dataesr/scientific-paragraphs-categorization huggingface dataset:
Identification of prolific flocks and ewes Seven prolific families were identified in the Ile de France breed, which showed a prevalence of 0. 38% triplet delivery on 20 229 recorded matings in the Brazilian Sheep Breeders Association databank. From these prolific families, 25 ewes with a history of delivering at least one triplet and recurrent multiple delivery were selected for genetic screening. These ewes were genotyped for the Booroola and Embrapa polymorphisms, which are the two SNPs affecting OR so far demonstrated to be segregating in Brazilian flocks  (Souza et al. 2009). All tested females were non-carriers of both Booroola and Embrapa mutations, which justified the sequencing of the GDF9 and BMP15 genomic DNA to investigate the presence of known polymorphisms or the existence of new SNPs that could explain their increased prolificacy.
767 (cut off = À3) and PROVEAN score of À4. 667 (cut off = À2. 5). The arginine at residue 315 in sheep GDF9 is highly conserved among vertebrates ranging from fish to mammals (Fig. 1 ), and the Vacaria mutation disrupts the PCSK cleavage site RHRR to a CHRR, which is predicted to abolish the production of the mature protein according to PROP 1. 0 software analysis (http:// www. cbs. dtu. dk/services/ProP/). Six other polymorphisms were detected in the GDF9 sequence analysis (Table  2 ), and all of them were predicted to have no effect on protein function by the PANTHER and PROVEAN softwares. These polymorphisms (G1, G2, G3, G4, G5, G6) have been previously reported as without association with increased OR/LS or sterility  (Hanrahan et al. 2004). The BMP15 resequencing revealed the presence of a deletion at position 28-30 of the coding region, resulting in a deletion of a leucine at residue 10 of the prodomain.
(2007). The populations of P. nigra covered three of the five subspecies considered by  Jalas & Suominen (1973) : P. nigra subsp. salzmannii, Pinus nigra subsp. nigra J. F. Arnold and Pinus nigra subsp. dalmatica (Vis. ) Businsky. Three needles were randomly sampled from three randomly selected adult trees per population. A 5-mm-long section of each needle was boiled in water for 1 h, macerated in Schulze's solution  (Kerp, 1990) , hand-cleaned with a lancet and mounted in glycerine on a microscope slide for observation by transmission light microscopy. Epidermal and stomatal analyses were performed using a digital camera and employing Leica Application Suite software (LAS version 3. 2. 0, Leica Microsystems). The outer cuticle of some additional samples was examined by scanning electron microscopy (SEM) to clarify some epidermal features.
0. Pore diameters were measured at 50 x 3. 3 magnification directly from frozen video images using Leika Application Suite 3. 2. 0 software. The longest diameter of the pore (p) was recorded for ten pores per needle. To analyse the variance, all p values were log-transformed to meet the requirements of independence, normality and constant variance of the residuals  (Sokal & Rohlf, 1995). Two analyses of vari-  ance involving the nested factors species, population, tree and needle were then undertaken: (1) a variance components analysis of random effects  (Sokal & Rohlf, 1995; McDonald, 2009) , performed using Microsoft Office Excel, 2007 (Supporting Information file 'spreadsheets_nestedanova. xls'), which provided information on the contribution of each factor to the variability as a whole; and (2) a linear mixed effects model (LME) analysis employing the factor species as a fixed effect factor and the remaining factors as random effects factors  (Bates & Maechler, 2009; R Development CoreTeam, 2009) , which was used to make pairwise comparisons between the means of the groups defined by the factor species  (Crawley, 2007).
, 2009a, b)  were measured for ten stomata per needle, following the same procedure described for variable p. Two kinds of multivariate analysis were then performed. (1) For understanding the general behaviour of the measured variables, the spontaneous grouping of stomata, needles and trees was studied by cluster analysis of single measures and by the cluster analysis of means of stomatal variables for needles and trees [UPGMA method with Euclidean distances; PC-ORD v. 4. 0 software  (McCune & Mefford, 1999) ]. (2) For establishing their taxonomic value, discriminant analysis (SPSS v. 15. 0. 1 software) was performed to observe the grouping of stomata by species. This last analysis determined the taxonomic contribution of each variable, providing a primitive predictive tool for the classification of unknown stomata.
Because the receivers' clocks are not synchronized with GPS time, to match the calculated and GPS-measured positions accurately, the data needed to be synchronized. For each of the three days of testing, each calculated position was matched with its spatially closest GPS-measured position, and the time differences between the matched positions were averaged for that day. These daily averages were used to correct VPS time to GPS time. To assess the probability of location, each test tag transmission not positioned by the VPS had to be located; the location of the test tag was obtained from the GPS-measured track of the boat at the precise time when the tag transmitted (every 25 s). For transmissions that were positioned by the VPS, the calculated position was used as the location of the test tag.
The probability of location over the entire surface of the reservoir was interpolated from calculated positions and transmissions not positioned using an inverse distance weighted technique (cell size = 10 m; power = 0. 1; search radius = the ten nearest points)  [21]. The positioning error was mapped in the same way as the probability of location. A Wilcoxon nonparametric test was used to compare the difference in the positioning error inside and outside the receiver array, computed with R software  [22]. Spatial analysis and representations were performed with ArcGIS 10 (ESRI, Redlands, CA).
Validation of adenine methylation at the GATC sites within the transposase gene To confirm the variability of adenine methylation between orange and green variants, fragments A1 and A6 were selected for further analysis. Based on the nucleotide sequence of A1 in the A. pisum EST database (accession number EST-CV840801), three putative GATC sites of potential adenine methylation were identified within and upstream of the original A1 sequence (marked as A1M1-A1M3 in Additional file 2: Figures S1 and Additional file 3: Figure  S2a ). The A1 fragment (including the extended sequence obtained from the NCBI database based on WP_002757529. 1 and YP_001863818. 1) was used in a subsequent comparative study of the green and orange aphid variants. Genomic DNA (gDNA) was purified from orange and green adult aphids (42 individual aphids in total: 21 orange and 21 green-including 24 wingless and 18 winged Vicia faba plants kept at 10°C.
Validation of adenine methylation at GATC sites within the helicase gene A sequence analysis similar to that described above for the A1 fragment was applied to the extended nucleotide sequence of the A6 fragment obtained from the R. insecticola genome (94% identity; accession number WP_006705384. 1). Three putative GATC sites were identified and further examined for adenine methylation (A6M1-A6M3; Figure  4a ) using 12 A. pisum aphids (6 orange and 6 green). All tested aphids demonstrated a strong amplicon signal using A6F3 and A6R2 primers (positive control, no GATC site; Figure  4b-c  and Table 2 ). Variation between the two aphid variants was detected within the A6M1 site by PCR amplification (using primers A6F1 and A6R1) of DpnI-digested DNA: strong amplicon intensity was obtained for the 6 orange aphids, whereas 5 green aphids demonstrated low to medium amplicon intensities, and no amplification was found for the 6th one (Figure  4d -e; Table  2 ).
Acknowledgments We thank the  Baylor College of Medicine  for allowing open access to the A. pisum genome database. This work was supported by an  ANR  grant "exsidum" and a postdoctoral fellowship from  Ministère de la Recherche et Enseignement Supérieur  to AD, and a Ph. D. fellowship from the  Signalife LabEx program of Nice University  to VR. Received: 10 April 2014 Accepted: 4 November 2014 Published: 19 November 2014.
Optimization Approach First, the mathematical model is programmed in CPLEX. Then, MAPPOINT software is used to represent manufacturers and depot locations geographically. Then, the software provides a distance matrix between the various locations according to their address. Then, this distance matrix with other data from the case study are introduced in the model in the optimization software CPLEX. The execution of our optimization program provides the optimal routes according to environmental criteria. To operate our case study, we used a set of parameters, summarized in table 2:.
Material All the experiments, except for experiment 2B, used the same apparatus. The participant's head was held by a chinrest so that his or her eyes were approximately 55 cm from the screen's centre. The stimuli were projected on a ‫״22‬ CRT screen, with a resolution of 1024  768 pixels and with a frame rate of 120 Hz. The experiments were programmed in MATLAB using the Psychophysics and Eyelink Toolbox extensions  (Brainard, 1997; Cornelissen, Peters, & Palmer, 2002; Pelli, 1997) , and were run on an Apple computer. Participants' eye movements were recorded with an eye-tracking system (SR research Eyelink 1000 monocular, 35 mm lens) at 1000 Hz sampling rate. The eye-tracker was always calibrated for the participant's dominant eye (9-point calibration. Eye dominance was assessed with an aiming task).
Object selection The object selection procedure we used in this study was similar to that presented in  Perdreau and Cavanagh, (2013b). Part of the set of possible and impossible objects used in the present study was taken from previous collections  (Schacter et al. , 1991; Soldan, Hilton, & Stern, 2009; used with authors' permission). The other objects were outlined versions of impossible objects provided by an Internet database ("Impossible world" website), and one of the authors (PF) designed corresponding possible versions using Adobe Illustrator CS4. At the end, our collection included a possible and an impossible version of 260 objects (total: 520) with an original size of 1667  1667 pixels. In order to reduce the ambiguity about the structural possibility or the impossibility of the objects used in our experiments, we asked 20 independent observers, not participating in this study, to judge all our line-drawn objects as being structurally possible or not.
Finally, we computed the drawing's accuracy as the mean of the percentage root-mean-square error (%RMSE) computed on each axis (x and y) between the 16 points in the original and in the drawing: 2 ( ) 100 %RMSE , d o o C C n n C ∑ - = × Σ (1) where Cd are the transformed coordinates of the copied house, Co the transformed coordinates of the original house and n the number of selected points (n 5 16). Smaller root-mean-square errors mean better drawing accuracy. We next evaluated this geometrical measure by comparing it to human observers' subjective judgments of accuracy. To do so, we designed an online experiment where randomly selected pairs of drawings were presented to participants (n 5 245) as well as the original picture. Online experiments are known to yield to a similar data quality compared to experiments run in laboratories  (Germine et al.
39 (SE: 0. 44), ²(1) 5 8. 59, p. 004] and a significant main effect of object size [ 5 1. 08 (SE: 0. 51), ²(1) 5 14. 26, p . 0002]. However, we found no significant interaction between object size and drawing accuracy [ 5 20. 44 (SE: 0. 37), ²(1) 5 1. 38, p 5. 24]. These results show that more skilled participants needed overall 1 Linear mixed-effects models are extensions of linear regression models, including both fixed effects (linear regression part) and random effects that allow random individual variations across a grouping factor's levels (as in repeated-measures ANOVA). Linear mixed-effects models presented in this study were computed using the lme4 R package with an ML procedure  (Bates, Maechler, & Bolker, 2012). Main effects and interaction effects were tested by using a likelihood ratio-test, which compares the residual deviance of both the full model and the reduced model (full model without the factor of interest) and approaches a ² distribution.
Stimuli Experimental conditions were identical to the visual masking task with possible/impossible objects. However, instead of using these line-drawn objects we used French words and non-words. These words and non-words were collected from a French database (LEXIQUE 3. 55;  New, Pallier, Brysbaert, & Ferrand, 2004). More particularly and to avoid any ambiguities of an effect of words frequency, and possibly of participants' education, on participants' performances, we selected words with a frequency greater than 100 times per million words, based on appearances in books, subtitles, webpages, etc. Likewise, for non-words we selected actual French trigrams (sequences of letters making a pronounceable non-word) that had the same mean frequency of occurrence in French as that of the words we used in this task.
Individual animals were maintained in dechlorinated tap water. Shelter and food was provided in the form of washed rotting sycamore leaves (1 leaf per container). TPS Dig2  (Rohlf, 1997)  software was employed to place landmarks on digital images where a substantial change of direction (>20 degrees) occurred. Sketches of track direction were used to order landmarks correctly. In this way the number of changes of direction, individual distances travelled and total distance travelled were recorded.
ACKNOWLEDGEMENTS The authors thank  Leeds City Council  and  Bradford Metropolitan District Council  for granting land access. Thanks to  Robert Jones  for assistance with laboratory work and  Emily Imhoff ,  Katie Arundell ,  Aurore Dubuffet , and  Paula Rosewarne  for help with analysis. This work was funded by a  National Environmental Research Council (NERC)  CASe partnership with the  Environment Agency  and a  NERC IAA  grant.
Recently, Sun and colleagues reported that delivery of a FOXN1expression plasmid to the aged thymus by intrathymic injection resulted in increased thymus size. However, as cellular composition, architecture and function of the thymus were not examined, that study was not informative regarding the effect of FOXN1 upregulation on hallmarks of thymic involution, including altered TEC phenotype and function  (Sun et al. , 2010). The importance of evaluating these parameters is highlighted by the findings of Griffiths and colleagues, discussed above, that the degenerative changes characteristic of ageassociated thymic involution persist despite increased thymic size during castration-induced thymic rebound  (Griffith et al. , 2012). In a separate study, Zook and colleagues reported that overexpression of FOXN1 from the human keratin 14 (hK14; KRT14 -Human Gene Nomenclature Database) promoter, which can drive broad expression in fetal and postnatal TECs including cTECs  (Laufer et al.
Flow cytometry Analysis Mouse fetal TECs were processed for flow cytometric analysis as described  (Bennett et al. , 2002; Nowell et al. , 2011) ; adult TECs were enzymatically digested to single cell suspensions as described  (Gray et al. , 2008)  and processed for cytometric analysis without further enrichment. Naive T cells (CD3 + CD62L + CD44 lo )  (Budd et al. , 1987)  and RTEs (CD3 + CD4 + CD62L + CD45RB int )  (Boursalian et al. , 2004)  were identified among splenocytes as described. Data were acquired using LSR Fortessa (BD Biosciences) and analyzed using FlowJo software (Tree Star).
Funding This work was supported by  Leukaemia and Lymphoma Research  (C. C. B. , C. S. N. and N. B. ); the  Darwin Trust of Edinburgh  (N. B. ); the  Medical Research Council [MRC Centre of Excellence in Regenerative Medicine , grant number  G0300058  and renewal  MR/K017047/10 ]; the  National Institutes of Health  [ PO1 1P01AI076514-01A1 ; N. B. and C. C. B. ]; and the  European Union Seventh Framework Programme  [FP7/2007-2013] under grant agreements  200720  (EuroSyStem) and 223098 (OptiStem). Deposited in PMC for immediate release.
InSAR Data The TerraSAR-X (TSX) satellite was tasked to acquire "StripMap" SAR images of the region following the eruption on both ascending and descending orbits. The TSX satellite uses an active X band SAR antenna with a wavelength of 31 mm, the incidence angle of the beam varies across the scene, between 25. 1 • to 30. 5 • and 31. 7 • to 34. 8 • for the ascending and descending tracks, respectively. Each fringe within an interferogram corresponds to a change in range of ∼15 mm between the ground and the satellite. Each SAR scene is 30 km wide and 50 km long, large enough to cover the BVC and the surrounding area, with a minimum pixel size corresponding to 3 m on the ground. We used a data set of 25 images acquired between 1 July 2011 to 5 October 2012 on descending orbit 046 and complemented these with 19 images from ascending orbit 130 spanning the period between 6 July 2011 and 10 October 2012.
Methods We manually picked arrival times of the P and S waves at every seismic station for each distinguishable earthquake using SAC software  [Goldstein and Snoke, 2005]. We found that the traces did not need to be filtered before analysis due to the high data quality. As part of the process, we assigned a quality value of 0, 1, 2, and 3 to the measurement, based on an estimated P wave arrival time error of 0. 05, 0. 1, 0. 015, and 0. 2 s, respectively. For S waves, the 0 to 3 quality values were assigned to values of 0. 1, 0. 175, 0. 25, and 0. 3 s, for the estimated error in arrival time. These values were used as weights in the location inversion performed by the Hypo2000 algorithm  [Klein, 2002]  (Figure  5 ). During the 38 day recording period we detected a total of 658 earthquakes on Nabro caldera and in the surrounding area.
g. ,  Kanamori [1977] , following the method of  Keir et al. [2011]. We computed lower hemisphere focal mechanisms to constrain the orientation of crustal strains using FOCMEC  [Snoke, 2003]. The program uses the station location, take off angles, and P and S H wave polarities to perform a grid search for the best-fit double-couple solution  [Snoke, 2003; Ebinger et al. , 2008]. Using an incremental step of 10 • , all fault plane solutions have an error of ≤ ± 20 o in strike and dip of the nodal planes. We were able to estimate 46 robust fault plane solutions beneath Nabro's caldera. We could not determine solutions for events away from the caldera due to the configuration of seismic stations. Data from the seismic station with a failed GPS system (NAB7) were included in the data set as the arrival time of the wave was not relevant for this analysis, but the position of the station was useful for determining the strike of the nodal planes.
Joint Interpretation of InSAR and Seismicity In this study we have measured the crustal response to the 2011 eruption of Nabro volcano. Using the high-resolution InSAR data in conjunction with seismicity, we are able to create a working model of the magmatic plumbing system and how it interacts with faults (Figure  11 ). We observe a circular subsidence signal which is offset to the SW of the caldera topography and the vent region, suggesting that the magma reservoir is not located directly beneath the eruption center. The subsidence signal suggests ongoing depressurization of the magma chamber following the eruption. The spatial pattern and sporadic nature of the hypocenters located at shallow depths (less than 6 km) under Nabro, are likely caused by the bending and episodic fracturing of brittle rocks within the volcanic edifice  [Dzurisin et al.
Modes of Caldera Subsidence The structure and evolution of calderas provide information on the behavior magma reservoir, and therefore, understanding their geometries is crucial in predicting future behavior  [Cole et al. , 2005; Acocella, 2007]. We can compare the mode of subsidence implied by the focal mechanisms to models of caldera response. The seismic data reveal fault structures in the shallow subsurface (less than 6 km deep), the magnitudes of the earthquakes which delineate the fault have a maximum magnitude of 3. Earthquakes of this size at ∼ 5 km depth cause less than 1 mm of deformation at the surface, which is not resolvable in the InSAR data. We also assess the temporal evolution of these faults through interpretation of the cross-correlated waveforms. In Figure  9 , a thrust fault is observed to crosscut the caldera floor 1 km above the center of the magma source.
Conclusions Our InSAR analysis of ascending and descending images, acquired after the eruption by the TSX satellite between 1 July 2011 and 10 October 2012, shows a concentric subsidence signal centered on Nabro's caldera with a maximum rate of 20 cm/year. The InSAR data can be modelled as a Mogi source at a depth of 6. 9 ± 1. 1 km. However, this may be an oversimplified model of magma reservoir geometry. We located 658, and relocated 456 earthquakes recorded over a 38 day period beginning on 31 August 2011. From the distribution of seismicity, we observe fracturing of brittle rock above the magma chamber. In conjunction with focal mechanisms, we delineate a major fault plane with a NE-SW strike which dips 45 • to the SE, crosscutting the caldera floor. A deep cluster of seismicity suggests a link to a deeper magma source.
Molecular characterization of HmCalR The analysis of Hirudo medicinalis genome allowed in silico prediction of mRNA databases according to intro-exon boundaries. Based on the candidate sequence detected, forward and reverse primers were designed to frame the complete sequence of predicted mRNA. From total RNA extracted from leech nerve cord using TRIzol ® reagent and according to the manufacturer's procedure (Invitrogen, USA), cDNA were synthesized using an oligo(dT) priming. The calreticulin-related molecule was amplified by PCR using the specific forward (5'GGTAGCAATACGTGCAGTTTG3') and reverse (5'GCAACCAAGAGTAGGCAACC3') primers and the Platinum ® Taq DNA Polymerase according to the manufacturer's instructions (Invitrogen, USA). Selected PCR products were ligated into pGEM T-easy vector and cloned into JM109 cells according to the manufacturer's instructions (Promega, USA).
Fluorescent in situ hybridization (FISH) Nerve cords were fixed for one hour at 4°C in 4% paraformaldehyde just after dissection. The 5' biotin-labeled specific antisense probe and sense probe (negative control) were generated from the 842-1479 nucleotides sequence of hmcalr mRNA (Genbank Accession Number KF709537). After PCR amplification and the insertion of the product in pGEM-T easy vector system (Promega, USA), the RNA sequence of interest was obtained by in vitro transcription using DIG/Biotin RNAlabeling kit according to the manufacturer's instructions (Roche, Switzerland). The hybridization protocol was performed as previously described  [30]. Nerve cords were incubated with a secondary anti-biotin antibody conjugated to Alexa Fluor 488 (dilution 1: 5000 in PBS) (Invitrogen, USA). Samples were rinsed with PBS.
Hmcalr mRNA (Genbank KF709537) encodes a 420-amino-acid sequence with a theoretical molecular weight of 48 610 Da. The protein sequence presents a putative signal peptide and a calreticulin domain in Met 1 -Ser 19 and in Val 23 -Ile 334 amino-acid regions, respectively (Figure  1A ). In addition, the analysis of HmCalR protein using a BLAST-P program shows a high conservation with human calreticulin, particularly in different domains that are already described for mammalian calreticulins  [32]. As presented in Figure  1B , HmCalR might possess a single disulfide bridge (Cys 107 -Cys 139 ) and contains a single histidine residue (His 172 ). These residues were also described in an N-domain of the human mature calreticulin in Cys 88 -Cys 120 and His 153 positions, respectively, (numerated from the signal peptide-free sequence) and were demonstrated as essential for the chaperoning function  [33, 34].