template to query non-annotated C. pomonella sequences from genome and transcriptome data (unpublished), which led to the identification of a final CDS of 3126 bp including a start codon. To confirm the stop codon, we extended the sequence 4166 bp from the 3 0 end by RACE-PCR, but no additional stop codon in frame with the partial CDS appeared.
The full sequence of CpTRPA5 has been submitted to Genbank (accession number KU130118). Comparison of the preliminary CpTRPA5 genomic locus with antennal RNA-seq data produced an overview of intron/exon boundaries within the CpTRPA5 locus (Fig. 3 ). The locus is constituted of four exons separated by three medium-sized introns. Interestingly, RNA-seq but not preliminary genomic assembly revealed 15 additional nucleotides (5 0 -CTCCATCGGCCTGGC-3 0 ) within the third exon, indicating that they could originate from mRNA editing. For the 1041 length translated amino acid sequence of CpTRPA5, the TMHMM model predicted six transmembrane domains (between amino acids 619 and 641; 654 and 676; 691 and 713; 720 and 738; 753 and 775; 826 and 848), an N-terminal cytoplasmic region (from 1 to 618) and a C-terminal cytoplasmic region (from 849 to 1041), all of which would be expected for TRPs.
RT-PCR on Adult Body Parts and Confirmation of CpTRPA5 Splice Forms PCR of E. coli colonies transformed with pDONR221 containing the expected full-length CDS of CpTRPA5 revealed several positive clones containing what appeared to be different size transcripts of CpTRPA5 (data not shown). Sequencing of plasmids purified from positive clones revealed eleven rearrangements of the CDS, suggesting possible generation of splice forms from the original CpTRPA5. RT-PCR on adult male and female body parts confirmed the existence of five out of the eleven potential splice forms (CpTRPA5_M4, CpTRPA5_M17, CpTRPA5_M43, CpTRPA5_M418 and CpTRP A5_F1117) in at least two cDNA samples reverse-transcribed from independent body part RNAs. Sequences of these five splice forms have been submitted to Genbank (accession numbers KU130119, KU130120, KU130121, KU130122, and KU130123 respectively).
Acknowledgments We thank  Andrea Campisano ,  Research and Innovation Centre -Fondazione Edmund Mach , for suggestions on RT-PCR. We thank  Ed Genomics ,  Edinburg (Scotland, UK)  for sequencing and for access to unpublished data. Partial financial support for this project was provided by the  direction of the PhD course in Chemistry, Biochemistry and Ecology of Pesticides (CBEA) of DeFENS: Department of Food, Nutritional and Environmental Sciences, Universit a degli Studi di Milano. Additional funding was provided by the  Italian Ministry of Education, Universities and Research (MIUR)  [project " Analisi integrate dei processi molecolari e cellulari responsabili dell'elaborazione di segnali sensoriali in condizioni normali e patologiche " (no. 2010599KBR_005 , prin 2011)]. We also want to acknowledge  Universit a di Cagliari  and the government of  Regione Autonoma della Sardegna (Italy)  for further financial support in phase of manuscript preparation [project "L'endemismo sardo-corso Papilio hospiton e sue piante-ospite: studio integrato per la conservazione" (L.
The most famous examples are French wines such as Champagne which is the name of the region where the wine is produced. PGI (Protected geographical indications) are awarded to products which are processed on-site but might be blended with some external ingredients. PGI refers to an agricultural or food product originating from a region with a given quality, reputation or any other characteristics which can be attributed to this origin; also, the production and/or processing stages must take place inside the defined geographical area. At least one of the stages of production, processing or preparation takes place in the area. The list approved by European Commission is provided by the DOOR database. In class 1. 5 of this database which registers all fats and oils are listed the most recent registered oils and fats, i.
Moreover, with its environmental benefits, organic agriculture can contribute a larger share in sustainably feeding the world. The European Database of Origin & Registration (DOOR) contains food names registered as a protected designation of origin (PDO), protected geographical indication (PGI) and traditional specialty guaranteed (TSG). Since 2007, EU registered a total of 1528 products. As example there are 250 cheeses, 175 fresh meats and 22 beers. One can also find 142 oils and fats which are labelled (PDO and PGI), accounting for a total market of 346 million euros in 2010. France was the first seller with 129 465 million euros in 2010  (Europa agriculture, 2016). As an example, the production value of the olive oil marketed using a protected designation of origin or protected geographical indication from 2006 to 2008 was 215 million Euros per year (Economic analysis of the olive sector, 2012).
Identification and Phylogenetic Analysis of Starch Metabolism Genes Members of starch metabolism gene families were identified using predicted proteomes of twelve plant species (Supplementary Table  S1 ): M. acuminata (Musaceae, order Zingiberales); rice, Brachypodium, sorghum and maize (Poaceae, order Poales); date palm (Arecaceae, order Arecales), Arabidopsis, grapevine, tomato, potato, peach and woodland strawberry. Protein sequences were identified by combining a BLASTP clustering strategy using a list of reference proteins (Supplementary Table  S2 ) and information from Pathway tools databases  (Karp et al. , 2002) , MusaCyc 1   (Droc et al. , 2013) , the Greenphyl database 2   (Rouard et al. , 2011)  and InterProScan  (Quevillon et al. , 2005)  to confirm and complement clustering results.
Protein sequences were aligned with MAFFT version 6. 717b  (Katoh et al. , 2009). Maximum-likelihood phylogenetic analysis was performed with PhyML version 3. 0  (Guindon et al. , 2010)  using the LG evolution model and gamma distributed substitution rates. The WAG model  (Whelan and Goldman, 2001)  was used for the BAM family. Tree topology was built based on best of nearest neighbor interchange and subtree pruning and re-graphing methods. An approximate likelihoodratio test with a Shimodaira-Hasegawa-like procedure  (Guindon et al. , 2010)  was used to estimate branch supports. Sequences from Chlamydomonas reinhardtii (Chlorophytae, green algae), Physcomitrella patens (Bryophytae, moss) and Selaginella mollendorffii (Plantae, Lycophyta) were retrieved from the Greenphyl database v. 4. 0 2  (Rouard et al.
Identification of Gene Duplication Modes Duplicated gene pairs resulting from banana WGD were identified based on Musa ancestral blocks available at http:// banana-genome. cirad. fr/dotplot (D'Hont et al. , 2012)  and in the Plant Genome Duplication Database (PGDD 4  ,  Lee et al. , 2013). WGD gene pairs were identified as deriving from α or β Musa WGD using available α and β blocks  (Garsmeur et al. , 2014). Additional paralogous relationships were detected using SynMap 5  with default parameters and a 3 to 3 quotaalign ratio for banana  (Tang et al. , 2011). Gene scale duplications corresponding to two consecutive duplicated genes (tandem duplications) and duplicated genes separated by twenty or fewer gene loci (proximal duplications) were detected based on the order of gene identifiers along the chromosomes using an in house-script.
Expression Profiling for Banana Starch Metabolism Genes Using Published RNA-Seq Data Banana RNA-Seq data correspond to fourteen libraries that were produced using the method detailed in the supplementary material of D  'Hont et al. (2012). They are available at NCBI SRA under accession number ERP0116302. Illumina reads were mapped onto banana gene models. Expression levels for banana starch metabolism genes were normalized in RPKM (reads per kilobase of exon per million mapped reads on banana gene models) and visualized using the MeV application (version 4. 9) from the TM4 software suite  (Howe et al. , 2011).
The banana MaActin2 (GSMUA_Achr1G05990_001) was used as a reference gene. Computations of normalized transcript abundance [A = E target (-Cptarget) /E reference (-Cpreference) ] were performed with LightCycler R 480 SW software version 1. 5. After a logarithmic transformation of raw data, statistical analysis was performed with an ANOVA followed by a Tukey's test.
ACKNOWLEDGMENTS We thank  Mr. Poumaroux  for providing access to his banana plot,  Olivier Hubert  ( CIRAD, Guadeloupe, France ) for monitoring of banana growth,  Corinne DaSilva  ( Genoscope, Evry, France ) for normalization of RNA-Seq data,  Olivier Garsmeur  for critical reading of the manuscript, and the  SouthGreen Bioinformatics Platform  (http://www. southgreen. fr/)for the banana genome hub (http://banana-genome-hub. southgreen. fr/)and for computational resources.
ID:440 An LCA study consists of four steps: 1. Defining the goal and scope of the study. 2. Life cycle inventory (LCI): Making a model of the product life cycle with all the environmental inputs and outputs (data collection) 3. Life cycle impact assessment (LCIA): understanding the environmental relevance of all the inputs and outputs. 4. Interpretation of the results. The LCA study was performed using SimaPro software (version 7. 3) with the CML 2 Baseline 2000 V2. 05/ World 1990, one of the most widely used and acknowledged impact assessment methods  (Claussen et al. 2011).
The model is described by a function with two parameters, ß 0 and ß 1 : p ¼ e b0 þb1 x 1 þ e b0 þb1 x where the parameter ß 1 is similar to a slope parameter (ß 1 equal, minor o greater than zero indicates none, negative or positive relationship, respectively). The program Statistica  [22]  was employed for all statistical analysis. Proportions were arcsin-transformed prior to all analyses.
Acknowledgments We thank  Verónica Wada  (former UNLP student) for laboratory aid and  Patricia Sarmiento  ( Servicio de Microscopía Electrónica de Barrido, Museo de Ciencias Naturales, FCNyM, UNLP ) for technical assistance. Julia Rouaux  and  Laura Morote  kindly helped with artwork. This research was partially funded by  ANPCyT  ( IM40-2000  and  PICT 2012-1624 ),  CONICET  ( PIP 0112 2012-2015 ),  UNLP  ( SA N706 2013-2016 ) and  IPRABIO  Project ( Marie Curie Actions-International Research Staff Exchange Scheme, IRSES ,  2011-2014 ).
Acknowledgments We thank those in the lettuce genetics and breeding community who reviewed and commented on data for this paper. We thank  Dr. R. van Treuren ,  Centre for Genetic Resources , the  Netherlands (CGN) , for input on germplasm information. L. Parra thanks  Becas Chile  for a Scholarship from the  National Commission for Science Research and Technology (CONICYT, Chile). Additional financial support was provided by a grant to RWM from  USDA NIFA SCRI #   2010-51181-21631  and to AL from  MSM 6198959215 (Ministry of Education, Youth and Sports of the Czech Republic)  and the internal Grant of Palacky ´University in Olomouc (IGA_PrF_2016_001). Compliance with ethical standards.
Visualization We created digital visualizations by first thresholding and surfacing data with the SPIERS software suite (www. spiers-software. org), following the methods of  Garwood & Sutton (2012). The resulting models were exported as VAXML datasets  (Sutton et al. 2012 ) (Supporting information Appendix S1). Subsequently, STLs from these were imported into the open source raytracer Blender (www. blender. org) following the methods of  Garwood & Dunlop (2014). Due to the low-relief nature of the fossils, we present two different lighting schemes to highlight surface topography. Both employ Blender internal renderer. The first uses a single constant falloff spotlight at a low angle to the surface, with a low-powered hemi light located close to the camera to lighten shadows. The other uses blue, red, green, and yellow spotlights at 90°to each other.
Acknowledgments. We thank  Cristiano Sampaio-Costa  for the scanning electron micrograph of the onychophoran antenna. We acknowledge the assistance provided by the Manchester X-ray Imaging Facility, which was funded in part by the  EPSRC  (grants  EP/F007906/1 ,  EP/F001452/1 , and  EP/I02249X/1 ). Tomasz Goral  ( Imaging and Analysis Centre, NHM ) conducted SEM imaging. RG is a Scientific Associate at the  Natural History Museum, London , and a member of the  Interdisciplinary Centre for Ancient Life (UMRI). Associate Editor  Greg Rouse  and two anonymous referees provided comments that helped improve this article.
0 kV. The vaporizer temperature of the source was set to 120°C and the capillary temperature to 280°C. In full MS mode, the resolution was set at 100 000 (FWHM at m/z 400), whereas in MS/MS mode it was set at 30 000. MS data were processed using XCALIBUR 2. 1 software and METWORKS 1. 2. 1 software (Thermo Fisher Scientific) to screen spectra for metal containing molecules. To get accurate masses, MS and MS/MS spectra were recalibrated offline using precursor/fragment ions with known formulae, which resulted in the determination of a unique chemical formula for each metal complex. These formulae were checked against a natural compounds database (Dictionary of Natural Products Online, http://dnp. chemnetbase. com) to identify the organic ligands, knowing that ligands can be present several times in a metal complex.
Metal column recovery was checked regularly and good recoveries (60-90%, depending on the element) were obtained for the targeted elements in these two types of sample. Note that quantitative recoveries are important for quantification but not necessarily for the identification of endogenous metal species. To confirm that < 100% recovery was not affecting data interpretation, columns saturated with the metal ions of interest (resulting in a metal recovery of 150-500%) were tested. No significant changes were observed either in terms of the morphology of chromatograms with ICP-MS detection (only general intensity increased) or in terms of the species identification by ESI-MS in comparison with normal conditions. The absence, in these particular samples, of changes in metal speciation when metal recoveries stay within a reasonable range (60-200%) is likely to be due to the presence of higher than stoichiometric concentrations of the relevant ligands.
Two types of fluids, xylem sap and embryo sac liquid, were obtained from P. sativum and were analyzed by means of the different couplings and in the different modes described in the Materials and Methods section. Peaks corresponding to the metal-containing species were searched for in the ESI MS spectra for several elements by the recognition of specific isotopic patterns (exact inter-isotopic mass differences and isotopic ratios) when applicable (except for monoisotopic elements). Using the accurate masses of the precursor ions, as well as their corresponding fragments, empiric molecular formulae could be determined for all the metal species detected. Taking into account that metals can be bound to one or to several (identical or different) ligands, these formulae were checked against a natural products database to identify the organic ligands.
A conservative cutoff value (< 2%) was set for minor species because their low peak areas are difficult to measure precisely below this threshold. Fe(II)-and Co(III)complexes were in too low concentrations compared to Fe(III)-and Co(II)complexes to be distinguished and quantified in HILIC-ICP-MS chromatograms. 1 ) from pea (Pisum sativum) xylem exudates. Citric (m/z 191. 02) and malic (m/z 133. 01) acid are detectable after sample acidification at complex retention times whereas the free forms of these organic acids are observed to elute a few minutes later by SEC chromatography (data not shown).
Some other molecules, aminoadipic acid and pipecolic acid, were detected as potential Ca chelators. However, the lack of similarity between the peak shapes of these complexes by HILIC-ICP-MS and HILIC-ESI-MS chromatographic profiles seems to indicate that the formation of these complexes may be just opportunistic and could occur in the ion source. Finally, chromatograms with ICP-MS detection were also recorded for K, Ti and Sr (data not shown) and they exhibited similar shapes/ peak retention times as for Mg and Ca, which seems to indicate that they have the same binding targets.
Conclusions Using the largest seismic data set available, we have generated a unified stratigraphic and structural framework for the entire offshore Corinth Rift. We document variations in rift depocenter development and fault activity at unprecedented 100 kyr time scales, producing a high-precision history of rift evolution over the past circa 2 Myr. The most significant structural change is the rapid transition from a structurally complex rift to a predominantly asymmetric rift over a 300 kyr period, starting at circa 620 ka. Since circa 620 ka, two phases of offshore rift development have dominated: (1) a change in rift symmetry and then (2) progressive localization deformation. The change in rift symmetry involved rapid (~200-300 kyr period) yet progressive transfer of deformation from south dipping to north dipping faults causing depocenter migration and the generation of a basin-wide synrift unconformity.
Acknowledgments We acknowledge funding from  NERC  (grants  NE/J006564/1  and  NER/B/S/ 2001/00269 ) and the  Royal Society. We thank the positive and constructive reviews of  Douglas Paton ,  Chris Morley , and an anonymous reviewer as well as excellent feedback from the associate editor  Taylor Schildgen. The authors are grateful to  Cindy Ebinger  and  Patience Cowie  for their helpful comments and encouragement. We also thank  HCMR  and all the participants of an ECORD funded Corinth workshop whose fruitful discussions helped focus key ideas. All data used are documented in listed references, tables, and supporting information.
Comparison of PDE-based formulation with classic quasi-steady Messinger approach on experimental wind tunnel test in glaze ice conditions do not showcase dramatic improvements for either one. Physics of glaze ice accretion remains extremely complex and icing codes nowadays are only able to obtain qualitative results in such icing conditions. In this paper we present the icing code developed in the structured compressible and multi-block Navier-Stokes solver NSMB  [15]. Supercooled water droplets field and impingement areas are obtained by means of an Eulerian approach solved implicitly using solvers BiGSTAB or SIP. The ice thickness is calculated based on an iterative Messinger model upgraded by an improved water runback scheme for threedimensional and multi-block ice accretion simulations.
A. 1 Rime Ice Accretion Simulation Rime icing is simulated on a two-dimensional NACA23012 airfoil and compared with experiments of Broeren et al. [17]  The choice of these particular validation cases was motivated by comparing our numerical results with recent high fidelity experimental ice shapes. The O-grid generated by NS-GRID software (citation) is shown in Fig. 2. The NACA23012 mesh has a chord of c = 1. 828m and contains 512 × 256 cells divided into two blocks. The parameters of the simulations ( Cases 1 & 2) are summarized on Table  1. Visualization of Liquid Water Content distribution for case 2 is shown in Fig. 3. Shadow zones observed evince dried areas where liquid water content is nearly zero. The Collection efficiency curves are shown in Fig. 4. Ice shapes obtained after a single icing step are compared with experimental results in Figs.