dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Figures  3  and 4  show an overview of the four simulations performed at the Col de Porte in terms of snow depth, SWE, surface albedo, and soil temperature at 10 cm. A quick look at the time series indicates that all of the model versions match the observations relatively well. However, an-nual statistics show a clear hierarchy between the four experiments. The snow depth statistics show that the new snow compaction/densification algorithm has a positive impact on the snowpack simulation. Indeed, both the CPT and NEW experiments exhibit the lowest bias and c-rmse for 12 of the 18 years. However, the comparison to SWE data does not allow a discrimination between the four simulations, even if the c-rmse of the NEW experiment is the best for 7 of the 10 years. The surface albedo from the NEW simulation is clearly better than the albedo from the other experiments; bias and c-rmse are the best for all years (Fig.
Numerical experiment design and observational data set The experimental design used here is close to that proposed by  Brun et al. (2013). The region considered (35 to 85 • N, 25 to 180 • E) covers eastern Europe, Russia, and Siberia (Fig. 7 ). The ISBA land surface model is run at a 0. 5 • by 0. 5 • spatial resolution using the Interim Reanalysis (ERA-I; http://www. ecmwf. int/en/research/ climate-reanalysis/era-interim,  Dee et al. , 2011). ERA-I meteorological variables are extracted with a 3-hourly frequency in order to represent the diurnal cycle. This reanalysis covers the time period from 1979 to the present. Many details about ERA-I can be found in  Dee et al. (2011)  and an evaluation of its performance is provided in  Berrisford et al. (2011). For precipitation, the monthly ERA-I precipitation values are rescaled to match the observed Global Precipitation Climatology Center (GPCC) Full Data Product V5 (http://gpcc.
ARCSS078,  Zhang et al. , 2001). Data coverage extends from the 1800s through 1990, but is not continuous. We compared our model results over the 1979-1990 period. Similar to snow depth, soil temperature stations are subject to WMO standards and are located in open area sites. We used the same criteria as for snow depth. Only stations with local elevations close to the ERA-I altitude (less than 100 m difference) are used. In addition, only stations with at least 36 months of observations (at least 3 years out of 12) are kept. Most soil temperature sites are collocated with snow depth sites (Fig. 7 ). Measurements were taken at depths of 20, 80, 160, and 320 cm. For each depth, 95, 48, 48, and 82 stations, respectively, were available for model evaluation. The spatial distribution of these stations is shown in Fig.
Model configuration Three experiments using the ISBA land surface model forced by the ERA-I-scaled GPCC atmospheric data set are performed using the same configuration. In addition to the CTL (old snow scheme) and NEW (new snow scheme) experiments already described in Sect. 4, we performed one simulation using the parameterization of the impact of the soil organic carbon on the hydrologic and thermal soil properties. This last experiment, called NEW-SOC (soil organic carbon), uses the new snow and soil property schemes described in Sects. 3. 1 and 3. 2, respectively. As previously done, the model determines the temperature, liquid water, and ice content evolution in each of the 14 soil layers corresponding to a total soil depth of 12 m. The model is run with a 15 min time step from 1 January 1979 to 31 December 2013.
More details can be found in  Decharme and Douville (2006b)  and  Decharme et al. (2013). For all of the simulations, the grid-cell fraction covered by snow evolves according to the simulated snow depth and is different for bare soil and vegetated areas (Appendix C) in each land cover patch. As was the case for the Col de Porte experiment, the effective roughness length of snow retains its usual value of 0. 001 m. The land surface parameters used by ISBA are specified according to the 1 km resolution ECOCLIMAP-II database  (Faroux et al. , 2013). LAI, vegetation height, and vegetation/soil albedos are prescribed for the 12 vegetation sub-grid patches based on a mean annual cycle at a 10-day time step. The rooting depth is specified for each vegetation type according to  Canadell et al. (1996).
Acknowledgements. This work is supported by the  APT  project from the  BNP-Paribas foundation , the program CLASSIQUE of the  French Agence Nationale pour la Recherche , the  Centre National de Recherches Météorologiques (CNRM) of Méteo France , and the  Centre National de la Recherche Scientifique (CNRS)  of the French research ministry. The authors would like to thank in particular  Vincent Vionnet ,  Matthieu Lafaysse ,  Yves Lejeune , and  Jean-Michel Panel  ( CNRM-GAME/Centre d'Etudes de la Neige ) for useful comments on snowpack modeling and their contribution to data acquisition at Col de Porte since 1993. Thanks are also due to anonymous reviewers. Edited by:  G. Chambon.
Mapping of sRNA sequence reads to the Ectocarpus genome and transcriptome The filtered reads were mapped against the Ectocarpus genome using Bowtie2  (28)  with default parameters. Only fully mapped reads were retained (-end-to-end option in Bowtie2). Read coverage for genomic feature (exons, introns, rRNA, tRNA, snoRNA and intergenic regions) was obtained using Samtools  (29). Ectocarpus snoRNA loci were predicted using ACAseeker and CDseeker. Coordinates of other genomic features, including rRNA and tRNA loci, were obtained from the Ectocarpus genome database at Orcae (http://bioinformatics. psb. ugent. be/orcae/overview/Ectsi)  (30). Sliding window analysis of sRNA read coverage was calculated using a custom script and a non-overlapping sliding window of 25 kb. The data is presented as sRNA read counts per window.
Visual analysis of the mapping pattern of the sRNA reads onto the genome indicated that it was not consistent with more than a very limited level of contamination by degraded mRNA fragments. This conclusion was also supported by the fact that 47% of the reads that mapped to mRNA-encoding regions of the genome mapped to the antisense strand compared to the mRNA transcript (data not shown). Expression levels (transcript abundance) of proteincoding genes in male and female gametophytes were determined using the Illumina RNA-seq dataset described by Ahmed et al. (24).
Identification and characterization of miRNA loci in Ectocarpus Ectocarpus is distantly related to both land plants and animals. Screens for miRNAs therefore employed both miRD-eep2  (31) , which implemented criteria for the identification of animal miRNAs, and miRDeep-p (32), a modified version of miRDeep that was adapted for the identification of plant miRNAs by allowing extended precursor sequences. After filtering, the reads from all six samples (Supplementary Table  S1 ) were combined into a single dataset and provided as input for each program. Candidate miRNA precursors were then extracted from the output files and the miRDeep-2 and miRDeep-p outputs compared using Blast to identify and remove redundant candidate miRNA precursors that had been identified by both programs. Custom scripts, which incorporated Bowtie  (28) , were used to align all the sRNA sequence reads to the candidate precursor miRNA loci, with no mismatches allowed.
For each miRNA locus, the sRNA species with the highest read count was compared with miRBase using Blast and the most similar match recovered if matches were detected. The entire precursor sequence was folded with Vienna RNAfold (33) and a further script was implemented to combine the output of this analysis with the sRNA read mapping results and miRBase Blast search results. Similar analyses of sRNA read mapping were also carried out for 23 Ectocarpus miRNA loci recently reported by Billoud et al. (23).
Thus the candidate miRNAs identified by Billoud et al. are most likely siRNAs. Quantitative PCR is commonly used to validate candidate miRNAs identified by bioinformatic approaches due to its low cost. The analysis carried out in this study identified limitations of this approach and demonstrated the importance of validation using sRNA read data. sRNA read data allows key criteria such as evidence for the existence of both miRNA and miRNA* species, homogeneity of 5 processing and pre-miRNA processing consistent with dicer activity, to be tested. Whilst quantitative PCR is clearly useful for the quantification of known miRNAs, as a tool to validate novel candidate miRNA loci it suffers from the weakness of not being able to distinguish miRNAs from rare RNA species, siRNAs or degraded products of diverse RNA transcripts.
Blastn search results were analysed for matching regions that exhibited at least partial conservation of the miRNA and/or miRNA* sequences and could potentially encode RNAs with hairpin structures, but no clear matches were found in any of the four species analysed. Recent estimates indicate that these four species of stramenopiles may all have diverged from the brown algal lineage more than 400 Mya  (83). It is therefore possible that extensive divergence over this length of evolutionary time may have obscured homologies. However, given that subsets of both animal and land plant miRNA loci have been strongly conserved over similar periods of time  (15, 40, 41, 49) , this is unlikely to have been the case for all of the miRNA loci. Moreover, recent extensive searches of three diatom genomes failed to find any strong candidate miRNA loci, indicating that this stramenopile group does not possess a miRNA regulatory system  (21, 22).
2. Data and Methodologies Data 2. 1. The present safety evaluation of GM carnation SHD-27531-4 by the EFSA GMO Panel is based on the information provided in notification C/NL/13/01, including e. g. additional information 5  provided by the notifier, the assessment report of the Dutch competent authority, the concerns raised by Member States, relevant scientific publications and the experience gained in assessing GM carnations with similar traits  (EFSA, 2006 (EFSA, , 2008;; EFSA GMO Panel, 2014a,b,c).
Evaluation of relevant scientific data Toxicology (a) Toxicological assessment of newly expressed proteins Bioinformatic analyses of the amino acid sequences of the three proteins newly expressed in carnation SHD-27351-4 (ALS, DFR and F3′5′H) reveal no significant similarities to known toxins to humans (see Section 3. 1. 3). These three new proteins have been previously assessed by the EFSA GMO Panel and no reasons for concern were identified in the context of the limited scope of previous notifications  (EFSA, 2006 (EFSA, , 2008 (EFSA, , 2014b,c),c). 6 Of the characteristics tested for significant differences, eleven were measured in both trials (plant height at flowering, length of 5th node, leaf length, 3rd from flower, flower diameter, calyx length, number of petals per flower, petal length, petal width, number of styles, style length and days to flowering), eight only in the first trial (number of internodes per stem, thickness of 5th node, height of corolla, calyx diameter, number of lobes per calyx, number of viable anthers, filament length and number of filaments), and four only in the second trial (stem length, stem diameter, leaf width and flower height).
, 1993). In addition, seeds of Dianthus species are generally relatively short-lived  (Mondoni et al. , 2011)  and so the consequences of changes in germination characteristics will vary with different populations and niches. The EFSA GMO Panel considered that small changes in seed germination characteristics induced by ALS tolerance are unlikely to be outside the current range of seed germination characteristics currently expressed by non-GM carnations and thus is unlikely to have an ecological impact. EFSA Journal 2015;13(12):4358 In addition, fitness advantages and higher weediness of the GM plants in the presence of sulfonylurea herbicides and herbicides with similar mode of action are not considered significant since these herbicides are not known to be used on cultivated carnations. The notifier provided data on 26 quantitative morphological characteristics of carnation SHD-27531-4 compared with its parental variety from two trials in Australia in 2010 (see Section 3.
No evidence has been found that that the flower colour and herbicide tolerant traits introduced by the genetic modification into carnation SHD-27531-4 would result in increased persistence and invasiveness of this or any other Dianthus species. Moreover, the EFSA GMO Panel is not aware of any scientific reports of increased spread and establishment of (GM) carnations or of any change in survival capacity, including overwintering (COGEM report 10 ; EFSA, 2006, 2008, 2014a,b,c). In addition, D. caryophyllus with double flowers has been imported into all EU countries as a garden ornamental plant and cut flower for many decades and EFSA is not aware of any reports of feral populations that have established outside of cultivation. Considering the scope of notification C/NL/13/01 and the data available, the EFSA GMO Panel considered that there would be no changes in plant characteristics of any ecological significance.
e. Petunia, Viola and Nicotiana tabacum (tobacco) (for more details, see Section 3. 1. 2). Owing to the absence of DNA with high similarity to that of bacteria, there is no indication of facilitated transfer of recombinant genes to bacteria when it is compared with the transfer of genes from non-GM carnations. Thus, based on the data provided by the notifier, no increased likelihood of horizontal gene transfer from carnation SHD-27531-4 to environmental bacteria is expected. The EFSA GMO Panel could not identify any selective advantage which would be provided to environmental bacteria when receiving the recombinant DNA of carnation SHD-27531-4. Considering the scope of notification C/NL/13/01, the EFSA GMO Panel therefore concluded that the unlikely, but theoretically possible, horizontal gene transfer of recombinant genes from carnation SHD-27531-4 to environmental bacteria does not give rise to environmental safety concerns.
Moreover, the reproductive biology of Dianthus  (OGTR, 2006)  and the information 11 provided by the notifier suggest that pollen production by flowers and pollen viability are low. The data indicate that pollen transfer to other carnations is very unlikely to occur owing to very low fertility levels in most carnations. Therefore EFSA GMO Panel is of the opinion that the potential spread of pollen of the GM carnation by Lepidoptera to wild Dianthus spp. is highly unlikely to occur and, if it did occur, it is very unlikely that viable hybrids would be produced, survive and cause adverse environmental effects. In addition, viable seed production of cut flowers is very unlikely and has not been observed to date with carnation SHD-27531-4, most probably because of its limited life time (i. e. three weeks) in comparison with the time needed for complete seed development (i.
Based on a comprehensive information package (e. g. notification C/NL/13/01, additional datasets, initial assessment report by The Netherlands), the EFSA GMO Panel concludes that the molecular characterisation data establish that carnation SHD-27531-4 contains one insert, consisting of three expression cassettes responsible for the intended trait (purple flower colour) conferred by the dfr and f3′5′h genes, and herbicide tolerance conferred by the mutated als gene. The stability of the newly introduced trait was observed over multiple vegetative generations. Carnation flowers have a long history of use as ornamentals. Carnation SHD-27351-4 differs from its parental variety in that it synthesises different levels of anthocyanins in the petals, e. g. an increased content of delphinidin, cyanidin and petunidin (common pigments in many ornamental flowers and food plants).
Growth rates The growth rate of three independent mutants and wild-type cells was measured by growth curve experiments in 100 mL of rich media with a Tecan Sunrise robot in triplicates. Data availability bz-rates was developed in Python with the Django v1. 6 framework. It is a free Web tool distributed under the terms of the GNU General Public License. bz-rates is accessible at http://www. lcqb. upmc. fr/bzrates. The source code, available at https://github. com/gillet/bzrates, can be easily modified to implement other estimators and clones of the tool can be set up elsewhere.
Experimental testing A fluctuation assay was performed with a yeast strain carrying a genetic system that is designed to generate a functional copy of an auxotrophic gene when the cells undergo a specific chromosomal rearrangement (a reciprocal translocation, see Materials and Methods). The resulting mutant cells have a strong growth defect relatively to wild-type cells, probably as the result of the translocation, that was experimentally measured to 0. 76 (Materials and Methods). The form of Figure  1A  is filled with the data of the 30 tubes fluctuation assay that was undertaken. We neglected to specify the relative growth rate of the mutants to compare the predicted relative growth rate of bz-rates to the experimental measure. Figure  1B  shows bz-rates results. The plot indicates a good fit between the statistical distribution of the mutants and the experimental data.
Published datasets and simulations To test our implementation and the stability of the GF estimator in bz-rates, we tested two published datasets: (i) the first dataset corresponds to a historical fluctuation assay composed of 42 parallel cultures performed by Luria and Delbrück (Figure  1C ). With this dataset, bz-rates predicts a mutation rate (4. 11 • 10 28 ) close to the one calculated by  Luria and Delbrück (1943)  (2. 48 • 10 28 ). The value of m (7. 19) and b (1. 022) are very close to the range of values reported in  Hamon and Ycart (2012)   [(5. 2228. 89) for m and (0. 7421. 22) for b]. We also tested one larger fluctuation dataset from  Boe et al. (1994)  that is composed of 1102 cultures (Figure  1D ). In this case, bz-rates reports a m value of 0. 705, which is close to the one calculated in  Hamon and Ycart (2012) (0.
6520. 77 ) and the one calculated in Zheng (2005) (0. 71). The mutant differential growth rate value is 1. 315, which is a bit greater than the one reported by  Zheng (2005)  with a ML approach  (b = 1. 193). The performance of bz-rates also was tested on simulated datasets. We generated simulated fluctuation assays for different couples of m and b with either  16, 32, 48, 96, 192 , or 384 parallel cultures (Figure  2 ). As expected, the precision of the estimator increases with increasing numbers of parallel cultures. The general trend that can be inferred from these plots is that the precision on the estimation of m (and by consequence the estimation of m) is higher for the smallest values of m. Therefore, users should not outgrow the cultures in order to limit the number of mutants that grow on selective plates.
Quantitative PCR Analysis Total RNA was extracted using the RNeasy Kit (Qiagen) per manufacturer's instructions, and 1 μg of RNA was used for cDNA synthesis. 25-50 ng of the cDNA was used to perform expression analyses with Taqman on the StepOnePlus System (Applied Biosystems) or using the ViiA 7 Real-Time PCR System (Life Technology) and using SYBR Green on the LightCycler 1536 (Roche). All data were analyzed using Qbase + software (Biogazelle). Quantitative PCR (qPCR) primers used for the analysis were purchased from Applied Biosystems or Primer Design. A set of 12 candidate reference genes (Primer Design) was tested, and the most stably expressed genes were determined using the geNorm tool of the Qbase + software. These were used as reference to establish individual gene expression values (2 -ΔΔCT ).
Specific protein bands were visualized using luminol-based substrates (Uptilight US, Cheshire Sciences), and images were obtained using a G:BOX Chemi XT16 system (Syngene). β-actin, GAPDH, and tubulin were used as protein-loading controls. All densitometric analyses of specific protein bands were made using exposure times within the linear range and the integrated density measurement function of ImageJ software  [26, 27].
Morphometric Analysis Muscle fiber size and central nucleation were visualized by collagen type-IV and Hoechst immunofluorescence staining of frozen muscle sections. Individual microscope fields of view were montaged using ImageJ to present whole cross-sections through the muscle. Image analysis was performed on these composite images using Fiji and ImageJ open-source software (US National Institutes of Health). A macro was developed to sequentially (i) subtract background components to minimize noise that could interfere with further analysis; (ii) apply band-pass thresholds to separate color channels; (iii) dilate borders to close inconsistent gaps; (iv) skeletonize these borders; (v) apply a convolution filter to translate pixels uniformly for border detection; (v) generate a mask of the muscle fiber borders using the analyze particles function, simultaneously eliminating stray "non-border" signals; and (vi) overlay threshold-delimited nuclei over the border mask, before another analyze particles command was used to measure morphometric variables including "area" and "minimum Feret diameter.
Bone Morphometric Analyses (4 wk) Mice tibias were imaged by means of μCT (XT H 225, X-Tek Systems), and a complete data acquisition was performed (V = 50-55 kV, I = 95-110 μA, voxel size = 6-8 μm, rotational step = 0. 19°/360°, acquisition time = 90 min). The regions of interest used for the morphometric assessment were selected to include both the cancellous and cortical bones in the proximal tibias and the cortical bones in the mid-shaft of the tibias, similarly to the methodology used in  [3]. Image processing was performed using the seeded region growing (SRG) technique (ImageJ) to automate segmentation of the bone tissue from the background. The morphometric parameters measured were bone volume fraction (BV/TV), trabecular bone thickness, and Tb. Sp.
During these test phases, one of the familiar objects was replaced by a novel object, with a different shape and color. During the 5-min testing, exploration of an object was defined as pointing the nose to the object and/or touching the object with the nose. The total time spent with each object and number of times each object was explored were recorded and scored using fully automated EthoVision XT 10. 0 video tracking software (Noldus Information Technologies). Data are presented as the discrimination index (time or frequency exploring novel object × 100/total object exploration time or frequency).
010). Myogenin levels were elevated compared to mdx and in line with Pf-mdx/P2X7 -/-(Fig 2C ; G-mdx/P2X7 -/-versus mdx, p < 0. 001), while CK levels (Fig 2D ; G-mdx/P2X7 -/-versus mdx, p = 0. 111) and sarcolemma permeability to IgG, albeit lower, were not statistically significantly different. The intermediate effects seen in G-mdx/P2X7 -/-as compared to Pf-mdx/P2X7 -/-mice confirmed the association between decreased P2RX7 expression and the phenotypic improvements. Moreover, we analyzed F1 Pf-mdx/P2X7 +/-males. These heterozygous mice had intermediate levels of muscle P2RX7 expression (S1A Fig), exactly as shown before in immune cells  [33]. Again, this intermediate level corresponded with the intermediate Feret diameter values in these mice (S1B Fig). F1 and G-mdx/P2X7 -/-data also confirmed that the improvements found in double-mutants are not due to the genetic background variation resulting from mdx-P2X7 -/-breeding, as this would have had an impact in all mouse lines.