dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments KC received a PhD grant by the  Emergence-UPMC   2011 research program  and the  "R egion Bretagne". JYT and DJ  benefited from funding provided by  Institut Paul Emile Victor (IPEV)  ( KREVET-1039 program ) and also by the  "R egion Bretagne" (SAD-1 -DRAKAR program ). The authors would like to thank all the staff at IPEV and the crew on the ship Astrolabe for their help during different Antarctic campaigns in Terre Ad elie. Authors also thank  Melody S. Clark  and  Diala Abu Awad  for their critical reading of the manuscript and are particularly grateful to the referee #1 who helped us to greatly improve the manuscript.
Colour Colour was recorded using a Konica Minolta CM 2500d (Japan) spectrocolorimeter in the CIELAB colour space (D65-10˚-L*a*b*-d/8 SCE). The instrument was calibrated at 0 (in the air) and with white standard (No. 7009694). Colour was measured on the top of the DFS slices. For each product formulation, the colour data reported here corresponded to the average of 15 local measurements performed on three whole product slices.
Texture DFS quality was evaluated through texture measurements on non-frozen 30 × 20 × 50 mm parallelepiped samples extracted from 29-day-old products. A TA. XT Plus universal texture analyser (Stable Micro Systems Ltd. , Surrey, England) was used to perform the texture profile analysis (TPA) tests at room temperature. The 20 mm-high parallelepiped samples were placed under the compression plate surface (flat 490 mm 2 cross-section plunger) and twice compressed axially to 50% of their original height with a time interval of 2 s between the two successive compressions. The TPA parameters obtained using the XT. RA Dimension software package delivered with the experimental device were hardness, fragility, elasticity and cohesiveness. Texture measurements were performed in six samples.
Statistical Analyses Hierarchical cluster analysis (HCA), calculated using Ward's method on STATISTICA 10-V2014 software, was applied to all measured raw values to make the figures easier to To assess the effect of each factor (fat and salt contents, and SFO use) and of some interactions between the factors (salt content × fat content, and salt content × SFO content) on each variable measured in this study, statistical analyses of the results were performed by analysis of variance (ANOVA) using STATISTICA 10-V2014 software. Note that we have firstly checked that the factor "formulation" had no significant effect (p > 0. 05) on each physicochemical and biochemical parameter measured in this study. When ANOVA found a significant effect (p < 0. 05), post-hoc procedures were used and multiple comparisons among means were examined by the Tukey test to determine the level of significance between groups.
Beyond day 21, PI values decreased for all formulation classes. To be sure that this decrease was not due to a problem with the experimental technique used, we measured PI in some samples using the classic Kjeldhal method, which confirmed the decrease in PI values over the last week of process (data not shown). This indicates that some end-products of proteolysis had disappeared, likely consumed by microorganisms present in the products at that point in time, and so could not be detected by the measurement techniques used. The HCA applied to PI values of all formulations segregated four classes of formulations but with lower between-class differences in time-course patterns of PI (Figure  1(a) ). The first group that leads to the lowest PI values is formed by the Control, likely reflecting the well-known inhibitor effect of salt against proteolytic enzyme activity.
Acknowledgements The research leading to these results received funding from the  European Union Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement No. 289397  ( TeRiFiQ  project) and from the " Conseil Régional d'Auvergne" within the framework of the Scientific Communication program  " 1182 " under grant agreement No. 939. 92-6574/13968. The authors thank  H. Ismail ,  R. Agouninessouk  and the ADIV staff for their technical assistance, and  ATT  for proofreading the manuscript.
Background: Geographic and demographic factors as well as specialisation to a new host-plant may lead to host-associated differentiation in plant-feeding insects. We explored the phylogeography of a protected moth, Graellsia isabellae, and its two recognised host-plant species (Pinus sylvestris and P. nigra) in order to seek for any concordance useful to disentangle the evolutionary history of this iconic lepidopteran. Results: DNA variation in one mitochondrial marker and nine nuclear microsatellite loci revealed a strong phylogeographic pattern across 28 populations of G. isabellae studied in Spain and France comprising six groups mostly distributed along different mountain ranges. Reanalysis of a previously published chloroplast microsatellite dataset revealed a three and two-group structure for Spanish P.
Methods To achieve aim 1, we Sanger sequenced the second half of the cytochrome c oxidase subunit I gene (COI), a mitochondrial marker widely used in insect population genetics, and genotyped nine microsatellite markers specifically developed for Graellsia isabellae  [20]. To attain our second aim, we used the genetic structure of Pinus sylvestris and P. nigra as a background. For this, we revised the available organelle and nuclear evidence for both pines at European level. We also surveyed the structure of their Iberian populations by reanalysing the chloroplast (cpDNA) microsatellite dataset published by Soto et al. [21].
Genetic diversity and population structure Nucleotide and haplotype diversities were analysed for the mitochondrial COI dataset with DNASP 5. 1  [26]. Nuclear gene diversity and F IS values for each sampling location were calculated with FSTAT 2. 9. 3. 2  [27]. Allelic richness and allelic private richness were obtained using HP-RARE  [28]. Analyses of Hardy-Weinberg equilibrium (HWE) as well as tests for gametic phase disequilibrium were computed using the web version of GENEPOP 4. 2  [29]. Genetic differentiation between populations was estimated using pairwise Φ ST and F ST as implemented in ARLEQUIN 3. 5. 1. 2 [30]. We explored global genetic structure using both the mitochondrial and nuclear datasets. We applied the Spatial Analysis of Molecular Variance (SAMOVA 1. 0)  [31]  to the former by using 100 simulated annealing processes for K values (groups of populations) from two to 10.
Each run was repeated three times to check for consistency. In addition, we carried out population mixture analyses using the spatial clustering modules implemented for DNA sequence data in BAPS 6. 0  [32, 33] , both for individuals and groups of individuals (sampling localities). We ran the program ten times each, using K = 10, K = 15 and K = 20 as upper bounds to the number of populations. In each repetition the program explores the space of partitions and informs of the optimal one (highest log marginal likelihood value). Two Bayesian clustering algorithms were used to infer population structure from the microsatellite dataset: STRUCTURE 2. 3. 4  [34]  and BAPS 6. 0. The former was run under the admixture model with correlated allele frequencies between populations  [35]. We set a burn-in of 100,000 iterations followed by 500,000 iterations for parameter estimation.
The strict clock model was tested against the non-clock model in this way, and once determined that our dataset evolved in a clock-like manner, we obtained a calibrated tree using the rate dating approach, based on the divergence rate of 3. 54 % My -1 estimated for the COI gene in tenebrionid beetles  [45] , essentially due to changes in 1 st or 3 rd coding positions. The output cladogram summarizing the trees was visualized with FIGTREE 1. 4. 2 [46] , retaining branch length information and expressing nodal support as posterior probabilities. Mean ages and 95 % highest posterior density (HPD) intervals of mtDNA phylogroups are used as estimates of divergence times.
Historical demography We investigated the effects of fluctuations in population size on the genetic variation of the population clusters defined in this work. On the one hand, we used the COI dataset to plot the observed frequency distribution of pairwise nucleotide differences with their expected distribution by performing a mismatch analysis. We estimated the demographic parameters θ 0 , θ 1 and τ from the mismatch distribution using MISMATCHHETMUTRATE  [47] , based on a finite-sites model with heterogeneity of mutation rates; confidence intervals around the estimated parameters were obtained by bootstrapping (1000 samples). Goodness of fit to the expected mismatch distribution under different theoretical demographic scenarios was tested using the sum of squared deviations (SSD), by comparing observed values with those yielded by 1000 simulated populations.
As a separate approach, BOTTLENECK 1. 2. 02  [51]  was used to detect reductions in population size using our microsatellite dataset as follows. Expected heterozygosities at mutation-drift equilibrium (h MD ), obtained from the observed number of alleles at each locus through simulating the coalescent process for n loci, are compared to heterozygosities at HWE (h HW ). During a bottleneck the number of alleles decreases faster than gene diversity, and therefore h HW should be higher than h MD. The analyses were performed across 10,000 iterations under both the infinite allele model (IAM) and the stepwise mutation model (SMM), which respectively correspond to the least and most stringent conditions to detect a bottleneck. We assessed the significance of the results using the Wilcoxon's signed ranks test, implemented in the program.
Phylogeography of Pinus sylvestris and P. nigra as from published genetic data With regard to Pinus sylvestris, we inspected the mitochondrial results published by Sinclair et al. ([53]  haplotypes obtained by RFLP analysis of COI), Soranzo et al. [54]  and Cheddadi et al. [16] , both of whom analysed one intron (nad1, exon B/C). Then we surveyed the dataset from Naydenov et al. ([55]  haplotypes revealed by the combination of the nad7 intron 1 and the nad1 intron B/ C) and Pyhäjärvi et al. [56] , whose mitochondrial haplotypes were combinations of the ones published by Soranzo et al. [54]. Then, we revised the interpretation of the results about population structure of Iberian Scots pine by Robledo-Arnuncio et al. [57]  using chloroplast SSR and Prus-Glowacki et al. [58]  based on isoenzyme data.
To the best of our knowledge, the only mitochondrial data from Pinus nigra related to forests of South Spain and Morocco  [59]. In addition, we also revised the interpretation of the chloroplast SSR results by Afzal-Rafii & Dodd  [17]  and the genomic ISSR data by Rubio-Moraga et al. [60]. Genetic structure of Pinus sylvestris and P. nigra as from cpDNA We reanalysed the cpDNA SSR dataset published by Soto et al. [21]  for Iberian P. sylvestris and P. nigra. The former consisted of 706 individuals, sampled in 30 natural forests and genotyped for six loci. We excluded locus PT1254 from our analyses as it contained 20. 25 % of missing data. The percentage of missing data for the other five loci ranged between 0. 56 (PT30204) and 2. 12 (PT1936). The available cpDNA SSR dataset for P. nigra consisted of 326 individuals, sampled in 14 natural forests and genotyped for the same six markers.
The population structure of Pinus nigra in the South of Spain and Morocco inferred by Jaramillo-Correa et al. [59]  was based on the same six markers we reanalysed from Soto et al. [21]. However, the population structure of P. sylvestris in the Northern Meseta (NW spain) surveyed by Robledo-Arnuncio et al. [57]  relied on the five loci we reanalysed for P. sylvestris plus a sixth one, not included in Soto et al. [21]. So, concerning P. sylvestris, the only difference in terms of molecular markers is the exclusion of locus PT1254 in our dataset and the information provided by locus PT26081 in Robledo-Arnuncio et al. [57]. Lastly, it should be noted that 12 out of the 14 Spanish sites sampled by Prus-Glowacki et al. [58]  and all (13) localities surveyed by Robledo-Arnuncio et al. [57]  are included in the dataset by Soto et al.
The most likely partition of the microsatellite dataset was six groups (EI, EP, WP, FA, SI and CI), as from STRUCTURE (Fig. 3a , upper panel, Additional file 6). A second partition (K = 2) was supported only by Evanno's method: the first cluster joined the French Alps, Eastern Pyrenees and Western Pyrenees (FA-EP-WP), whereas the second one grouped Eastern Iberia, Central Iberia, and Southern Iberia (EI-CI-SI) (Fig. 3a , lower panel). However, the overall population structure characterised by BAPS yielded K = 19 as the best partition (Fig. 3c ). Three of these clusters were formed by a single individual (sampled at Ademuz L1, Bronchales L2 and La Sarra L11, respectively). Cluster and sampling locality only matched at Rascafría L21 and Sierra-María L28.
The SI cluster was the second most diverse group in our dataset. Conversely, the CI cluster was mitochondrially monomorphic and its nuclear diversity was intermediate between the FA and EP groups. The genetic pattern of the EI cluster points to the Iberian System as genetic sanctuary  [69]  for G. isabellae. This hypothesis is congruent with the basal position of haplotype EI. 4 and the rich diversity and highly reticulated pattern displayed by the EI haplotypes (Fig. 1b ). The ancestral character states of the EI cluster are also supported by the evolutionary history of P. sylvestris (Additional file 7). The reticulated pattern of cluster EI was due to some haplotypes connected to variants from other clusters (WP, EP and FA) as well as to loops caused by ambiguous phylogenetic relationships.
e. some kind of post-zygotic mechanism lowering the fitness of those Spanish Moon Moths with "southern lineage" mitochondrial haplotypes when carrying certain "northern" (EI) nuclear genotypes. Given the amount of non-synonymous substitutions in the "southern" lineage it is hardly surprising that selection favoured a specific "southern-mito + southern-nuclear" genetic combination during the period that those populations remained isolated from the rest of conspecifics. After the posterior mating between individuals from SI/CI and EI, the finding of a "southern-mito + northern-nuclear" combination would be expected in our dataset. That absence suggests that selection may have only allowed the "northern-mito + southern-nuclear" combination currently present at the Eastern Iberian System. The differential effect of specific mito-nuclear combinations on the fitness of interpopulation hybrids has been proved in other arthropods such as the copepod Tigriopus californicus, Drosophila (Sophophora) melanogaster and the seed beetle Callosobruchus maculatus (revised by  [91, 92] ).
This seems to be the case for the populations of the Spanish Moon Moth from the Eastern Pyrenees and French Alps, which likely derived from the Holocene fragmentation of the continuous forest of P. nigra connecting different populations of P. sylvestris in Northeastern Spain and Southeastern France. The Central Iberian system descends from Betic ancestors, whose populations showed genetic footprints of both a population expansion and posterior bottlenecks. Subsequent gene flow between both the Central/Betic mountains and the Eastern Iberian System was revealed by the nuclear dataset and was compatible with the overlapping potential distribution area of the Scots and Black pines during the Holocene. The mito-nuclear discordance involving the Eastern Iberian cluster is congruent with male-biased gene flow and/or a secondary contact after the evolution of mito-nuclear incompatibilities in geographically isolated areas.
Acknowledgements We thank  N Remón  and  E Magnoux  for help in the laboratory. J Baixeras ,  J Casaponsa ,  MA Gómez ,  S Ibáñez ,  DC Lees ,  R Maciá , MICROFAUNA,  Y Monasterio ,  E Murria ,  JC Nevado ,  A Sáez ,  J Sevilla ,  T Latasa ,  J Ylla  and, especially,  F Goussard  contributed to fieldwork with their advice, assistance and equipment. We appreciate the invaluable help provided by  E Villagrasa  ( Parque Nacional de Ordesa y Monteperdido ) and  J Mestre  ( Parc Natural dels Ports ). The male of G. isabellae included in Fig. 1c was photographed by  T Decaens. U Kodandaramaiah  and his team kindly provided controls for detection of  Wolbachia. A Dolsa  and  J Baixeras  generously sent us 13 of the samples tested for this intracellular parasite. This work benefited from the discussions held with  D Buckley ,  M García-París ,  S González-Martínez ,  A Martínez-Abraín ,  W Nässig ,  JJ Pino ,  R Rougerie  and  J Rousselet.
Availability of data and materials The mitochondrial haplotypes supporting the results of this article have been deposited on GenBank under accession numbers KX302361-KX302402 (see Additional file 3) and KX348010, whereas the microsatellite dataset is available in the figShare repository (entry DOI: 10. 6084/m9. figshare. 3423001 [97] ). A fasta file containing the 41 mitochondrial haplotypes of G. isabellae can be found at figShare repository (entry DOI: 10. 6084/m9. figshare. 3423142 [98] ).
The chemical composition of the statolith crystals were additionally analysed with a Quantax Energy Dispersive Spectrometer (EDS) (Bruker AXS). The software used to analyse the spectra was Esprit 1. 8 (Bruker AXS). Quantification and Data analysis. We considered for the analysis the region comprising the sensory areas of the statocyst. The length of the area comprising hair cells was determined for each sample, and 900 μ m 2 (30 × 30 μ m) sampling squares were placed along the centre length of the area at 5, 25, 50, and 75% of the length on axe of the statocyst (Figs  2  and 3 ). The hair cell bundle densities at the most proximal tip of the area (from 75% -in C. tuberculata-and 50% -in R. pulmo-of length measured) were too high to accurately quantify; therefore, we chose not to attempt quantification of hair bundle density and damage in this area.
Damage due to sound exposure was tested using permutation tests. Data was summed over all regions. Damage was measured as the percentage of extruded and missing hair cells. Permutation tests were repeated multiple times with N = 1000. The influence of recovery time after sound exposure in groups of animals sacrificed 48 h vs 96 h after sound exposure was tested using permutation tests repeated multiple times with N = 1000. The difference in damage between regions was measured as the percentage of extruded and missing hair cells per region 5% vs 25% region at 48 h and 96 h after sound exposure using permutation tests repeated multiple times with N = 1000.
Acknowledgements We would like to thank  Eduard Escolar  of the vessel  Nova Míriam  for their assistance with the collection of A. aurita, C. tuberculata and R. pulmo specimens and  Sebastià Serra  for drawing the image of Sciphozoan medusa rhopalium (Fig. 1A). This work was developed in the frame of the collaborative project  AQUO  ( Achieve QUieter Oceans  by shipping noise footprint reduction), funded by the  European Commission  within the Call FP7 SST. 2012. 1. 1-1:Assessment and mitigation of noise impacts of the maritime transport on the marine environment, Grant agreement no. 314227 , coordinated topic "The Ocean of Tomorrow". The content of this paper does not reflect the official opinion of the  European Union. Responsibility for the information and views expressed in the paper lies entirely with the authors.
1). For this purpose, a list of potential functions for the main torrential protection technics described throughout this paper can be drawn. Elements are extracted from the previous historical analysis (see part 2), completed by the corresponding detailed paper on check dams  [8] , a detailed international analysis of open check dams  [53, 54] , on the RTM database, on the Austrian standard to maintain torrential protection structures  [68]  and on the French technical manual to manage protective forests in the Alps  [69]. We also propose scale of capacity assessment which is the measurable ability related to a function  [4]. Indeed, it is needed to quantify the protective effect on hazard and related risk  [8]. Torrent control works typically consist in implementing structural measures such as protection forests, check dams, open check dams, dykes and bank protection.
Statistical analysis The temperature resulting in 50% mortality of the experimental populations at low temperature exposures (the LT 50 ) was determined using Probit analysis in MINITAB, version 17 (Minitab Inc. , State College, Pennsylvania). Handling controls resulted in 99-100% survival across all treatments. The natural response rate was therefore assumed to be close to zero and not included in the model. Significant differences in mortality were identified by non-overlapping 95% fiducial limits  [24, 47]. To analyse aphid behaviour in a declining temperature regime, categorical data were analysed using a chi-square test in MINITAB version 17 to determine if the proportion of individuals exhibiting each behaviour type differed between the treatment groups and species. Of the aphids which dropped from the wheat, the temperature at which this occurred was analysed to determine any effect of parasitism on this behaviour.
Acknowledgments The authors gratefully acknowledge  Stephanie Llopis ,  Herve Amat ,  Jean-Luc Foulon ,  Thierry Fontaine  and  Fouad Nassur  for technical assistance. Additional thanks to  Stephanie Llopis  and  Charlotte Alford  for help with parasitizing aphids. This work was funded by a  Marie Curie Intra-European Fellowship  for the project ' Climland ' ( FP7-PEOPLE-2012-IEF-326943 ) awarded to  L Alford ,  F Burel  and  J van Baaren.
Image Acquisition for Setting Up the In-Focus Droplet Criterion For establishing the in-focus droplet criterion, images were taken at different distances from the focal plane using all nozzles and settings given in Table  1. This was done by moving the translation stage (lens) towards and away from the focal plane in the range between 420 and 430 mm in steps of 50 µm (Figure  2 ). Thus, in this manner sequences of 200 "out-in-out of focus" images were taken with every nozzle/setting combination (Table  1 ). An example of images in continuous mode acquired using the nozzle orifice size of 65 µm at 5. 0 V and 8. 0 kHz, generating 222. 9 µm droplets, at three distances from the focal plane is shown in Figure  3. Once the images were acquired, a sequence of steps was employed to process and analyze them using Matlab and its image processing toolbox (Figure  4 ).
Image Pre-Processing Image pre-processing aims at resolving problems due to lighting patterns or dirt on the lens, given that the light source can be non-homogeneous  [23]. An image background was reconstructed from a set of 70 images with droplets. For each of these images, the background was selected based Once the images were acquired, a sequence of steps was employed to process and analyze them using Matlab and its image processing toolbox (Figure  4 ). Once the images were acquired, a sequence of steps was employed to process and analyze them using Matlab and its image processing toolbox (Figure  4 ).
Quantitative real-time PCR (qRT-PCR) analysis of gene transcription VvGME, VvVTC2, VvL-GalDH, VvGLDH, VvL-IdnDH (transcript of interest) and VvEFαI, VvUbiquitin (reference genes) transcript levels were measured by real-time qRT-PCR, using the IQ-SYBR green supermix on a CFX96 ™ Real-Time PCR Detection System (Bio-Rad, Marnes La Coquette, France) monitored via Bio-Rad CFX manager 3. 0 software. The reaction mixture (20 μL) contained 5 μL cDNA template and 0. 25 μM of the forward and reverse primers specific to each gene (Additional file 3: Table  S1 ). The thermal cycling conditions and primers for all genes studied are shown in Additional file 3: Table  S1. Amplification specificity was verified for each gene product at the end of each run with melt curves. To verify the specificity of the primers, the amplification products were loaded onto a gel in order to verify the presence of a single band, and they were also sequenced at Eurofins MWG Operon (Ebersberg, Germany).